feat: legacy fallback tests and docs (PR 3)

- Add test_tool_instances_legacy.py with 8 unit tests: - dockerfile definition type builds from template - dockerfile build failure raises HTTP 500 - compose definition type renders template - manifest compiler is NOT called for legacy types - start_instance legacy/compose/dockerfile types all skip manifest flow - start_instance manifest type correctly invokes compiler - Mark T3.2 and T3.3 tasks complete in OpenSpec - Add openspec/docs/tool-workshop-guide.md with user guide covering definition types, manifest creation workflow, base definitions, migration path, and permissions
feat: Tool Workshop manifest editor (PR 2)
2026-05-28 14:54:32 +02:00 · 2026-05-28 14:35:04 +02:00 · 2026-05-28 13:37:34 +02:00 · 2026-05-28 10:58:18 +02:00 · 2026-05-28 10:56:43 +02:00 · 2026-05-28 10:56:33 +02:00
340 changed files with 30067 additions and 4910 deletions
@@ -0,0 +1,195 @@
+---
+name: sift-backlog
+description: Triage and organize backlog tasks into actionable plans. Use when asked to review the backlog, prioritize tasks, create plans from backlog items, or move tasks from backlog to open status. Handles the full workflow of listing backlog tasks, grouping related tasks into plans, setting priorities and dependencies, activating plans, and changing task status from backlog to open.
+---
+
+# Sift Backlog
+
+Triage backlog tasks: prioritize, group into plans, set dependencies, and activate.
+
+## Overview
+
+1. List backlog tasks (`sf task backlog`)
+2. Clarify and enrich each task (titles, descriptions)
+3. Identify groupings and create draft plans
+4. Add tasks to plans and set dependencies
+5. Activate plans
+6. Set task status to open
+
+## Workflow
+
+### Step 1: List Backlog Tasks
+
+```bash
+sf task backlog
+```
+
+### Step 2: Clarify and Enrich Tasks
+
+Backlog tasks often have only a brief title with no description. Before organizing, ensure each task is well-defined.
+
+**For each task, evaluate:**
+
+- Is the title clear and actionable?
+- Is there a description? Check with `sf task describe <task-id> --show`
+- Is the scope unambiguous?
+
+**If the title is unclear**, update it:
+
+```bash
+sf update <task-id> --title "Clear, actionable title"
+```
+
+**Add a description** with context, scope, and acceptance criteria:
+
+```bash
+sf task describe <task-id> --content "Description with:
+- What needs to be done
+- Why it matters
+- Acceptance criteria
+- Any relevant context"
+```
+
+**Use your best judgment** to interpret tasks and make reasonable decisions about scope, grouping, and priority. You have context about the codebase, project patterns, and typical development practices—leverage this knowledge rather than deferring to the user for routine decisions.
+
+**Only ask the user for clarity when absolutely necessary:**
+
+- The task is fundamentally ambiguous (multiple mutually exclusive interpretations)
+- Critical business logic or user-facing behavior that could go wrong in meaningful ways
+- External dependencies or integrations you cannot verify
+
+**Do NOT ask about:**
+
+- Implementation details you can reasonably infer
+- Priority or grouping decisions—use your judgment
+- Standard development practices (testing, code style, etc.)
+- Tasks where a reasonable interpretation exists
+
+### Step 3: Create Draft Plans
+
+Group related tasks into plans using your best judgment. Plans start as drafts (tasks won't be dispatched until activated).
+
+**Grouping guidance:**
+
+- Group tasks that share a common theme, feature area, or goal
+- Consider technical dependencies when grouping (tasks that touch the same files/modules)
+- Separate unrelated work into distinct plans for parallel execution
+- Don't over-group—if tasks are truly independent, separate plans enable better parallelism
+- Don't under-group—related tasks benefit from shared context and coordinated execution
+
+```bash
+sf plan create --title "Plan Name"
+```
+
+**Example:**
+
+```bash
+sf plan create --title "Authentication Improvements"
+# Output: Created plan el-abc123
+```
+
+### Step 4: Add Tasks to Plans
+
+```bash
+sf plan add-task <plan-id> <task-id>
+```
+
+**Example:**
+
+```bash
+sf plan add-task el-abc123 el-task1
+sf plan add-task el-abc123 el-task2
+```
+
+### Step 5: Set Dependencies Between Tasks
+
+Use `blocks` dependency when one task must complete before another can start.
+
+```bash
+sf dependency add <blocked-id> <blocker-id> --type blocks
+```
+
+**Semantics:** The first ID is blocked BY the second ID. The blocker must complete first.
+
+**Example:** Task 2 can't start until Task 1 completes:
+
+```bash
+sf dependency add el-task2 el-task1 --type blocks
+```
+
+### Step 6: Update Priorities
+
+Set priorities based on your assessment of impact, urgency, and dependencies. Use your judgment—you don't need user confirmation for routine prioritization.
+
+**Priority guidance:**
+
+- **Critical (1):** Blocking issues, security vulnerabilities, production bugs
+- **High (2):** Important features with deadlines, significant user impact
+- **Medium (3):** Standard feature work, most tasks default here
+- **Low (4):** Nice-to-haves, minor improvements, tech debt
+- **Minimal (5):** Backlog cleanup, documentation, exploratory work
+
+```bash
+sf update <task-id> --priority <1-5>
+```
+
+| Value | Level    |
+| ----- | -------- |
+| 1     | Critical |
+| 2     | High     |
+| 3     | Medium   |
+| 4     | Low      |
+| 5     | Minimal  |
+
+### Step 7: Activate Plans
+
+Once tasks are organized with dependencies set, activate plans to enable dispatch.
+
+```bash
+sf plan activate <plan-id>
+```
+
+### Step 8: Set Task Status to Open
+
+Move tasks from backlog to open so they become ready for work.
+
+```bash
+sf update <id> --status open
+```
+
+## Other Actions
+
+**Close obsolete tasks:**
+
+```bash
+sf task close <id> --reason "Won't do: <reason>"
+```
+
+**Defer tasks:**
+
+```bash
+sf task defer <id> --until <date>
+```
+
+**View existing plans:**
+
+```bash
+sf plan list
+```
+
+**View tasks in a plan:**
+
+```bash
+sf plan tasks <plan-id>
+```
+
+## Tips
+
+- **Use your best judgment** for grouping, prioritization, and task interpretation—don't defer routine decisions to the user
+- **Only escalate to the user** when ambiguity is fundamental and could lead to wasted work (mutually exclusive interpretations, critical business decisions)
+- Make reasonable inferences about implementation details, scope, and priority based on codebase context
+- Create plans before setting dependencies to avoid dispatch race conditions
+- Always activate plans after dependencies are set
+- Focus on oldest backlog items first (sorted by creation date)
+- Every task should have a clear title and description before activation
+- When uncertain about a minor detail, make a reasonable choice and document it in the task description—workers can ask if needed
@@ -48,3 +48,6 @@ apps/web/dist/
 # OS
 .DS_Store
 Thumbs.db
+/.stoneforge/.worktrees/
+# Local Pi runtime state
+.atl/
@@ -0,0 +1 @@
+{}
@@ -0,0 +1,2 @@
+262629
+1779624255076
@@ -0,0 +1,6 @@
+# Runtime data
+*.db
+*.db-journal
+*.db-wal
+*.db-shm
+daemon-state.json
@@ -0,0 +1,20 @@
+# Stoneforge Configuration
+
+database: stoneforge.db
+sync:
+  auto_export: true
+  elements_file: elements.jsonl
+  dependencies_file: dependencies.jsonl
+playbooks:
+  paths:
+    - playbooks
+identity:
+  mode: soft
+merge:
+  auto_merge: true
+  target_branch: null
+  require_approval: false
+workflow:
+  preset: auto
+agents:
+  permission_model: unrestricted
@@ -0,0 +1,43 @@
+{"blockedId":"el-1of","blockerId":"el-258","type":"parent-child","createdAt":"2026-05-24T09:44:58.759Z","createdBy":"el-2jua"}
+{"blockedId":"el-5fe","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:40.892Z","createdBy":"el-2jua"}
+{"blockedId":"el-1nj","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.010Z","createdBy":"el-2jua"}
+{"blockedId":"el-1bn","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.127Z","createdBy":"el-2jua"}
+{"blockedId":"el-4hr","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.244Z","createdBy":"el-2jua"}
+{"blockedId":"el-62c","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.372Z","createdBy":"el-2jua"}
+{"blockedId":"el-5z8","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.490Z","createdBy":"el-2jua"}
+{"blockedId":"el-1t7","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.607Z","createdBy":"el-2jua"}
+{"blockedId":"el-5j5","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.726Z","createdBy":"el-2jua"}
+{"blockedId":"el-2xl","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.844Z","createdBy":"el-2jua"}
+{"blockedId":"el-4bc","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.959Z","createdBy":"el-2jua"}
+{"blockedId":"el-107","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.074Z","createdBy":"el-2jua"}
+{"blockedId":"el-32e","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.195Z","createdBy":"el-2jua"}
+{"blockedId":"el-3ou","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.311Z","createdBy":"el-2jua"}
+{"blockedId":"el-14w","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.425Z","createdBy":"el-2jua"}
+{"blockedId":"el-1ou","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.541Z","createdBy":"el-2jua"}
+{"blockedId":"el-1nj","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.651Z","createdBy":"el-2jua"}
+{"blockedId":"el-1bn","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.761Z","createdBy":"el-2jua"}
+{"blockedId":"el-4hr","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.868Z","createdBy":"el-2jua"}
+{"blockedId":"el-62c","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:42.979Z","createdBy":"el-2jua"}
+{"blockedId":"el-62c","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:43.092Z","createdBy":"el-2jua"}
+{"blockedId":"el-5z8","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:43.205Z","createdBy":"el-2jua"}
+{"blockedId":"el-5z8","blockerId":"el-4hr","type":"blocks","createdAt":"2026-05-24T12:44:43.313Z","createdBy":"el-2jua"}
+{"blockedId":"el-1t7","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:43.422Z","createdBy":"el-2jua"}
+{"blockedId":"el-1t7","blockerId":"el-4hr","type":"blocks","createdAt":"2026-05-24T12:44:43.529Z","createdBy":"el-2jua"}
+{"blockedId":"el-1t7","blockerId":"el-62c","type":"blocks","createdAt":"2026-05-24T12:44:43.647Z","createdBy":"el-2jua"}
+{"blockedId":"el-5j5","blockerId":"el-1t7","type":"blocks","createdAt":"2026-05-24T12:44:43.758Z","createdBy":"el-2jua"}
+{"blockedId":"el-2xl","blockerId":"el-1t7","type":"blocks","createdAt":"2026-05-24T12:44:43.876Z","createdBy":"el-2jua"}
+{"blockedId":"el-4bc","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:43.987Z","createdBy":"el-2jua"}
+{"blockedId":"el-4bc","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:44.096Z","createdBy":"el-2jua"}
+{"blockedId":"el-4bc","blockerId":"el-62c","type":"blocks","createdAt":"2026-05-24T12:44:44.208Z","createdBy":"el-2jua"}
+{"blockedId":"el-107","blockerId":"el-5z8","type":"blocks","createdAt":"2026-05-24T12:44:44.319Z","createdBy":"el-2jua"}
+{"blockedId":"el-32e","blockerId":"el-5j5","type":"blocks","createdAt":"2026-05-24T12:44:44.429Z","createdBy":"el-2jua"}
+{"blockedId":"el-32e","blockerId":"el-2xl","type":"blocks","createdAt":"2026-05-24T12:44:44.539Z","createdBy":"el-2jua"}
+{"blockedId":"el-3ou","blockerId":"el-4bc","type":"blocks","createdAt":"2026-05-24T12:44:44.650Z","createdBy":"el-2jua"}
+{"blockedId":"el-3ou","blockerId":"el-107","type":"blocks","createdAt":"2026-05-24T12:44:44.761Z","createdBy":"el-2jua"}
+{"blockedId":"el-14w","blockerId":"el-32e","type":"blocks","createdAt":"2026-05-24T12:44:44.873Z","createdBy":"el-2jua"}
+{"blockedId":"el-1ou","blockerId":"el-3ou","type":"blocks","createdAt":"2026-05-24T12:44:44.987Z","createdBy":"el-2jua"}
+{"blockedId":"el-1ou","blockerId":"el-14w","type":"blocks","createdAt":"2026-05-24T12:44:45.107Z","createdBy":"el-2jua"}
+{"blockedId":"el-375","blockerId":"el-26p","type":"replies-to","createdAt":"2026-05-24T13:21:42.486Z","createdBy":"el-2i1s"}
+{"blockedId":"el-3n4","blockerId":"el-31p","type":"replies-to","createdAt":"2026-05-24T13:21:46.044Z","createdBy":"el-13ju"}
+{"blockedId":"el-3jer","blockerId":"el-1xx","type":"replies-to","createdAt":"2026-05-24T13:24:47.580Z","createdBy":"el-4350"}
+{"blockedId":"el-1afv","blockerId":"el-1ozw","type":"replies-to","createdAt":"2026-05-24T13:32:42.658Z","createdBy":"el-51a8"}
@@ -87,6 +87,31 @@ Do not claim completion without verification evidence.

 ## Git workflow

+### Branching strategy
+
+For every spec change or new functionality:
+
+1. Create a new branch from `dev` with a proper prefix:
+   - `feat/` for new features (e.g., `feat/tool-workshop`)
+   - `fix/` for bug fixes (e.g., `fix/terminal-tty`)
+   - `refactor/` for refactors (e.g., `refactor/api-cleanup`)
+   - `docs/` for documentation (e.g., `docs/api-guide`)
+   - `chore/` for maintenance (e.g., `chore/update-deps`)
+2. Branch name should reference the OpenSpec change name when applicable.
+3. Do not commit directly to `main` or `dev`.
+
+### Completion and merge
+
+When implementation is complete and verified:
+
+1. Ensure all tests pass and quality gates are met.
+2. Stage all changes with `git add -A`.
+3. Create a commit with a proper conventional commit message (see below).
+4. Switch to `dev`: `git checkout dev`.
+5. Merge the feature branch: `git merge --no-ff <branch-name>`.
+6. Push to remote: `git push origin dev`.
+7. Delete the local feature branch if desired: `git branch -d <branch-name>`.
+
 ### Auto-commit on spec completion

 When an OpenSpec change is fully implemented and all tasks are complete:
@@ -27,6 +27,7 @@ WORKDIR /app
 RUN apt-get update && apt-get install -y --no-install-recommends \
    libpq5 \
    git \
+    openssh-client \
    netcat-openbsd \
    ca-certificates \
    curl \
@@ -0,0 +1,29 @@
+"""add probe_result to tool_instances
+
+Revision ID: 0013_add_probe_result
+Revises: 0012_default_port_req
+Create Date: 2026-05-22 21:45:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0013_add_probe_result"
+down_revision: Union[str, None] = "0012_default_port_req"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "tool_instances",
+        sa.Column("probe_result", postgresql.JSON, nullable=True)
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_instances", "probe_result")
@@ -0,0 +1,23 @@
+"""merge migration heads
+
+Revision ID: 0014_merge_heads
+Revises: 0013_add_probe_result, 8ed7dd80973d
+Create Date: 2026-05-22 21:50:00.000000
+
+"""
+from typing import Sequence, Union
+
+
+# revision identifiers, used by Alembic.
+revision: str = "0014_merge_heads"
+down_revision: Union[str, Sequence[str], None] = ("0013_add_probe_result", "8ed7dd80973d")
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    pass
+
+
+def downgrade() -> None:
+    pass
@@ -0,0 +1,109 @@
+"""replace interfaces with interface_type and add requires_port
+
+Revision ID: 0015_single_interface
+Revises: 0014_merge_heads
+Create Date: 2026-05-22 22:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0015_single_interface"
+down_revision: Union[str, Sequence[str], None] = "0014_merge_heads"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def _get_dialect() -> str:
+    """Get the current database dialect name."""
+    conn = op.get_bind()
+    return conn.dialect.name
+
+
+def upgrade() -> None:
+    dialect = _get_dialect()
+    
+    # Add new columns
+    op.add_column('tool_types', sa.Column('interface_type', sa.String(20), nullable=True))
+    op.add_column('tool_types', sa.Column('requires_port', sa.Boolean(), nullable=False, server_default='true'))
+    
+    # Migrate data: take first element from interfaces JSON array
+    if dialect == 'postgresql':
+        op.execute("""
+            UPDATE tool_types 
+            SET interface_type = COALESCE(
+                (SELECT elem FROM jsonb_array_elements_text(interfaces::jsonb) AS elem LIMIT 1),
+                'web'
+            ),
+            requires_port = CASE 
+                WHEN COALESCE(
+                    (SELECT elem FROM jsonb_array_elements_text(interfaces::jsonb) AS elem LIMIT 1),
+                    'web'
+                ) = 'web' THEN true
+                ELSE false
+            END
+        """)
+    else:
+        # SQLite: interfaces is stored as JSON text, extract first array element
+        op.execute("""
+            UPDATE tool_types 
+            SET interface_type = COALESCE(
+                (SELECT json_extract(value, '$[0]') 
+                 FROM json_each(interfaces) AS value 
+                 WHERE json_valid(interfaces) 
+                 LIMIT 1),
+                'web'
+            ),
+            requires_port = CASE 
+                WHEN COALESCE(
+                    (SELECT json_extract(value, '$[0]') 
+                     FROM json_each(interfaces) AS value 
+                     WHERE json_valid(interfaces) 
+                     LIMIT 1),
+                    'web'
+                ) = 'web' THEN true
+                ELSE false
+            END
+        """)
+    
+    # Make interface_type non-nullable after data migration
+    op.alter_column('tool_types', 'interface_type', nullable=False)
+    
+    # Drop old interfaces column
+    op.drop_column('tool_types', 'interfaces')
+    
+    # Add CHECK constraint for interface_type (only on PostgreSQL; SQLite supports it too)
+    op.create_check_constraint('chk_interface_type', 'tool_types', sa.text("interface_type IN ('web', 'terminal')"))
+
+
+def downgrade() -> None:
+    dialect = _get_dialect()
+    
+    # Drop CHECK constraint
+    op.drop_constraint('chk_interface_type', 'tool_types', type_='check')
+    
+    # Add back interfaces column
+    if dialect == 'postgresql':
+        op.add_column('tool_types', sa.Column('interfaces', postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default='["web"]'))
+        
+        # Migrate data back: wrap interface_type in array
+        op.execute("""
+            UPDATE tool_types 
+            SET interfaces = jsonb_build_array(interface_type)
+        """)
+    else:
+        op.add_column('tool_types', sa.Column('interfaces', sa.JSON(), nullable=False, server_default='["web"]'))
+        
+        # Migrate data back: wrap interface_type in array for SQLite
+        op.execute("""
+            UPDATE tool_types 
+            SET interfaces = json_array(interface_type)
+        """)
+    
+    # Drop new columns
+    op.drop_column('tool_types', 'requires_port')
+    op.drop_column('tool_types', 'interface_type')
@@ -0,0 +1,129 @@
+"""add pi agent tool type
+
+Revision ID: 20260527_160017_add_pi_agent
+Revises: f3d2dc90ba3a
+Create Date: 2026-05-27T16:00:17
+
+"""
+
+import json
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+import uuid
+
+# revision identifiers, used by Alembic.
+revision: str = "20260527_160017_add_pi_agent"
+down_revision: Union[str, None] = "2026_05_27_external_repos"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+PI_AGENT_ID = uuid.UUID("d07b8376-2151-4119-8c1d-27f792aae9a3")
+
+
+def upgrade() -> None:
+    # Check if pi-agent already exists
+    conn = op.get_bind()
+    result = conn.execute(
+        sa.text("SELECT id FROM tool_types WHERE name = 'pi-agent'")
+    ).fetchone()
+    
+    if result is None:
+        conn.execute(
+            sa.text("""
+                INSERT INTO tool_types (
+                    id, name, display_name, description, category,
+                    interface_type, requires_port, default_port,
+                    definition_type, compose_template, dockerfile_template, required_variables,
+                    created_at, updated_at
+                ) VALUES (
+                    :id, :name, :display_name, :description, :category,
+                    :interface_type, :requires_port, :default_port,
+                    :definition_type, :compose_template, :dockerfile_template, :required_variables,
+                    now(), now()
+                )
+            """),
+            {
+                "id": PI_AGENT_ID,
+                "name": "pi-agent",
+                "display_name": "Pi Agent",
+                "description": "Pi coding agent terminal environment with nvim, ranger, and tmux",
+                "category": "development",
+                "interface_type": "terminal",
+                "requires_port": False,
+                "default_port": 0,
+                "definition_type": "dockerfile",
+                "compose_template": """services:
+  app:
+    build: .
+    stdin_open: true
+    tty: true
+    volumes:
+      - ${REPO_PATH}:/workspace
+    working_dir: /workspace
+    command: /bin/bash""",
+                "dockerfile_template": """# Pi Coding Agent - Terminal-based coding harness
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install base dependencies
+RUN apt-get update && apt-get install -y \\
+    curl \\
+    wget \\
+    git \\
+    neovim \\
+    ranger \\
+    tmux \\
+    htop \\
+    tree \\
+    jq \\
+    ca-certificates \\
+    python3 \\
+    python3-pip \\
+    build-essential \\
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Node.js (required for Pi)
+RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \\
+    && apt-get install -y nodejs \\
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Pi Coding Agent globally
+RUN npm install -g --ignore-scripts @earendil-works/pi-coding-agent
+
+# Create non-root user
+RUN useradd -m -s /bin/bash user
+WORKDIR /home/user
+
+# Set up git
+RUN git config --global init.defaultBranch main \\
+    && git config --global user.email "dev@headquarter.local" \\
+    && git config --global user.name "Developer"
+
+# Create default tmux config
+RUN echo 'set -g mouse on\\nset -g default-terminal "screen-256color"' > /home/user/.tmux.conf
+
+# Create default ranger config
+RUN mkdir -p /home/user/.config/ranger \\
+    && echo 'set preview_files true\\nset use_preview_script true' > /home/user/.config/ranger/rc.conf
+
+# Set up Pi config directory
+RUN mkdir -p /home/user/.pi/agent
+
+USER user
+
+# Default to bash (Pi is invoked manually via `pi` command)
+CMD ["/bin/bash"]""",
+                "required_variables": json.dumps(["REPO_PATH"]),
+            }
+        )
+
+
+def downgrade() -> None:
+    conn = op.get_bind()
+    conn.execute(
+        sa.text("DELETE FROM tool_types WHERE name = 'pi-agent'")
+    )
@@ -0,0 +1,36 @@
+"""add_clone_mode_and_ssh_key_id
+
+Revision ID: 2026_05_22_add_clone_mode
+Revises: 0014_merge_heads
+Create Date: 2026-05-22 20:30:00.000000
+"""
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '2026_05_22_add_clone_mode'
+down_revision = '0015_single_interface'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # Add ssh_key_id to git_repositories
+    op.add_column('git_repositories', sa.Column('ssh_key_id', postgresql.UUID(), nullable=True))
+    op.create_foreign_key('fk_git_repositories_ssh_key', 'git_repositories', 'ssh_keys', ['ssh_key_id'], ['id'])
+    
+    # Add clone_mode and branch to tool_instances
+    op.add_column('tool_instances', sa.Column('clone_mode', sa.String(20), nullable=False, server_default='mount'))
+    op.add_column('tool_instances', sa.Column('branch', sa.String(255), nullable=True, server_default='main'))
+
+
+def downgrade() -> None:
+    # Drop columns from tool_instances
+    op.drop_column('tool_instances', 'branch')
+    op.drop_column('tool_instances', 'clone_mode')
+    
+    # Drop ssh_key_id from git_repositories
+    op.drop_constraint('fk_git_repositories_ssh_key', 'git_repositories', type_='foreignkey')
+    op.drop_column('git_repositories', 'ssh_key_id')
@@ -0,0 +1,25 @@
+"""remove_is_builtin_from_tool_types
+
+Revision ID: 2026_05_23_remove_is_builtin
+Revises: 2026_05_22_add_clone_mode
+Create Date: 2026-05-23 14:30:00.000000
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision = '2026_05_23_remove_is_builtin'
+down_revision = 'f3d2dc90ba3a'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # Drop the is_builtin column from tool_types
+    op.execute("ALTER TABLE tool_types DROP COLUMN IF EXISTS is_builtin")
+
+
+def downgrade() -> None:
+    # Add the is_builtin column back to tool_types
+    op.add_column('tool_types', sa.Column('is_builtin', sa.Boolean(), nullable=False, server_default='false'))
@@ -0,0 +1,30 @@
+"""add startup_command to tool_types
+
+Revision ID: 2026_05_24_220141
+Revises: 6fc7bfcf199f
+Create Date: 2026-05-24 22:01:41.000000
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_24_220141"
+down_revision: Union[str, Sequence[str], None] = "6fc7bfcf199f"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "tool_types",
+        sa.Column("startup_command", sa.Text(), nullable=True),
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_types", "startup_command")
@@ -0,0 +1,86 @@
+"""add_config_profiles
+
+Revision ID: 2026_05_24_add_config_profiles
+Revises: f3d2dc90ba3a
+Create Date: 2026-05-24 14:00:00.000000
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_24_add_config_profiles"
+down_revision: Union[str, Sequence[str], None] = "f3d2dc90ba3a"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # Create config_profiles table
+    op.create_table(
+        "config_profiles",
+        sa.Column("id", postgresql.UUID(as_uuid=True), server_default=sa.text("gen_random_uuid()"), nullable=False),
+        sa.Column("user_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("users.id", ondelete="CASCADE"), nullable=False),
+        sa.Column("name", sa.String(255), nullable=False),
+        sa.Column("description", sa.Text(), nullable=True),
+        sa.Column("project_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("projects.id", ondelete="CASCADE"), nullable=True),
+        sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("tool_types.id", ondelete="CASCADE"), nullable=True),
+        sa.Column("env_vars", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
+        sa.Column("runtime_hints", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
+        sa.Column("mounts", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="[]"),
+        sa.Column("files", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
+        sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
+    )
+
+    # Create indexes for config_profiles
+    op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
+    op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
+    op.create_index("idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"])
+
+    # Create config_profile_includes table
+    op.create_table(
+        "config_profile_includes",
+        sa.Column("id", postgresql.UUID(as_uuid=True), server_default=sa.text("gen_random_uuid()"), nullable=False),
+        sa.Column("profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False),
+        sa.Column("included_profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False),
+        sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("profile_id", "included_profile_id", name="uq_config_profile_includes"),
+    )
+
+    # Create indexes for config_profile_includes
+    op.create_index("idx_config_profile_includes_profile", "config_profile_includes", ["profile_id"])
+    op.create_index("idx_config_profile_includes_included", "config_profile_includes", ["included_profile_id"])
+
+    # Add selected_config_profile_id to tool_instances
+    op.add_column(
+        "tool_instances",
+        sa.Column("selected_config_profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True),
+    )
+    op.create_index("idx_tool_instances_config_profile", "tool_instances", ["selected_config_profile_id"])
+
+
+def downgrade() -> None:
+    # Remove selected_config_profile_id from tool_instances
+    op.drop_index("idx_tool_instances_config_profile", table_name="tool_instances")
+    op.drop_column("tool_instances", "selected_config_profile_id")
+
+    # Drop config_profile_includes table
+    op.drop_index("idx_config_profile_includes_included", table_name="config_profile_includes")
+    op.drop_index("idx_config_profile_includes_profile", table_name="config_profile_includes")
+    op.drop_table("config_profile_includes")
+
+    # Drop config_profiles table
+    op.drop_index("idx_config_profiles_tool_type", table_name="config_profiles")
+    op.drop_index("idx_config_profiles_project", table_name="config_profiles")
+    op.drop_index("idx_config_profiles_user", table_name="config_profiles")
+    op.drop_table("config_profiles")
@@ -0,0 +1,28 @@
+"""add_git_mounts_to_config_profiles
+
+Revision ID: 2026_05_26_add_git_mounts
+Revises: f3d2dc90ba3a
+Create Date: 2026-05-26 12:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_26_add_git_mounts"
+down_revision: Union[str, Sequence[str], None] = "2026_05_24_220141"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "config_profiles",
+        sa.Column("git_mounts", sa.JSON(), nullable=True, default=list),
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("config_profiles", "git_mounts")
@@ -0,0 +1,41 @@
+"""make_project_id_nullable_in_git_repositories
+
+Revision ID: 2026_05_27_external_repos
+Revises: 2026_05_26_add_git_mounts
+Create Date: 2026-05-27 08:30:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_27_external_repos"
+down_revision: Union[str, Sequence[str], None] = "2026_05_26_add_git_mounts"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # Expand alembic_version version_num to avoid truncation errors
+    op.execute("ALTER TABLE alembic_version ALTER COLUMN version_num TYPE VARCHAR(64)")
+    
+    # Make project_id nullable to allow external repositories
+    op.alter_column(
+        "git_repositories",
+        "project_id",
+        existing_type=sa.UUID(),
+        nullable=True,
+    )
+
+
+def downgrade() -> None:
+    op.alter_column(
+        "git_repositories",
+        "project_id",
+        existing_type=sa.UUID(),
+        nullable=False,
+    )
+    op.execute("ALTER TABLE alembic_version ALTER COLUMN version_num TYPE VARCHAR(32)")
@@ -0,0 +1,381 @@
+"""add tool definition manifests
+
+Revision ID: 2026_05_28_add_tool_definition_manifests
+Revises: 20260527_160017_add_pi_agent
+Create Date: 2026-05-28T11:00:00
+
+"""
+
+import json
+import uuid
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_28_add_tool_definition_manifests"
+down_revision: Union[str, None] = "20260527_160017_add_pi_agent"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+BASE_UBUNTU_ID = uuid.UUID("a1b2c3d4-e5f6-7890-abcd-ef1234567890")
+PI_AGENT_MANIFEST_ID = uuid.UUID("d07b8376-2151-4119-8c1d-27f792aae9a3")
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+
+    # ── Create tool_definition_manifests table ───────────────────────
+    op.create_table(
+        "tool_definition_manifests",
+        sa.Column("id", sa.UUID(), nullable=False),
+        sa.Column("name", sa.String(64), nullable=False),
+        sa.Column("display_name", sa.String(128), nullable=False),
+        sa.Column("description", sa.Text(), nullable=True),
+        sa.Column("category", sa.String(64), nullable=True),
+        sa.Column("interface_type", sa.String(16), nullable=False),
+        sa.Column("base_image", sa.String(256), nullable=True),
+        sa.Column("base_definition_id", sa.UUID(), nullable=True),
+        sa.Column(
+            "base_version", sa.String(32), nullable=False, server_default="latest"
+        ),
+        sa.Column("manifest", sa.JSON(), nullable=False),
+        sa.Column("dockerfile_cache", sa.Text(), nullable=True),
+        sa.Column("compose_cache", sa.Text(), nullable=True),
+        sa.Column("version", sa.String(32), nullable=False, server_default="v1"),
+        sa.Column("is_base", sa.Boolean(), nullable=False, server_default="false"),
+        sa.Column("created_by_id", sa.UUID(), nullable=True),
+        sa.Column(
+            "created_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
+        ),
+        sa.Column(
+            "updated_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
+        ),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("name"),
+        sa.ForeignKeyConstraint(
+            ["base_definition_id"], ["tool_definition_manifests.id"]
+        ),
+        sa.ForeignKeyConstraint(["created_by_id"], ["users.id"]),
+        sa.CheckConstraint(
+            "(base_image IS NOT NULL) OR (base_definition_id IS NOT NULL)",
+            name="ck_tool_definition_manifests_base_required",
+        ),
+    )
+
+    # ── Add columns to tool_types ────────────────────────────────────
+    # Check if manifest_id exists before adding
+    conn = op.get_bind()
+    result = conn.execute(
+        sa.text("""
+            SELECT column_name FROM information_schema.columns
+            WHERE table_name = 'tool_types' AND column_name = 'manifest_id'
+        """)
+    )
+    if not result.fetchone():
+        op.add_column("tool_types", sa.Column("manifest_id", sa.UUID(), nullable=True))
+        op.create_foreign_key(
+            "fk_tool_types_manifest_id",
+            "tool_types",
+            "tool_definition_manifests",
+            ["manifest_id"],
+            ["id"],
+        )
+
+    # Update definition_type to allow 'legacy' and 'manifest'
+    result = conn.execute(
+        sa.text("""
+            SELECT constraint_name FROM information_schema.check_constraints
+            WHERE constraint_name = 'chk_definition_type'
+        """)
+    )
+    if result.fetchone():
+        op.drop_constraint("chk_definition_type", "tool_types", type_="check")
+
+    op.execute("ALTER TABLE tool_types ALTER COLUMN definition_type TYPE VARCHAR(16)")
+    op.execute(
+        "ALTER TABLE tool_types ALTER COLUMN definition_type SET DEFAULT 'legacy'"
+    )
+
+    # ── Add columns to tool_instances ────────────────────────────────
+    result = conn.execute(
+        sa.text("""
+            SELECT column_name FROM information_schema.columns
+            WHERE table_name = 'tool_instances' AND column_name = 'manifest_compiled_at'
+        """)
+    )
+    if not result.fetchone():
+        op.add_column(
+            "tool_instances",
+            sa.Column(
+                "manifest_compiled_at", sa.TIMESTAMP(timezone=True), nullable=True
+            ),
+        )
+
+    result = conn.execute(
+        sa.text("""
+            SELECT column_name FROM information_schema.columns
+            WHERE table_name = 'tool_instances' AND column_name = 'image_tag'
+        """)
+    )
+    if not result.fetchone():
+        op.add_column(
+            "tool_instances",
+            sa.Column("image_tag", sa.String(256), nullable=True),
+        )
+
+    # ── Data migration: create base definition + pi-agent manifest ───
+    conn.execute(
+        sa.text(
+            """
+            INSERT INTO tool_definition_manifests
+            (id, name, display_name, description, interface_type, base_image,
+             manifest, is_base, version, created_at, updated_at)
+            VALUES
+            (:base_id, 'ubuntu-24.04-dev', 'Ubuntu 24.04 Dev Base',
+             'Base development environment with build tools', 'terminal',
+             'ubuntu:24.04', :base_manifest, true, 'v1', now(), now())
+        """
+        ),
+        {
+            "base_id": BASE_UBUNTU_ID,
+            "base_manifest": json.dumps(
+                {
+                    "name": "ubuntu-24.04-dev",
+                    "display_name": "Ubuntu 24.04 Dev Base",
+                    "interface_type": "terminal",
+                    "base_image": "ubuntu:24.04",
+                    "packages": {
+                        "apt": [
+                            "curl",
+                            "wget",
+                            "git",
+                            "build-essential",
+                            "ca-certificates",
+                            "python3",
+                            "python3-pip",
+                        ]
+                    },
+                    "user": {
+                        "name": "user",
+                        "uid": 1000,
+                        "gid": 1000,
+                        "create_home": True,
+                        "shell": "/bin/bash",
+                    },
+                    "env": {"DEBIAN_FRONTEND": "noninteractive"},
+                }
+            ),
+        },
+    )
+
+    conn.execute(
+        sa.text(
+            """
+            INSERT INTO tool_definition_manifests
+            (id, name, display_name, description, category, interface_type,
+             base_definition_id, base_version, manifest, version, created_at, updated_at)
+            VALUES
+            (:manifest_id, 'pi-agent', 'Pi Agent',
+             'Terminal-based coding harness with nvim, ranger, tmux',
+             'development', 'terminal', :base_id, 'v1', :manifest, 'v1',
+             now(), now())
+        """
+        ),
+        {
+            "manifest_id": PI_AGENT_MANIFEST_ID,
+            "base_id": BASE_UBUNTU_ID,
+            "manifest": json.dumps(
+                {
+                    "name": "pi-agent",
+                    "display_name": "Pi Agent",
+                    "description": "Terminal-based coding harness",
+                    "category": "development",
+                    "interface_type": "terminal",
+                    "base_definition_id": str(BASE_UBUNTU_ID),
+                    "base_version": "v1",
+                    "packages": {
+                        "apt": [
+                            "neovim",
+                            "ranger",
+                            "tmux",
+                            "htop",
+                            "tree",
+                            "jq",
+                        ],
+                        "node": {"version": "20"},
+                        "npm_global": ["@earendil-works/pi-coding-agent"],
+                    },
+                    "user": {
+                        "name": "user",
+                        "uid": 1001,
+                        "gid": 1001,
+                        "create_home": True,
+                        "shell": "/bin/bash",
+                    },
+                    "env": {"DEBIAN_FRONTEND": "noninteractive"},
+                    "scripts": {
+                        "build": [
+                            "git config --global init.defaultBranch main && git config --global user.email 'dev@headquarter.local' && git config --global user.name 'Developer'",
+                            "mkdir -p /home/user/.config/ranger && echo 'set preview_files true' > /home/user/.config/ranger/rc.conf",
+                        ],
+                        "startup": [
+                            "if [ -d /workspace ]; then sudo chown -R user:user /workspace 2>/dev/null || true; fi",
+                        ],
+                    },
+                    "mounts": [
+                        {
+                            "name": "workspace",
+                            "target": "/workspace",
+                            "source_type": "repo",
+                            "writable": True,
+                            "owner": "user",
+                        },
+                        {
+                            "name": "ssh_keys",
+                            "target": "/home/user/.ssh",
+                            "source_type": "ssh_key",
+                            "mode": "0700",
+                            "file_mode": "0600",
+                            "readonly": True,
+                        },
+                        {
+                            "name": "pi_state",
+                            "target": "/tmp/.pi/agents",
+                            "source_type": "instance",
+                            "writable": True,
+                        },
+                        {
+                            "name": "pi_config",
+                            "target": "/home/user/.pi",
+                            "source_type": "git_mount",
+                            "git_mount_ref": "dotfiles",
+                            "writable": True,
+                            "owner": "user",
+                        },
+                    ],
+                    "runtime": {
+                        "command": ["/bin/bash"],
+                        "stdin_open": True,
+                        "tty": True,
+                        "working_dir": "/workspace",
+                    },
+                }
+            ),
+        },
+    )
+
+    # ── Update existing pi-agent tool_type ───────────────────────────
+    conn.execute(
+        sa.text(
+            """
+            UPDATE tool_types
+            SET manifest_id = :manifest_id,
+                definition_type = 'manifest',
+                dockerfile_template = NULL,
+                compose_template = NULL
+            WHERE name = 'pi-agent'
+        """
+        ),
+        {"manifest_id": PI_AGENT_MANIFEST_ID},
+    )
+
+
+def downgrade() -> None:
+    conn = op.get_bind()
+
+    # Restore pi-agent templates if manifest_id column exists
+    result = conn.execute(
+        sa.text("""
+            SELECT column_name FROM information_schema.columns
+            WHERE table_name = 'tool_types' AND column_name = 'manifest_id'
+        """)
+    )
+    has_manifest_id = result.fetchone() is not None
+
+    if has_manifest_id:
+        conn.execute(
+            sa.text(
+                """
+                UPDATE tool_types
+                SET manifest_id = NULL,
+                    definition_type = 'dockerfile',
+                    dockerfile_template = :dockerfile,
+                    compose_template = :compose
+                WHERE name = 'pi-agent'
+            """
+            ),
+            {
+                "dockerfile": """# Pi Coding Agent - Terminal-based coding harness
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y \\
+    curl wget git neovim ranger tmux htop tree jq \\
+    ca-certificates python3 python3-pip build-essential \\
+    && rm -rf /var/lib/apt/lists/*
+
+RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \\
+    && apt-get install -y nodejs \\
+    && rm -rf /var/lib/apt/lists/*
+
+RUN npm install -g --ignore-scripts @earendil-works/pi-coding-agent
+
+RUN useradd -m -s /bin/bash user
+WORKDIR /home/user
+
+RUN git config --global init.defaultBranch main \\
+    && git config --global user.email "dev@headquarter.local" \\
+    && git config --global user.name "Developer"
+
+RUN echo 'set -g mouse on\\nset -g default-terminal "screen-256color"' > /home/user/.tmux.conf
+
+RUN mkdir -p /home/user/.config/ranger \\
+    && echo 'set preview_files true\\nset use_preview_script true' > /home/user/.config/ranger/rc.conf
+
+RUN mkdir -p /home/user/.pi/agent
+
+USER user
+
+CMD ["/bin/bash"]
+""",
+                "compose": """services:
+  app:
+    build: .
+    stdin_open: true
+    tty: true
+    volumes:
+      - ${REPO_PATH}:/workspace
+    working_dir: /workspace
+    command: /bin/bash""",
+            },
+        )
+
+    # Drop columns conditionally
+    result = conn.execute(
+        sa.text("""
+            SELECT column_name FROM information_schema.columns
+            WHERE table_name = 'tool_instances' AND column_name = 'image_tag'
+        """)
+    )
+    if result.fetchone():
+        op.drop_column("tool_instances", "image_tag")
+
+    result = conn.execute(
+        sa.text("""
+            SELECT column_name FROM information_schema.columns
+            WHERE table_name = 'tool_instances' AND column_name = 'manifest_compiled_at'
+        """)
+    )
+    if result.fetchone():
+        op.drop_column("tool_instances", "manifest_compiled_at")
+
+    if has_manifest_id:
+        op.drop_constraint(
+            "fk_tool_types_manifest_id", "tool_types", type_="foreignkey"
+        )
+        op.drop_column("tool_types", "manifest_id")
+
+    op.drop_table("tool_definition_manifests")
@@ -0,0 +1,23 @@
+"""merge_remove_is_builtin_and_add_config_profiles
+
+Revision ID: 6fc7bfcf199f
+Revises: 2026_05_23_remove_is_builtin, 2026_05_24_add_config_profiles
+Create Date: 2026-05-24 18:00:43.990361
+"""
+
+
+
+
+# revision identifiers, used by Alembic.
+revision = '6fc7bfcf199f'
+down_revision = ('2026_05_23_remove_is_builtin', '2026_05_24_add_config_profiles')
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    pass
+
+
+def downgrade() -> None:
+    pass
@@ -0,0 +1,23 @@
+"""merge_single_interface_and_clone_mode
+
+Revision ID: f3d2dc90ba3a
+Revises: 0015_single_interface, 2026_05_22_add_clone_mode
+Create Date: 2026-05-24 10:43:14.000000
+
+"""
+from typing import Sequence, Union
+
+
+# revision identifiers, used by Alembic.
+revision: str = "f3d2dc90ba3a"
+down_revision: Union[str, Sequence[str], None] = ("0015_single_interface", "2026_05_22_add_clone_mode")
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    pass
+
+
+def downgrade() -> None:
+    pass
@@ -48,7 +48,7 @@ async def login(next: str = "/") -> RedirectResponse:
        redirect_uri=redirect_uri,
        state=state,
    )
-    logger.info("Auth login initiated: redirect_uri=%s, next=%s", redirect_uri, next)
+    logger.debug("Auth login initiated: redirect_uri=%s, next=%s", redirect_uri, next)
    response = RedirectResponse(location)
    response.set_cookie("auth_state", state, httponly=True, samesite="lax")
    response.set_cookie("auth_next", next, httponly=True, samesite="lax")
@@ -63,7 +63,7 @@ async def callback(
    auth_next: str | None = Cookie(default="/"),
    session: AsyncSession = Depends(get_db_session),
 ) -> RedirectResponse:
-    logger.info("Auth callback received: code=%s... state=%s", code[:10] if code else "None", state[:10] if state else "None")
+    logger.debug("Auth callback received: code=%s... state=%s", code[:10] if code else "None", state[:10] if state else "None")
    
    if auth_state is None or auth_state != state:
        logger.warning("State mismatch: cookie=%s, param=%s", auth_state, state)
@@ -71,7 +71,7 @@ async def callback(

    settings = Settings()
    redirect_uri = f"{settings.api_base_url}/auth/callback"
-    logger.info("Exchanging code for tokens (redirect_uri=%s)", redirect_uri)
+    logger.debug("Exchanging code for tokens (redirect_uri=%s)", redirect_uri)
    
    async with httpx.AsyncClient() as client:
        try:
@@ -92,7 +92,7 @@ async def callback(
                access_token=token_payload["access_token"],
                client=client,
            )
-            logger.info("User info fetched successfully")
+            logger.debug("User info fetched successfully")
        except Exception as exc:
            logger.error("User info fetch failed: %s", exc)
            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="failed to fetch user info")
@@ -100,19 +100,19 @@ async def callback(
    authentik_id = str(user_info.get("sub", ""))
    email = str(user_info.get("email", f"{authentik_id}@authentik.local"))
    name = str(user_info.get("name", email))
-    logger.info("User info: authentik_id=%s, email=%s, name=%s", authentik_id, email, name)
+    logger.debug("User info: authentik_id=%s, email=%s, name=%s", authentik_id, email, name)

    try:
        user = await session.scalar(select(User).where(User.authentik_id == authentik_id))
        if user is None:
-            logger.info("Creating new user: authentik_id=%s", authentik_id)
+            logger.debug("Creating new user: authentik_id=%s", authentik_id)
            user = User(email=email, name=name, authentik_id=authentik_id, avatar_url=None)
            session.add(user)
            await session.commit()
            await session.refresh(user)
            logger.info("New user created: id=%s", user.id)
        else:
-            logger.info("Existing user found: id=%s, updating info", user.id)
+            logger.debug("Existing user found: id=%s, updating info", user.id)
            user.email = email
            user.name = name
            await session.commit()
@@ -165,20 +165,20 @@ async def me(
    session_cookie: str | None = Cookie(default=None, alias="session"),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict[str, Any]:
-    logger.info("Auth /me called, cookie present: %s", bool(session_cookie))
+    logger.debug("Auth /me called, cookie present: %s", bool(session_cookie))
    
    if not session_cookie:
        logger.warning("Auth /me: missing session cookie")
        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing session")

    settings = Settings()
-    logger.info("Auth /me: cookie_domain=%s, cookie_secure=%s, cookie_samesite=%s", 
+    logger.debug("Auth /me: cookie_domain=%s, cookie_secure=%s, cookie_samesite=%s", 
                settings.cookie_domain, settings.cookie_secure, settings.cookie_samesite)
    
    try:
        payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
        user_id = payload["user_id"]
-        logger.info("Auth /me: decoded session for user_id=%s", user_id)
+        logger.debug("Auth /me: decoded session for user_id=%s", user_id)
    except ValueError as exc:
        logger.warning("Auth /me: invalid session: %s", exc)
        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail=str(exc))
@@ -8,6 +8,7 @@ from pydantic import BaseModel, Field, field_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession

+from src.api.shared_validators import validate_files as _validate_files, validate_mount_path as _validate_mount_path
 from src.auth.dependencies import get_current_user_id, get_db_session
 from src.models.config_folder import ConfigFolder

@@ -15,9 +16,6 @@ logger = logging.getLogger(__name__)

 router = APIRouter(prefix="/config-folders", tags=["config-folders"])

-MAX_FOLDER_SIZE_MB = 10
-MAX_FOLDER_SIZE_BYTES = MAX_FOLDER_SIZE_MB * 1024 * 1024
-

 class ConfigFolderCreate(BaseModel):
    name: str = Field(description="Folder name (unique per user)")
@@ -28,24 +26,12 @@ class ConfigFolderCreate(BaseModel):
    @field_validator("mount_path")
    @classmethod
    def validate_mount_path(cls, v: str) -> str:
-        if not v.startswith("/"):
-            raise ValueError("Mount path must be absolute (start with /)")
-        return v
+        return _validate_mount_path(v)

    @field_validator("files")
    @classmethod
    def validate_files(cls, v: dict) -> dict:
-        total_size = 0
-        for path, content in v.items():
-            # Check for path traversal
-            if ".." in path or path.startswith("/"):
-                raise ValueError(f"Invalid file path: {path}")
-            total_size += len(content.encode("utf-8"))
-        
-        if total_size > MAX_FOLDER_SIZE_BYTES:
-            raise ValueError(f"Total folder size exceeds {MAX_FOLDER_SIZE_MB}MB limit")
-        
-        return v
+        return _validate_files(v)


 class ConfigFolderUpdate(BaseModel):
@@ -58,29 +44,12 @@ class ConfigFolderUpdate(BaseModel):
    @field_validator("mount_path")
    @classmethod
    def validate_mount_path(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if not v.startswith("/"):
-            raise ValueError("Mount path must be absolute (start with /)")
-        return v
+        return _validate_mount_path(v)

    @field_validator("files")
    @classmethod
    def validate_files(cls, v: dict | None) -> dict | None:
-        if v is None:
-            return v
-        
-        total_size = 0
-        for path, content in v.items():
-            # Check for path traversal
-            if ".." in path or path.startswith("/"):
-                raise ValueError(f"Invalid file path: {path}")
-            total_size += len(content.encode("utf-8"))
-        
-        if total_size > MAX_FOLDER_SIZE_BYTES:
-            raise ValueError(f"Total folder size exceeds {MAX_FOLDER_SIZE_MB}MB limit")
-        
-        return v
+        return _validate_files(v)


 class ProjectOverrideCreate(BaseModel):
@@ -90,11 +59,7 @@ class ProjectOverrideCreate(BaseModel):
    @field_validator("mount_path")
    @classmethod
    def validate_mount_path(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if not v.startswith("/"):
-            raise ValueError("Mount path must be absolute (start with /)")
-        return v
+        return _validate_mount_path(v)


 class ConfigFolderResponse(BaseModel):
@@ -0,0 +1,723 @@
+"""Config profile API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, Query, status
+from pydantic import BaseModel, Field, field_validator
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.orm import selectinload
+
+from src.api.shared_validators import validate_env_vars as _validate_env_vars
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models.project import Project
+from src.models.tool_type import ToolType
+from src.services.config_profile_resolver import (
+    ConfigProfileCycleError,
+    check_include_cycle,
+    resolve_profile,
+    resolved_profile_to_dict,
+)
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
+
+MAX_PROFILE_SIZE_MB = 10
+MAX_PROFILE_SIZE_BYTES = MAX_PROFILE_SIZE_MB * 1024 * 1024
+
+
+def _validate_uuid(v: str | None) -> str | None:
+    if v is None:
+        return v
+    try:
+        uuid.UUID(v)
+    except ValueError:
+        raise ValueError(f"Invalid UUID: {v}")
+    return v
+
+
+def _calculate_profile_size(data: dict) -> int:
+    """Calculate approximate serialized size of profile data."""
+    total = 0
+    for key, value in data.get("env_vars", {}).items():
+        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
+    for key, value in data.get("runtime_hints", {}).items():
+        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
+    for mount in data.get("mounts", []):
+        total += len(str(mount.get("target", "")).encode("utf-8"))
+        total += len(str(mount.get("mode", "")).encode("utf-8"))
+        for path, content in mount.get("files", {}).items():
+            total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
+    for path, content in data.get("files", {}).items():
+        total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
+    return total
+
+
+class GitMountItem(BaseModel):
+    remote_url: str = Field(description="Git remote URL (HTTPS or SSH)")
+    source_path: str = Field(default=".", description="Path within repository (supports glob patterns)")
+    target_path: str = Field(description="Absolute path inside container")
+    branch: str | None = Field(default=None, description="Optional branch or tag name")
+
+    @field_validator("remote_url")
+    @classmethod
+    def validate_remote_url(cls, v: str) -> str:
+        if not v.startswith(("http://", "https://", "git@", "ssh://")):
+            raise ValueError("remote_url must be a valid git URL (https://, git@, or ssh://)")
+        return v
+
+    @field_validator("source_path")
+    @classmethod
+    def validate_source_path(cls, v: str) -> str:
+        if v.startswith("/"):
+            raise ValueError("source_path must be relative (no leading /)")
+        if ".." in v:
+            raise ValueError("source_path cannot contain path traversal (..)")
+        return v
+
+    @field_validator("target_path")
+    @classmethod
+    def validate_target_path(cls, v: str) -> str:
+        if ".." in v:
+            raise ValueError("target_path cannot contain path traversal (..)")
+        return v
+
+
+class MountItem(BaseModel):
+    target: str = Field(description="Absolute mount target path")
+    mode: str = Field(default="rw", description="Mount mode: ro or rw")
+    files: dict = Field(default_factory=dict, description="Files as {relative_path: content}")
+
+    @field_validator("target")
+    @classmethod
+    def validate_target(cls, v: str) -> str:
+        if not v.startswith("/"):
+            raise ValueError("Mount target must be absolute (start with /)")
+        return v
+
+    @field_validator("mode")
+    @classmethod
+    def validate_mode(cls, v: str) -> str:
+        if v not in ("ro", "rw"):
+            raise ValueError("Mount mode must be 'ro' or 'rw'")
+        return v
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict) -> dict:
+        for path in v.keys():
+            if ".." in path or not path:
+                raise ValueError(f"Invalid file path: {path}")
+            if path.startswith("/"):
+                raise ValueError(
+                    f"Mount file paths must be relative (got: {path}). "
+                    f"The mount target defines the absolute container path."
+                )
+        return v
+
+
+class ConfigProfileCreate(BaseModel):
+    name: str = Field(description="Profile name (unique per user)")
+    description: str | None = Field(default=None, description="Optional description")
+    project_id: str | None = Field(default=None, description="Optional project ID")
+    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
+    env_vars: dict = Field(default_factory=dict, description="Environment variables")
+    runtime_hints: dict = Field(default_factory=dict, description="Runtime hints")
+    mounts: list[MountItem] = Field(default_factory=list, description="Mount definitions")
+    files: dict = Field(default_factory=dict, description="Files as {relative_path: content}")
+    git_mounts: list[GitMountItem] = Field(default_factory=list, description="Git repository mounts")
+    is_default: bool = Field(default=False, description="Whether this is the default profile for its scope")
+
+    @field_validator("project_id", "tool_type_id")
+    @classmethod
+    def validate_uuids(cls, v: str | None) -> str | None:
+        return _validate_uuid(v)
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict) -> dict:
+        for path in v.keys():
+            if ".." in path or not path:
+                raise ValueError(f"Invalid file path: {path}")
+            if path.startswith("/"):
+                raise ValueError(
+                    f"File paths must be relative (got: {path}). "
+                    f"Use Mounts for absolute container paths."
+                )
+        return v
+
+    @field_validator("env_vars")
+    @classmethod
+    def validate_env_vars(cls, v: dict) -> dict:
+        result = _validate_env_vars(v)
+        if result is None:
+            raise ValueError("env_vars must be a JSON object")
+        return result
+
+    @field_validator("runtime_hints")
+    @classmethod
+    def validate_runtime_hints(cls, v: dict) -> dict:
+        if not isinstance(v, dict):
+            raise ValueError("runtime_hints must be a JSON object")
+        return v
+
+    @field_validator("mounts")
+    @classmethod
+    def validate_mounts(cls, v: list) -> list:
+        if not isinstance(v, list):
+            raise ValueError("mounts must be a JSON array")
+        return v
+
+
+class ConfigProfileUpdate(BaseModel):
+    name: str | None = Field(default=None, description="Profile name")
+    description: str | None = Field(default=None, description="Optional description")
+    project_id: str | None = Field(default=None, description="Optional project ID")
+    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
+    env_vars: dict | None = Field(default=None, description="Environment variables")
+    runtime_hints: dict | None = Field(default=None, description="Runtime hints")
+    mounts: list[MountItem] | None = Field(default=None, description="Mount definitions")
+    files: dict | None = Field(default=None, description="Files as {relative_path: content}")
+    git_mounts: list[GitMountItem] | None = Field(default=None, description="Git repository mounts")
+    is_default: bool | None = Field(default=None, description="Whether this is the default profile")
+
+    @field_validator("project_id", "tool_type_id")
+    @classmethod
+    def validate_uuids(cls, v: str | None) -> str | None:
+        return _validate_uuid(v)
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict | None) -> dict | None:
+        if v is None:
+            return v
+        for path in v.keys():
+            if ".." in path or path.startswith("/") or not path:
+                raise ValueError(f"Invalid file path: {path}")
+        return v
+
+
+class ConfigProfileIncludeUpdate(BaseModel):
+    includes: list[str] = Field(description="Ordered list of included profile IDs")
+
+    @field_validator("includes")
+    @classmethod
+    def validate_includes(cls, v: list) -> list:
+        for item in v:
+            try:
+                uuid.UUID(item)
+            except ValueError:
+                raise ValueError(f"Invalid UUID in includes: {item}")
+        return v
+
+
+class ConfigProfileResponse(BaseModel):
+    id: str
+    user_id: str
+    name: str
+    description: str | None
+    project_id: str | None
+    tool_type_id: str | None
+    env_vars: dict
+    runtime_hints: dict
+    mounts: list
+    files: dict
+    git_mounts: list
+    is_default: bool
+    includes: list[dict]
+    created_at: str
+    updated_at: str
+
+
+async def _get_profile_with_includes(session: AsyncSession, profile_id: uuid.UUID) -> ConfigProfile | None:
+    """Fetch a profile with includes eagerly loaded."""
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile_id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    return result.scalar_one_or_none()
+
+
+async def _check_access(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    project_id: uuid.UUID | None = None,
+    tool_type_id: uuid.UUID | None = None,
+) -> None:
+    """Verify user has access to referenced project and tool type."""
+    if project_id is not None:
+        project = await session.get(Project, project_id)
+        if project is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Project not found")
+        # Add ownership check if needed; for now just verify existence
+    if tool_type_id is not None:
+        tool_type = await session.get(ToolType, tool_type_id)
+        if tool_type is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Tool type not found")
+
+
+async def _validate_git_mounts(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    git_mounts: list[dict],
+    project_id: uuid.UUID | None = None,
+) -> None:
+    """Validate git mount URLs.
+    
+    Simply checks that remote_url looks like a valid git URL.
+    Actual clone validation happens at instance startup time.
+    """
+    for mount in git_mounts:
+        remote_url = mount.get("remote_url")
+        if not remote_url:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="Git mount missing remote_url",
+            )
+        
+        if not remote_url.startswith(("http://", "https://", "git@", "ssh://")):
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail=f"Invalid git URL: {remote_url}",
+            )
+
+
+def _profile_to_response(profile: ConfigProfile, includes: list[ConfigProfileInclude] | None = None) -> dict:
+    return {
+        "id": str(profile.id),
+        "user_id": str(profile.user_id),
+        "name": profile.name,
+        "description": profile.description,
+        "project_id": str(profile.project_id) if profile.project_id else None,
+        "tool_type_id": str(profile.tool_type_id) if profile.tool_type_id else None,
+        "env_vars": profile.env_vars or {},
+        "runtime_hints": profile.runtime_hints or {},
+        "mounts": profile.mounts or [],
+        "git_mounts": profile.git_mounts or [],
+        "files": profile.files or {},
+        "is_default": profile.is_default,
+        "includes": [
+            {
+                "id": str(inc.id),
+                "included_profile_id": str(inc.included_profile_id),
+                "order_index": inc.order_index,
+            }
+            for inc in (includes or profile.includes)
+        ],
+        "created_at": profile.created_at.isoformat() if profile.created_at else None,
+        "updated_at": profile.updated_at.isoformat() if profile.updated_at else None,
+    }
+
+
+@router.get("", response_model=list[ConfigProfileResponse])
+async def list_config_profiles(
+    project_id: str | None = Query(None, description="Filter by project compatibility"),
+    tool_type_id: str | None = Query(None, description="Filter by tool type compatibility"),
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """List config profiles, optionally filtered by compatibility."""
+    user_uuid = current_user_id
+    query = select(ConfigProfile).where(ConfigProfile.user_id == user_uuid).options(selectinload(ConfigProfile.includes))
+
+    if project_id or tool_type_id:
+        # Compatibility filter: include portable profiles and matching scoped profiles
+        project_uuid = uuid.UUID(project_id) if project_id else None
+        tool_uuid = uuid.UUID(tool_type_id) if tool_type_id else None
+
+        from sqlalchemy import or_
+
+        conditions: list = []
+        # Portable profiles (no project, no tool)
+        conditions.append(
+            (ConfigProfile.project_id.is_(None)) & (ConfigProfile.tool_type_id.is_(None))
+        )
+        if project_uuid:
+            # Profiles matching this project (with or without tool)
+            conditions.append(ConfigProfile.project_id == project_uuid)
+        if tool_uuid:
+            # Profiles matching this tool (with or without project)
+            conditions.append(ConfigProfile.tool_type_id == tool_uuid)
+        if project_uuid and tool_uuid:
+            # Exact match
+            conditions.append(
+                (ConfigProfile.project_id == project_uuid) & (ConfigProfile.tool_type_id == tool_uuid)
+            )
+
+        query = query.where(or_(*conditions))
+
+    result = await session.execute(query)
+    profiles = result.scalars().all()
+    return [_profile_to_response(p) for p in profiles]
+
+
+@router.post("", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED)
+async def create_config_profile(
+    data: ConfigProfileCreate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Create a new config profile."""
+    user_uuid = current_user_id
+
+    # Check for duplicate name
+    existing = await session.execute(
+        select(ConfigProfile).where(
+            ConfigProfile.user_id == user_uuid,
+            ConfigProfile.name == data.name,
+        ).options(selectinload(ConfigProfile.includes))
+    )
+    if existing.scalar_one_or_none() is not None:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"Profile with name '{data.name}' already exists",
+        )
+
+    # Validate references
+    project_uuid = uuid.UUID(data.project_id) if data.project_id else None
+    tool_uuid = uuid.UUID(data.tool_type_id) if data.tool_type_id else None
+    await _check_access(session, user_uuid, project_uuid, tool_uuid)
+    
+    # Validate git mounts reference existing repositories
+    if data.git_mounts:
+        git_mounts_data = [m.model_dump() if hasattr(m, "model_dump") else m for m in data.git_mounts]
+        await _validate_git_mounts(session, user_uuid, git_mounts_data, project_uuid)
+
+    # Check size
+    size = _calculate_profile_size(data.model_dump())
+    if size > MAX_PROFILE_SIZE_BYTES:
+        raise HTTPException(
+            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
+        )
+
+    profile = ConfigProfile(
+        user_id=user_uuid,
+        name=data.name,
+        description=data.description,
+        project_id=project_uuid,
+        tool_type_id=tool_uuid,
+        env_vars=data.env_vars,
+        runtime_hints=data.runtime_hints,
+        mounts=[m.model_dump() for m in data.mounts],
+        git_mounts=[m.model_dump() for m in data.git_mounts],
+        files=data.files,
+        is_default=data.is_default,
+    )
+    session.add(profile)
+    await session.commit()
+
+    # Re-fetch with includes to avoid lazy loading issues
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile.id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    profile = result.scalar_one()
+
+    logger.debug("Created config profile %s for user %s", profile.id, user_uuid)
+    return _profile_to_response(profile)
+
+
+@router.get("/{profile_id}", response_model=ConfigProfileResponse)
+async def get_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Get a config profile by ID."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
+    if profile.user_id != current_user_id:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
+    return _profile_to_response(profile)
+
+
+@router.put("/{profile_id}", response_model=ConfigProfileResponse)
+async def update_config_profile(
+    profile_id: str,
+    data: ConfigProfileUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
+    if profile.user_id != current_user_id:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
+
+    update_data = data.model_dump(exclude_unset=True)
+
+    # Handle name uniqueness
+    if "name" in update_data:
+        existing = await session.execute(
+            select(ConfigProfile).where(
+                ConfigProfile.user_id == profile.user_id,
+                ConfigProfile.name == update_data["name"],
+                ConfigProfile.id != profile.id,
+            )
+        )
+        if existing.scalar_one_or_none() is not None:
+            raise HTTPException(
+                status_code=status.HTTP_409_CONFLICT,
+                detail=f"Profile with name '{update_data['name']}' already exists",
+            )
+
+    # Validate references
+    project_uuid = (
+        uuid.UUID(update_data["project_id"])
+        if "project_id" in update_data and update_data["project_id"]
+        else (profile.project_id if "project_id" not in update_data else None)
+    )
+    tool_uuid = (
+        uuid.UUID(update_data["tool_type_id"])
+        if "tool_type_id" in update_data and update_data["tool_type_id"]
+        else (profile.tool_type_id if "tool_type_id" not in update_data else None)
+    )
+    await _check_access(session, profile.user_id, project_uuid, tool_uuid)
+    
+    # Validate git mounts reference existing repositories
+    if "git_mounts" in update_data and update_data["git_mounts"] is not None:
+        git_mounts_data = [
+            m.model_dump() if hasattr(m, "model_dump") else m 
+            for m in update_data["git_mounts"]
+        ]
+        await _validate_git_mounts(session, profile.user_id, git_mounts_data, project_uuid)
+
+    # Check size
+    current_data = _profile_to_response(profile)
+    merged = {**current_data, **update_data}
+    size = _calculate_profile_size(merged)
+    if size > MAX_PROFILE_SIZE_BYTES:
+        raise HTTPException(
+            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
+        )
+
+    # Apply updates
+    for field_name, value in update_data.items():
+        if field_name in ("project_id", "tool_type_id"):
+            value = uuid.UUID(value) if value else None
+        elif field_name == "mounts" and value is not None:
+            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
+        elif field_name == "git_mounts" and value is not None:
+            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
+        setattr(profile, field_name, value)
+
+    await session.commit()
+
+    # Re-fetch with includes to avoid lazy loading issues
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile.id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    profile = result.scalar_one()
+
+    logger.debug("Updated config profile %s", profile.id)
+    return _profile_to_response(profile)
+
+
+@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Delete a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
+    if profile.user_id != current_user_id:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
+
+    await session.delete(profile)
+    await session.commit()
+
+    logger.debug("Deleted config profile %s", profile_id)
+    return None
+
+
+@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
+async def update_profile_includes(
+    profile_id: str,
+    data: ConfigProfileIncludeUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update the ordered includes for a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
+    if profile.user_id != current_user_id:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
+
+    # Validate all included profiles exist and belong to the user
+    included_uuids = [uuid.UUID(inc_id) for inc_id in data.includes]
+    for inc_uuid in included_uuids:
+        inc_profile = await session.get(ConfigProfile, inc_uuid)
+        if inc_profile is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Included profile not found: {inc_uuid}",
+            )
+        if inc_profile.user_id != current_user_id:
+            raise HTTPException(
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail=f"Not authorized to include profile: {inc_uuid}",
+            )
+        if inc_uuid == profile.id:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="Profile cannot include itself",
+            )
+
+    # Check for cycles
+    cycle = await check_include_cycle(session, profile.id, None)
+    if cycle is None and included_uuids:
+        # Check each new include would not create a cycle
+        for inc_uuid in included_uuids:
+            cycle = await check_include_cycle(session, profile.id, inc_uuid)
+            if cycle is not None:
+                break
+
+    if cycle is not None:
+        cycle_str = " -> ".join(str(c) for c in cycle)
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"Include cycle detected: {cycle_str}",
+        )
+
+    # Remove existing includes
+    result = await session.execute(
+        select(ConfigProfileInclude).where(ConfigProfileInclude.profile_id == profile.id)
+    )
+    for existing in result.scalars().all():
+        await session.delete(existing)
+    await session.flush()
+
+    # Add new includes
+    for order_index, inc_uuid in enumerate(included_uuids):
+        include = ConfigProfileInclude(
+            profile_id=profile.id,
+            included_profile_id=inc_uuid,
+            order_index=order_index,
+        )
+        session.add(include)
+    await session.flush()
+
+    await session.commit()
+
+    # Re-fetch profile (includes loaded separately due to SQLite async issue)
+    result = await session.execute(
+        select(ConfigProfile).where(ConfigProfile.id == profile.id)
+    )
+    profile = result.scalar_one()
+
+    inc_result = await session.execute(
+        select(ConfigProfileInclude).where(ConfigProfileInclude.profile_id == profile.id)
+    )
+    direct_includes = inc_result.scalars().all()
+
+    logger.debug("Updated includes for config profile %s", profile.id)
+    return _profile_to_response(profile, list(direct_includes))
+
+
+@router.get("/{profile_id}/preview")
+async def preview_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Preview the resolved output of a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
+    if profile.user_id != current_user_id:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
+
+    try:
+        resolved = await resolve_profile(session, profile.id)
+    except ConfigProfileCycleError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=str(exc),
+        )
+
+    return resolved_profile_to_dict(resolved)
+
+
+@router.get("/defaults/resolve")
+async def resolve_default_profile(
+    project_id: str = Query(..., description="Project ID"),
+    tool_type_id: str = Query(..., description="Tool type ID"),
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Resolve the default config profile for a project/tool combination.
+
+    Selects by specificity:
+    1. project+tool explicit default
+    2. project explicit default
+    3. tool explicit default
+    4. global/user explicit default
+    5. first created compatible profile
+    6. none (returns null)
+    """
+    user_uuid = current_user_id
+    project_uuid = uuid.UUID(project_id)
+    tool_uuid = uuid.UUID(tool_type_id)
+
+    # Fetch all compatible profiles ordered by created_at
+    query = (
+        select(ConfigProfile)
+        .where(ConfigProfile.user_id == user_uuid)
+        .where(
+            (ConfigProfile.project_id.is_(None) & ConfigProfile.tool_type_id.is_(None))
+            | (ConfigProfile.project_id == project_uuid)
+            | (ConfigProfile.tool_type_id == tool_uuid)
+            | (
+                (ConfigProfile.project_id == project_uuid)
+                & (ConfigProfile.tool_type_id == tool_uuid)
+            )
+        )
+        .order_by(ConfigProfile.created_at)
+    )
+    result = await session.execute(query)
+    profiles = result.scalars().all()
+
+    if not profiles:
+        return {"profile_id": None, "profile_name": None}
+
+    # Check explicit defaults by specificity
+    explicit_defaults = [p for p in profiles if p.is_default]
+
+    # Most specific: project+tool
+    for p in explicit_defaults:
+        if p.project_id == project_uuid and p.tool_type_id == tool_uuid:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: project only
+    for p in explicit_defaults:
+        if p.project_id == project_uuid and p.tool_type_id is None:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: tool only
+    for p in explicit_defaults:
+        if p.project_id is None and p.tool_type_id == tool_uuid:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: global/user (no project, no tool)
+    for p in explicit_defaults:
+        if p.project_id is None and p.tool_type_id is None:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Fall back to first created compatible profile
+    first = profiles[0]
+    return {"profile_id": str(first.id), "profile_name": first.name}
@@ -10,11 +10,10 @@ from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession

-from src.auth.dependencies import get_current_user_id, get_db_session
+from src.auth.dependencies import _get_owned_project, _get_user, get_current_user_id, get_db_session
 from src.config import Settings
 from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.user import User
+from src.models.ssh_key import SSHKey
 from src.utils.git_files import (
    commit_file,
    get_file_content,
@@ -34,46 +33,13 @@ from src.utils.git_control import (
 )
 from src.utils.git_history import get_commit_detail, get_commit_history
 from src.utils.git_url_parser import parse_git_url
+from src.services.ssh_keys import _get_fernet

 router = APIRouter(prefix="/projects", tags=["git-repositories"])

 logger = logging.getLogger(__name__)


-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    """Fetch a user by ID or raise 401 if not found."""
-    user = await session.get(User, user_id)
-    if user is None:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
-    return user
-
-
-async def _get_owned_project(
-    project_id: uuid.UUID,
-    user_id: uuid.UUID,
-    session: AsyncSession,
-) -> Project:
-    """Fetch a project and verify ownership.
-
-    Args:
-        project_id: UUID of the project.
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        The project if found and owned by the user.
-
-    Raises:
-        HTTPException: If project not found or user is not the owner.
-    """
-    project = await session.get(Project, project_id)
-    if project is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="project not found")
-    if project.owner_id != user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not project owner")
-    return project
-
-
 def _get_repo_path(user_id: uuid.UUID, project_id: uuid.UUID, name: str) -> str:
    """Generate the filesystem path for a repository.

@@ -94,41 +60,97 @@ def _build_provider_clone_url(owner: str, repo: str) -> str:
    return f"git@git.commumedia.org:{owner}/{repo}.git"


-def _preflight_remote_repository(remote_url: str) -> None:
+def _prepare_ssh_env(ssh_key: SSHKey | None) -> dict | None:
+    """Prepare environment variables for git commands with SSH authentication.
+    
+    Returns a dict of extra env vars, or None if no SSH key provided.
+    The caller is responsible for cleaning up the temporary key file.
+    """
+    if ssh_key is None:
+        return None
+    
+    import tempfile
+    
+    # Decrypt private key
+    fernet = _get_fernet()
+    private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
+    
+    # Write to temp file with restricted permissions
+    fd, key_path = tempfile.mkstemp(prefix="ssh_key_")
+    try:
+        os.write(fd, private_key.encode())
+    finally:
+        os.close(fd)
+    os.chmod(key_path, 0o600)
+    
+    # Return env vars and the key path for cleanup
+    env = {
+        "GIT_SSH_COMMAND": f"ssh -i {key_path} -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
+    }
+    return env, key_path
+
+
+def _preflight_remote_repository(remote_url: str, ssh_key: SSHKey | None = None) -> None:
    """Verify a remote repository is reachable before cloning."""
+    env = None
+    key_path = None
+    
+    if ssh_key is not None:
+        ssh_result = _prepare_ssh_env(ssh_key)
+        if ssh_result:
+            env, key_path = ssh_result
+    
    try:
        result = subprocess.run(
            ["git", "ls-remote", remote_url],
            capture_output=True,
            text=True,
            timeout=60,
+            env={**os.environ, **env} if env else None,
        )
    except subprocess.TimeoutExpired:
        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="remote repository check timed out")
    except FileNotFoundError:
        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
+    finally:
+        if key_path and os.path.exists(key_path):
+            os.unlink(key_path)

    if result.returncode != 0:
+        logger.error("Preflight check failed for %s: stderr=%s", remote_url, result.stderr)
        raise HTTPException(
            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="repository not found or inaccessible",
+            detail=f"repository not found or inaccessible: {result.stderr}",
        )


-def _clone_working_repository(remote_url: str, repo_path: str) -> None:
+def _clone_working_repository(remote_url: str, repo_path: str, ssh_key: SSHKey | None = None) -> None:
+    env = None
+    key_path = None
+    
+    if ssh_key is not None:
+        ssh_result = _prepare_ssh_env(ssh_key)
+        if ssh_result:
+            env, key_path = ssh_result
+    
    try:
        result = subprocess.run(
            ["git", "clone", remote_url, repo_path],
            capture_output=True,
            text=True,
            timeout=300,
+            env={**os.environ, **env} if env else None,
        )
    except subprocess.TimeoutExpired:
        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="clone operation timed out")
    except FileNotFoundError:
        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
+    finally:
+        if key_path and os.path.exists(key_path):
+            os.unlink(key_path)

    if result.returncode != 0:
+        logger.error("Clone failed for %s: stderr=%s", remote_url, result.stderr)
        raise HTTPException(
            status_code=status.HTTP_400_BAD_REQUEST,
            detail=f"failed to clone repository: {result.stderr}",
@@ -175,6 +197,7 @@ class GitRepositoryCreate(BaseModel):
    name: str
    remote_url: str | None = None
    force_original_url: bool = False
+    ssh_key_id: str | None = None


 class URLParseRequest(BaseModel):
@@ -197,15 +220,166 @@ class GitRepositoryResponse(BaseModel):
    id: uuid.UUID
    name: str
    path: str
-    project_id: uuid.UUID
+    project_id: uuid.UUID | None
    owner_id: uuid.UUID
    is_mirror: bool
    remote_url: str | None
    last_push: datetime | None
+    ssh_key_id: uuid.UUID | None
    created_at: datetime
    updated_at: datetime


+@router.get(
+    "/repositories",
+    response_model=list[GitRepositoryResponse],
+    summary="List all user repositories",
+    description="List all git repositories owned by the user, including external repositories not tied to any project.",
+)
+async def list_user_repositories(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> list[GitRepository]:
+    """List all repositories owned by the user.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        List of all repositories owned by the user.
+    """
+    result = await session.execute(
+        select(GitRepository).where(GitRepository.owner_id == user_id)
+    )
+    return list(result.scalars().all())
+
+
+@router.post(
+    "/repositories/parse-url",
+    response_model=URLParseResponse,
+    summary="Parse a git URL",
+    description="Parse a git URL and detect if it's a browser URL that needs correction.",
+)
+async def parse_repository_url(data: URLParseRequest) -> URLParseResponse:
+    """Parse a git URL and detect if it's a browser URL that needs correction.
+
+    Args:
+        data: Request containing the URL to parse.
+
+    Returns:
+        Parsed URL information including whether it needs parsing and suggested corrections.
+    """
+    result = parse_git_url(data.url)
+    return URLParseResponse(**result)
+
+
+@router.post(
+    "/repositories",
+    response_model=GitRepositoryResponse,
+    status_code=status.HTTP_201_CREATED,
+    summary="Create an external repository",
+    description="Create a new external git repository (not tied to any project). Can clone from remote URL.",
+)
+async def create_external_repository(
+    data: GitRepositoryCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> GitRepository:
+    """Create a new external git repository.
+
+    External repositories are not tied to any project and can be used
+    across all projects for config profile git mounts.
+
+    Args:
+        data: Repository creation data including name and optional remote URL.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The newly created external repository.
+    """
+    _user = await _get_user(session, user_id)
+
+    # Check for duplicate name (external repos only)
+    existing = await session.execute(
+        select(GitRepository).where(
+            GitRepository.project_id.is_(None),
+            GitRepository.owner_id == user_id,
+            GitRepository.name == data.name,
+        )
+    )
+    if existing.scalar_one_or_none():
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="repository name already exists")
+
+    # Validate and potentially correct the URL
+    remote_url = data.remote_url
+    if remote_url and not data.force_original_url:
+        parse_result = parse_git_url(remote_url)
+        if parse_result["needs_parsing"] and parse_result["base_url"]:
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                detail={
+                    "message": "The provided URL appears to be a browser URL, not a git clone URL",
+                    "suggested_url": parse_result["base_url"],
+                    "original_url": remote_url,
+                    "error_code": "URL_NEEDS_PARSING",
+                },
+            )
+        if parse_result["base_url"]:
+            remote_url = parse_result["base_url"]
+
+    # Validate SSH key if provided
+    ssh_key_id = None
+    ssh_key = None
+    if data.ssh_key_id:
+        try:
+            ssh_key_id = uuid.UUID(data.ssh_key_id)
+        except ValueError:
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
+        
+        ssh_key = await session.get(SSHKey, ssh_key_id)
+        if ssh_key is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        if ssh_key.user_id != user_id:
+            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user")
+
+    if remote_url:
+        _preflight_remote_repository(remote_url, ssh_key)
+
+    # Create external repo with no project
+    repo = GitRepository(
+        name=data.name,
+        path="",  # Will be set after clone
+        project_id=None,
+        owner_id=user_id,
+        remote_url=remote_url,
+        ssh_key_id=ssh_key_id,
+    )
+    session.add(repo)
+    await session.flush()
+
+    # Set path and optionally clone
+    repo_path = f"/data/repos/external/{user_id}/{repo.id}"
+    repo.path = repo_path
+
+    if remote_url:
+        try:
+            _clone_working_repository(remote_url, repo_path, ssh_key)
+            repo.is_mirror = False
+        except Exception as exc:
+            await session.rollback()
+            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=f"Failed to clone repository: {exc}")
+    else:
+        # Initialize empty repo
+        os.makedirs(repo_path, exist_ok=True)
+        subprocess.run(["git", "init", repo_path], check=True, capture_output=True)
+        repo.is_mirror = False
+
+    await session.commit()
+    return repo
+
+
@router.get(
    "/{project_id}/repositories",
    response_model=list[GitRepositoryResponse],
@@ -275,25 +449,6 @@ async def delete_repository(
    return Response(status_code=status.HTTP_204_NO_CONTENT)


-@router.post(
-    "/repositories/parse-url",
-    response_model=URLParseResponse,
-    summary="Parse a git URL",
-    description="Parse a git URL and detect if it's a browser URL that needs correction.",
-)
-async def parse_repository_url(data: URLParseRequest) -> URLParseResponse:
-    """Parse a git URL and detect if it's a browser URL that needs correction.
-
-    Args:
-        data: Request containing the URL to parse.
-
-    Returns:
-        Parsed URL information including whether it needs parsing and suggested corrections.
-    """
-    result = parse_git_url(data.url)
-    return URLParseResponse(**result)
-
-
@router.post(
    "/{project_id}/repositories",
    response_model=GitRepositoryResponse,
@@ -349,8 +504,23 @@ async def create_repository(
        if parse_result["base_url"]:
            remote_url = parse_result["base_url"]

+    # Validate SSH key if provided
+    ssh_key_id = None
+    ssh_key = None
+    if data.ssh_key_id:
+        try:
+            ssh_key_id = uuid.UUID(data.ssh_key_id)
+        except ValueError:
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
+        
+        ssh_key = await session.get(SSHKey, ssh_key_id)
+        if ssh_key is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        if ssh_key.user_id != user_id and ssh_key.project_id != project_id:
+            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user or project")
+
    if remote_url:
-        _preflight_remote_repository(remote_url)
+        _preflight_remote_repository(remote_url, ssh_key)

    repo_path = _get_repo_path(user_id, project_id, data.name)

@@ -358,7 +528,7 @@ async def create_repository(
    os.makedirs(os.path.dirname(repo_path), exist_ok=True)

    if remote_url:
-        _clone_working_repository(remote_url, repo_path)
+        _clone_working_repository(remote_url, repo_path, ssh_key)
    else:
        _init_working_repository(repo_path)

@@ -369,6 +539,7 @@ async def create_repository(
        owner_id=user_id,
        is_mirror=False,
        remote_url=remote_url,
+        ssh_key_id=ssh_key_id,
    )
    session.add(repo)
    await session.commit()
@@ -376,6 +547,64 @@ async def create_repository(
    return repo


+class UpdateSSHKeyRequest(BaseModel):
+    ssh_key_id: str | None = None
+
+
+@router.patch(
+    "/{project_id}/repositories/{repo_id}/ssh-key",
+    response_model=GitRepositoryResponse,
+    summary="Update repository SSH key",
+    description="Update the SSH key associated with a repository.",
+)
+async def update_repository_ssh_key(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: UpdateSSHKeyRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> GitRepository:
+    """Update the SSH key for a repository.
+
+    Args:
+        project_id: UUID of the project.
+        repo_id: UUID of the repository.
+        data: Update data containing the new SSH key ID.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated repository.
+    """
+    _user = await _get_user(session, user_id)
+    _project = await _get_owned_project(project_id, user_id, session)
+
+    repo = await session.get(GitRepository, repo_id)
+    if repo is None or repo.project_id != project_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
+
+    # Validate SSH key if provided
+    if data.ssh_key_id:
+        try:
+            ssh_key_id = uuid.UUID(data.ssh_key_id)
+        except ValueError:
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
+
+        ssh_key = await session.get(SSHKey, ssh_key_id)
+        if ssh_key is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        if ssh_key.user_id != user_id and ssh_key.project_id != project_id:
+            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user or project")
+
+        repo.ssh_key_id = ssh_key_id
+    else:
+        repo.ssh_key_id = None
+
+    await session.commit()
+    await session.refresh(repo)
+    return repo
+
+
@router.get(
    "/{project_id}/repositories/{repo_id}/history",
    summary="Get repository history",
@@ -4,11 +4,10 @@ import time
 from datetime import datetime, timezone
 from typing import Any

-from fastapi import APIRouter, status
+from fastapi import APIRouter
 from pydantic import BaseModel, Field
 from sqlalchemy import text

-from src.config import Settings
 from src.database import SessionLocal

 router = APIRouter()
@@ -2,7 +2,6 @@

 import logging
 import uuid
-from typing import Any

 import httpx
 from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
@@ -7,23 +7,14 @@ from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession

-from src.auth.dependencies import get_current_user_id, get_db_session
+from src.auth.dependencies import _get_owned_project, _get_user, get_current_user_id, get_db_session
 from src.models.git_repository import GitRepository
 from src.models.project import Project
 from src.models.ssh_key import SSHKey
-from src.models.user import User

 router = APIRouter(prefix="/projects", tags=["projects"])


-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    """Fetch a user by ID or raise 401 if not found."""
-    user = await session.get(User, user_id)
-    if user is None:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
-    return user
-
-
 class ProjectCreate(BaseModel):
    name: str
    description: str | None = None
@@ -132,32 +123,6 @@ async def get_project(
    return await _get_owned_project(project_id, user_id, session)


-async def _get_owned_project(
-    project_id: uuid.UUID,
-    user_id: uuid.UUID,
-    session: AsyncSession,
-) -> Project:
-    """Fetch a project and verify ownership.
-
-    Args:
-        project_id: UUID of the project.
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        The project if found and owned by the user.
-
-    Raises:
-        HTTPException: If project not found or user is not the owner.
-    """
-    project = await session.get(Project, project_id)
-    if project is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="project not found")
-    if project.owner_id != user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not project owner")
-    return project
-
-
@router.patch(
    "/{project_id}",
    response_model=ProjectResponse,
@@ -0,0 +1,98 @@
+"""Shared Pydantic validators for API schemas."""
+
+
+MAX_FOLDER_SIZE_MB = 10
+MAX_FOLDER_SIZE_BYTES = MAX_FOLDER_SIZE_MB * 1024 * 1024
+
+
+def validate_mount_path(v: str | None) -> str | None:
+    """Validate that a mount path is absolute (starts with /).
+
+    Args:
+        v: Mount path string or None.
+
+    Returns:
+        The validated path, or None if input was None.
+
+    Raises:
+        ValueError: If path is not absolute.
+    """
+    if v is None:
+        return v
+    if not v.startswith("/"):
+        raise ValueError("Mount path must be absolute (start with /)")
+    return v
+
+
+def validate_files(v: dict | None, max_size_bytes: int = MAX_FOLDER_SIZE_BYTES) -> dict | None:
+    """Validate file dict for path traversal and size limits.
+
+    Args:
+        v: Dict of {path: content} or None.
+        max_size_bytes: Maximum total size in bytes.
+
+    Returns:
+        The validated dict, or None if input was None.
+
+    Raises:
+        ValueError: If path traversal detected or size limit exceeded.
+    """
+    if v is None:
+        return v
+
+    total_size = 0
+    for path, content in v.items():
+        # Check for path traversal
+        if ".." in path or path.startswith("/"):
+            raise ValueError(f"Invalid file path: {path}")
+        total_size += len(content.encode("utf-8"))
+
+    if total_size > max_size_bytes:
+        raise ValueError(f"Total folder size exceeds {max_size_bytes // (1024 * 1024)}MB limit")
+
+    return v
+
+
+def validate_env_vars(v: dict | None) -> dict | None:
+    """Validate that environment variables is a JSON object.
+
+    Args:
+        v: Dict of env vars or None.
+
+    Returns:
+        The validated dict, or None if input was None.
+
+    Raises:
+        ValueError: If not a dict.
+    """
+    if v is None:
+        return v
+    if not isinstance(v, dict):
+        raise ValueError("environment_variables must be a JSON object")
+    return v
+
+
+def validate_volumes(v: list | None) -> list | None:
+    """Validate volume mounts list.
+
+    Args:
+        v: List of volume dicts or None.
+
+    Returns:
+        The validated list, or None if input was None.
+
+    Raises:
+        ValueError: If not a list or missing required fields.
+    """
+    if v is None:
+        return v
+    if not isinstance(v, list):
+        raise ValueError("volumes must be a JSON array")
+    for i, vol in enumerate(v):
+        if not isinstance(vol, dict):
+            raise ValueError(f"Volume at index {i} must be an object")
+        if "source" not in vol:
+            raise ValueError(f"Volume at index {i} must have 'source' field")
+        if "target" not in vol:
+            raise ValueError(f"Volume at index {i} must have 'target' field")
+    return v
@@ -1,3 +1,4 @@
+import base64
 import uuid
 from datetime import datetime

@@ -9,22 +10,13 @@ from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession

-from src.auth.dependencies import get_current_user_id, get_db_session
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.config import Settings
 from src.models.ssh_key import SSHKey
-from src.models.user import User

 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])


-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    """Fetch a user by ID or raise 401 if not found."""
-    user = await session.get(User, user_id)
-    if user is None:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
-    return user
-
-
 def _get_fernet() -> Fernet:
    """Generate a valid Fernet key from the session secret."""
    import base64
@@ -74,6 +66,23 @@ class SSHKeyResponse(BaseModel):
    created_at: datetime


+class SignPayloadRequest(BaseModel):
+    payload: str
+
+
+class SignatureResponse(BaseModel):
+    signature: str
+
+
+class VerifySignatureRequest(BaseModel):
+    payload: str
+    signature: str
+
+
+class VerifySignatureResponse(BaseModel):
+    valid: bool
+
+
@router.post(
    "",
    response_model=SSHKeyResponse,
@@ -166,3 +175,80 @@ async def delete_ssh_key(

    await session.delete(ssh_key)
    await session.commit()
+
+
+@router.post(
+    "/{key_id}/sign",
+    response_model=SignatureResponse,
+    summary="Sign payload",
+    description="Sign a payload using the SSH private key.",
+)
+async def sign_payload(
+    key_id: uuid.UUID,
+    data: SignPayloadRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> SignatureResponse:
+    """Sign a payload with an SSH key.
+
+    Args:
+        key_id: UUID of the SSH key to use for signing.
+        data: Sign request containing the payload string.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Base64-encoded Ed25519 signature.
+    """
+    user = await _get_user(session, user_id)
+    ssh_key = await session.get(SSHKey, key_id)
+    if ssh_key is None or ssh_key.user_id != user.id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+
+    fernet = _get_fernet()
+    private_key_pem = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
+
+    private_key = serialization.load_ssh_private_key(
+        private_key_pem.encode(), password=None
+    )
+
+    signature = private_key.sign(data.payload.encode())
+    return SignatureResponse(signature=base64.b64encode(signature).decode())
+
+
+@router.post(
+    "/{key_id}/verify",
+    response_model=VerifySignatureResponse,
+    summary="Verify signature",
+    description="Verify a signature against a payload using the SSH public key.",
+)
+async def verify_signature(
+    key_id: uuid.UUID,
+    data: VerifySignatureRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> VerifySignatureResponse:
+    """Verify a signature with an SSH key's public key.
+
+    Args:
+        key_id: UUID of the SSH key to use for verification.
+        data: Verify request containing payload and base64-encoded signature.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Whether the signature is valid.
+    """
+    user = await _get_user(session, user_id)
+    ssh_key = await session.get(SSHKey, key_id)
+    if ssh_key is None or ssh_key.user_id != user.id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+
+    public_key = serialization.load_ssh_public_key(ssh_key.public_key.encode())
+
+    try:
+        signature = base64.b64decode(data.signature)
+        public_key.verify(signature, data.payload.encode())
+        return VerifySignatureResponse(valid=True)
+    except Exception:
+        return VerifySignatureResponse(valid=False)
@@ -4,17 +4,25 @@ import asyncio
 import logging
 import uuid

-from fastapi import APIRouter, Depends, HTTPException, WebSocket, WebSocketDisconnect, status
+from fastapi import APIRouter, Depends, HTTPException, WebSocket, status
 from sqlalchemy.ext.asyncio import AsyncSession

 from src.auth.dependencies import get_db_session
 from src.models.tool_instance import ToolInstance
+from src.models.tool_type import ToolType
 from src.services.terminal_manager import terminal_manager

 router = APIRouter()
 logger = logging.getLogger(__name__)


+class SessionRef:
+    """Mutable reference to a terminal session, allowing updates during reset."""
+
+    def __init__(self, session):
+        self.session = session
+
+
@router.websocket(
    "/ws/tool-instances/{instance_id}/terminal",
 )
@@ -26,6 +34,7 @@ async def terminal_websocket(
    """WebSocket endpoint for terminal access to a tool instance.

    Provides an interactive terminal session inside a running tool instance container.
+    Sessions persist across WebSocket disconnections.

    Args:
        websocket: The WebSocket connection.
@@ -35,8 +44,9 @@ async def terminal_websocket(
    Returns:
        None. Communicates via WebSocket messages.
    """
-    logger.info("Terminal WebSocket connection attempt for instance %s", instance_id)
+    logger.debug("Terminal WebSocket connection attempt for instance %s", instance_id)
    await websocket.accept()
+    logger.debug("Terminal WebSocket accepted for instance %s", instance_id)

    try:
        # Parse instance_id
@@ -70,32 +80,222 @@ async def terminal_websocket(
        await websocket.close(code=4004, reason="Instance not running")
        return

-    logger.info("Creating terminal session for instance %s (container_id=%s)", instance_id, instance.container_id)
-    # Create terminal session
+    logger.debug("Terminal auth passed for instance %s, user %s", instance_id, user_id)
+
+    # Fetch tool type to get startup_command
+    tool_type = await db_session.get(ToolType, instance.tool_type_id)
+    startup_command = tool_type.startup_command if tool_type else None
+    if startup_command:
+        logger.debug("Using startup command for instance %s: %s", instance_id, startup_command)
+
+    # Get or create terminal session
    try:
-        session = await terminal_manager.create_session(
+        session = await terminal_manager.get_or_create_session(
            instance_uuid,
            instance.container_id,
-            websocket,
+            startup_command=startup_command,
        )
-        logger.info("Terminal session created successfully for instance %s", instance_id)
+        logger.debug("Terminal session ready for instance %s (session_id=%s)", instance_id, session.session_id)
+
+        # Attach WebSocket to session
+        await terminal_manager.attach_websocket(session, websocket)
+        logger.debug("WebSocket attached to session for instance %s", instance_id)

        # Send connected status
        await websocket.send_json({"type": "status", "status": "connected"})
+        logger.debug("Sent connected status for instance %s", instance_id)

-        # Keep connection alive until session ends
-        # The terminal_manager handles I/O loops, we just wait here
-        while session.is_alive() and not session._closed:
-            await asyncio.sleep(0.5)
+        # Use mutable session reference so loops can survive reset
+        session_ref = SessionRef(session)
+
+        # Start I/O loops and heartbeat
+        read_task = asyncio.create_task(_read_loop(session_ref, websocket))
+        write_task = asyncio.create_task(_write_loop(session_ref, websocket, instance_id))
+        heartbeat_task = asyncio.create_task(_heartbeat_loop(websocket))
+        logger.debug("Started terminal loops for instance %s", instance_id)
+
+        # Wait for either task to complete (indicating disconnect or error)
+        done, pending = await asyncio.wait(
+            [read_task, write_task, heartbeat_task],
+            return_when=asyncio.FIRST_COMPLETED,
+        )
+        
+        logger.debug("Terminal loop completed for instance %s, done=%s", instance_id, len(done))
+        
+        # Cancel remaining tasks
+        for task in pending:
+            task.cancel()

    except Exception as exc:
        logger.error("Terminal session error for instance %s: %s", instance_id, str(exc), exc_info=True)
        await websocket.close(code=4000, reason=f"Error: {exc}")
    finally:
-        # Cleanup will be handled by the session manager
+        # Detach WebSocket, don't kill session
+        try:
+            if 'session' in locals():
+                await terminal_manager.detach_websocket(session, websocket)
+                logger.debug("WebSocket detached from session for instance %s", instance_id)
+        except Exception:
+            pass
+
+
+async def _read_loop(session_ref: SessionRef, websocket) -> None:
+    """Read output from the container and send to WebSocket."""
+    try:
+        while True:
+            session = session_ref.session
+            if not session.is_alive() or session._closed:
+                await asyncio.sleep(0.1)
+                continue
+            data = await session.read_output()
+            if data:
+                try:
+                    await websocket.send_bytes(data)
+                except Exception:
+                    break
+            else:
+                await asyncio.sleep(0.01)
+    except Exception:
        pass


+async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> None:
+    """Read input from WebSocket and send to container."""
+    try:
+        while True:
+            session = session_ref.session
+            if not session.is_alive() or session._closed:
+                await asyncio.sleep(0.1)
+                continue
+            message = await websocket.receive()
+            if message["type"] == "websocket.receive":
+                if "bytes" in message:
+                    await session.write_input(message["bytes"])
+                elif "text" in message:
+                    text = message["text"]
+                    if text.startswith("{"):
+                        # Control message (JSON)
+                        import json
+                        try:
+                            ctrl = json.loads(text)
+                            msg_type = ctrl.get("type")
+                            
+                            if msg_type == "resize":
+                                cols = ctrl.get("cols", 80)
+                                rows = ctrl.get("rows", 24)
+                                logger.debug(f"Received resize message for instance {instance_id}: {cols}x{rows}")
+                                await session.resize(cols, rows)
+                            elif msg_type == "reset":
+                                # Reset terminal session
+                                logger.debug("Resetting terminal session for instance %s", session.instance_id)
+                                await websocket.send_json({"type": "status", "status": "resetting"})
+                                
+                                # Reset the session
+                                new_session = await terminal_manager.reset_session(
+                                    session.instance_id,
+                                    session.container_id,
+                                    startup_command=session.startup_command,
+                                )
+                                
+                                # Update the mutable session reference so read_loop uses the new session
+                                session_ref.session = new_session
+                                
+                                # Attach to new session
+                                await terminal_manager.attach_websocket(new_session, websocket)
+                                await websocket.send_json({"type": "status", "status": "connected"})
+                                
+                                # Continue the loop with the new session
+                                continue
+                                
+                        except json.JSONDecodeError:
+                            # Not a valid JSON control message, treat as regular input
+                            await session.write_input(text.encode("utf-8"))
+                    else:
+                        await session.write_input(text.encode("utf-8"))
+            elif message["type"] == "websocket.disconnect":
+                break
+    except Exception:
+        pass
+
+
+async def _heartbeat_loop(websocket: WebSocket) -> None:
+    """Send periodic ping messages to detect disconnections."""
+    try:
+        while True:
+            await asyncio.sleep(30)  # Ping every 30 seconds
+            try:
+                await websocket.send_json({"type": "ping"})
+            except Exception:
+                # WebSocket is closed or broken
+                break
+    except Exception:
+        pass
+
+
+@router.post(
+    "/projects/{project_id}/repositories/{repo_id}/instances/{instance_id}/terminal/reset",
+    summary="Reset terminal session",
+    description="Reset the terminal session for a tool instance, killing the current shell and starting fresh.",
+)
+async def reset_terminal_session(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    instance_id: uuid.UUID,
+    db_session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Reset the terminal session for an instance.
+
+    Args:
+        project_id: UUID of the project.
+        repo_id: UUID of the repository.
+        instance_id: UUID of the tool instance.
+        db_session: Database session.
+
+    Returns:
+        Dictionary with status message.
+    """
+    # Get instance and verify it exists and is running
+    instance = await db_session.get(ToolInstance, instance_id)
+    if instance is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail="Instance not found"
+        )
+
+    if instance.status != "running" or not instance.container_id:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail="Instance is not running"
+        )
+
+    # Fetch tool type to get startup_command
+    tool_type = await db_session.get(ToolType, instance.tool_type_id)
+    startup_command = tool_type.startup_command if tool_type else None
+
+    try:
+        # Reset the session
+        new_session = await terminal_manager.reset_session(
+            instance_id,
+            instance.container_id,
+            startup_command=startup_command,
+        )
+        
+        logger.info("Terminal session reset for instance %s (new session_id=%s)", instance_id, new_session.session_id)
+        
+        return {
+            "status": "success",
+            "message": "Terminal session reset successfully",
+            "instance_id": str(instance_id),
+            "session_id": new_session.session_id,
+        }
+    except Exception as exc:
+        logger.error("Failed to reset terminal session for instance %s: %s", instance_id, str(exc), exc_info=True)
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+            detail=f"Failed to reset terminal session: {exc}"
+        )
+
+
 async def _get_user_from_websocket(
    websocket: WebSocket,
    db_session: AsyncSession,
@@ -1,6 +1,5 @@
 """Tool configuration API endpoints."""

-import logging
 import uuid

 from fastapi import APIRouter, Depends, HTTPException, status
@@ -8,12 +7,11 @@ from pydantic import BaseModel, Field, field_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession

+from src.api.shared_validators import validate_env_vars as _validate_env_vars, validate_volumes as _validate_volumes
 from src.auth.dependencies import get_current_user_id, get_db_session
 from src.models.tool_config import ToolConfig
 from src.models.tool_type import ToolType

-logger = logging.getLogger(__name__)
-
 router = APIRouter(prefix="/tool-configs", tags=["tool-configs"])


@@ -42,27 +40,12 @@ class ToolConfigCreate(BaseModel):
    @field_validator("environment_variables")
    @classmethod
    def validate_env_vars(cls, v: dict | None) -> dict | None:
-        if v is None:
-            return v
-        if not isinstance(v, dict):
-            raise ValueError("environment_variables must be a JSON object")
-        return v
+        return _validate_env_vars(v)

    @field_validator("volumes")
    @classmethod
    def validate_volumes(cls, v: list | None) -> list | None:
-        if v is None:
-            return v
-        if not isinstance(v, list):
-            raise ValueError("volumes must be a JSON array")
-        for i, vol in enumerate(v):
-            if not isinstance(vol, dict):
-                raise ValueError(f"Volume at index {i} must be an object")
-            if "source" not in vol:
-                raise ValueError(f"Volume at index {i} must have 'source' field")
-            if "target" not in vol:
-                raise ValueError(f"Volume at index {i} must have 'target' field")
-        return v
+        return _validate_volumes(v)


 class ToolConfigUpdate(BaseModel):
@@ -88,27 +71,12 @@ class ToolConfigUpdate(BaseModel):
    @field_validator("environment_variables")
    @classmethod
    def validate_env_vars(cls, v: dict | None) -> dict | None:
-        if v is None:
-            return v
-        if not isinstance(v, dict):
-            raise ValueError("environment_variables must be a JSON object")
-        return v
+        return _validate_env_vars(v)

    @field_validator("volumes")
    @classmethod
    def validate_volumes(cls, v: list | None) -> list | None:
-        if v is None:
-            return v
-        if not isinstance(v, list):
-            raise ValueError("volumes must be a JSON array")
-        for i, vol in enumerate(v):
-            if not isinstance(vol, dict):
-                raise ValueError(f"Volume at index {i} must be an object")
-            if "source" not in vol:
-                raise ValueError(f"Volume at index {i} must have 'source' field")
-            if "target" not in vol:
-                raise ValueError(f"Volume at index {i} must have 'target' field")
-        return v
+        return _validate_volumes(v)


 class ToolConfigResponse(BaseModel):
@@ -0,0 +1,424 @@
+"""Tool definition API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from pydantic import BaseModel, Field
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models.tool_definition_manifest import ToolDefinitionManifest
+from src.models.tool_type import ToolType
+from src.services.manifest_compiler import (
+    compile_compose,
+    compile_dockerfile,
+    compile_entrypoint,
+    compute_image_tag,
+    deep_merge,
+    resolve_base,
+)
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/tool-definitions", tags=["tool-definitions"])
+
+
+class CreateToolDefinitionRequest(BaseModel):
+    """Request body for creating a tool definition manifest."""
+
+    model_config = {"extra": "ignore"}
+
+    name: str = Field(description="Unique identifier (kebab-case)")
+    display_name: str = Field(description="Human-readable name")
+    description: str | None = Field(default=None)
+    category: str = Field(default="development")
+    interface_type: str = Field(default="terminal", description="web or terminal")
+    base_image: str | None = Field(default=None, description="Direct base image")
+    base_definition_id: str | None = Field(
+        default=None, description="Reference to a base definition"
+    )
+    base_version: str = Field(default="latest")
+    manifest: dict = Field(description="The full manifest JSON")
+
+
+class UpdateToolDefinitionRequest(BaseModel):
+    """Request body for updating a tool definition manifest."""
+
+    model_config = {"extra": "ignore"}
+
+    display_name: str | None = Field(default=None)
+    description: str | None = Field(default=None)
+    category: str | None = Field(default=None)
+    manifest: dict | None = Field(default=None)
+    base_version: str | None = Field(default=None)
+
+
+@router.post(
+    "",
+    summary="Create tool definition",
+    description="Create a new tool definition manifest.",
+)
+async def create_tool_definition(
+    data: CreateToolDefinitionRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Create a new tool definition manifest.
+
+    Args:
+        data: Manifest data.
+        user_id: Authenticated user ID.
+        session: Database session.
+
+    Returns:
+        Dictionary with created definition details.
+    """
+    # Validate base reference
+    if not data.base_image and not data.base_definition_id:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail="Either base_image or base_definition_id is required",
+        )
+
+    base_def_id = None
+    if data.base_definition_id:
+        try:
+            base_def_id = uuid.UUID(data.base_definition_id)
+        except ValueError:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail=f"Invalid base_definition_id: {data.base_definition_id}",
+            )
+
+        base_def = await session.get(ToolDefinitionManifest, base_def_id)
+        if not base_def:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Base definition not found: {data.base_definition_id}",
+            )
+        if not base_def.is_base:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="Referenced definition is not a base definition",
+            )
+
+    # Check name uniqueness
+    existing = await session.execute(
+        select(ToolDefinitionManifest).where(ToolDefinitionManifest.name == data.name)
+    )
+    if existing.scalar_one_or_none():
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"Tool definition '{data.name}' already exists",
+        )
+
+    definition = ToolDefinitionManifest(
+        name=data.name,
+        display_name=data.display_name,
+        description=data.description,
+        category=data.category,
+        interface_type=data.interface_type,
+        base_image=data.base_image,
+        base_definition_id=base_def_id,
+        base_version=data.base_version,
+        manifest=data.manifest,
+        created_by_id=user_id,
+    )
+
+    session.add(definition)
+    await session.commit()
+    await session.refresh(definition)
+
+    logger.info("Created tool definition %s (%s)", definition.id, definition.name)
+
+    return {
+        "id": str(definition.id),
+        "name": definition.name,
+        "display_name": definition.display_name,
+        "description": definition.description,
+        "category": definition.category,
+        "interface_type": definition.interface_type,
+        "base_image": definition.base_image,
+        "base_definition_id": str(definition.base_definition_id)
+        if definition.base_definition_id
+        else None,
+        "base_version": definition.base_version,
+        "manifest": definition.manifest,
+        "is_base": definition.is_base,
+        "created_at": definition.created_at.isoformat(),
+    }
+
+
+@router.get(
+    "",
+    summary="List tool definitions",
+    description="List all tool definition manifests.",
+)
+async def list_tool_definitions(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+    include_bases: bool = True,
+) -> dict:
+    """List all tool definition manifests.
+
+    Args:
+        user_id: Authenticated user ID.
+        session: Database session.
+        include_bases: Whether to include base definitions.
+
+    Returns:
+        Dictionary containing list of definitions.
+    """
+    query = select(ToolDefinitionManifest)
+    if not include_bases:
+        query = query.where(ToolDefinitionManifest.is_base == False)
+
+    result = await session.execute(
+        query.order_by(ToolDefinitionManifest.created_at.desc())
+    )
+    definitions = result.scalars().all()
+
+    return {
+        "definitions": [
+            {
+                "id": str(d.id),
+                "name": d.name,
+                "display_name": d.display_name,
+                "description": d.description,
+                "category": d.category,
+                "interface_type": d.interface_type,
+                "is_base": d.is_base,
+                "base_image": d.base_image,
+                "base_definition_id": str(d.base_definition_id)
+                if d.base_definition_id
+                else None,
+                "base_version": d.base_version,
+                "version": d.version,
+                "created_at": d.created_at.isoformat(),
+            }
+            for d in definitions
+        ]
+    }
+
+
+@router.get(
+    "/{definition_id}",
+    summary="Get tool definition",
+    description="Get a specific tool definition manifest.",
+)
+async def get_tool_definition(
+    definition_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get a specific tool definition manifest.
+
+    Args:
+        definition_id: UUID of the definition.
+        user_id: Authenticated user ID.
+        session: Database session.
+
+    Returns:
+        Dictionary with definition details.
+    """
+    definition = await session.get(ToolDefinitionManifest, definition_id)
+    if not definition:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"Tool definition not found: {definition_id}",
+        )
+
+    return {
+        "id": str(definition.id),
+        "name": definition.name,
+        "display_name": definition.display_name,
+        "description": definition.description,
+        "category": definition.category,
+        "interface_type": definition.interface_type,
+        "base_image": definition.base_image,
+        "base_definition_id": str(definition.base_definition_id)
+        if definition.base_definition_id
+        else None,
+        "base_version": definition.base_version,
+        "manifest": definition.manifest,
+        "dockerfile_cache": definition.dockerfile_cache,
+        "compose_cache": definition.compose_cache,
+        "version": definition.version,
+        "is_base": definition.is_base,
+        "created_at": definition.created_at.isoformat(),
+        "updated_at": definition.updated_at.isoformat(),
+    }
+
+
+@router.put(
+    "/{definition_id}",
+    summary="Update tool definition",
+    description="Update a tool definition manifest.",
+)
+async def update_tool_definition(
+    definition_id: uuid.UUID,
+    data: UpdateToolDefinitionRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a tool definition manifest.
+
+    Args:
+        definition_id: UUID of the definition.
+        data: Update data.
+        user_id: Authenticated user ID.
+        session: Database session.
+
+    Returns:
+        Dictionary with updated definition details.
+    """
+    definition = await session.get(ToolDefinitionManifest, definition_id)
+    if not definition:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"Tool definition not found: {definition_id}",
+        )
+
+    if data.display_name is not None:
+        definition.display_name = data.display_name
+    if data.description is not None:
+        definition.description = data.description
+    if data.category is not None:
+        definition.category = data.category
+    if data.manifest is not None:
+        definition.manifest = data.manifest
+    if data.base_version is not None:
+        definition.base_version = data.base_version
+
+    await session.commit()
+    await session.refresh(definition)
+
+    logger.info("Updated tool definition %s (%s)", definition.id, definition.name)
+
+    return {
+        "id": str(definition.id),
+        "name": definition.name,
+        "display_name": definition.display_name,
+        "manifest": definition.manifest,
+        "updated_at": definition.updated_at.isoformat(),
+    }
+
+
+@router.delete(
+    "/{definition_id}",
+    summary="Delete tool definition",
+    description="Delete a tool definition manifest.",
+)
+async def delete_tool_definition(
+    definition_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Delete a tool definition manifest.
+
+    Args:
+        definition_id: UUID of the definition.
+        user_id: Authenticated user ID.
+        session: Database session.
+
+    Returns:
+        Dictionary with deletion status.
+    """
+    definition = await session.get(ToolDefinitionManifest, definition_id)
+    if not definition:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"Tool definition not found: {definition_id}",
+        )
+
+    # Check if any tool types reference this manifest
+    result = await session.execute(
+        select(ToolType).where(ToolType.manifest_id == definition_id)
+    )
+    referencing = result.scalars().all()
+    if referencing:
+        tool_names = ", ".join(t.name for t in referencing)
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"Cannot delete: referenced by tool types: {tool_names}",
+        )
+
+    await session.delete(definition)
+    await session.commit()
+
+    logger.info("Deleted tool definition %s (%s)", definition.id, definition.name)
+
+    return {"status": "deleted", "id": str(definition_id)}
+
+
+@router.post(
+    "/{definition_id}/compile",
+    summary="Compile tool definition",
+    description="Compile a manifest to Dockerfile + Compose preview without building.",
+)
+async def compile_tool_definition(
+    definition_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Compile a manifest to Dockerfile + Compose preview.
+
+    Args:
+        definition_id: UUID of the definition.
+        user_id: Authenticated user ID.
+        session: Database session.
+
+    Returns:
+        Dictionary with compiled Dockerfile, Compose, and image tag.
+    """
+    definition = await session.get(ToolDefinitionManifest, definition_id)
+    if not definition:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"Tool definition not found: {definition_id}",
+        )
+
+    manifest = dict(definition.manifest)
+
+    # Resolve base if referenced
+    if definition.base_definition_id:
+        base_def = await session.get(
+            ToolDefinitionManifest, definition.base_definition_id
+        )
+        if base_def:
+            base_manifest = dict(base_def.manifest)
+            manifest = resolve_base(deep_merge(base_manifest, manifest))
+
+    # Compile
+    dockerfile = compile_dockerfile(manifest)
+    entrypoint = compile_entrypoint(manifest)
+    image_tag = compute_image_tag(definition.name, manifest)
+
+    # Dummy compose with placeholder variables
+    dummy_vars = {
+        "IMAGE_TAG": image_tag,
+        "INSTANCE_NAME": f"{definition.name}-preview",
+        "INSTANCE_DIR": "/data/instances/preview",
+        "REPO_PATH": "/data/repos/preview",
+        "SSH_PATH": "/data/instances/preview/.ssh",
+        "TOOL_PORT": "8080",
+        "EXTRA_ENV": {},
+        "EXTRA_VOLUMES": [],
+    }
+    compose = compile_compose(manifest, dummy_vars)
+
+    # Update cache
+    definition.dockerfile_cache = dockerfile
+    definition.compose_cache = compose
+    await session.commit()
+
+    return {
+        "id": str(definition.id),
+        "name": definition.name,
+        "dockerfile": dockerfile,
+        "entrypoint": entrypoint,
+        "compose": compose,
+        "image_tag": image_tag,
+    }
@@ -1,27 +1,23 @@
 import uuid
 from datetime import datetime

-import yaml
 from fastapi import APIRouter, Depends, HTTPException, status
 from pydantic import BaseModel, ConfigDict, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession

-from src.auth.dependencies import get_current_user_id, get_db_session
+from src.api.tool_types_validation import (
+    check_port_exposed,
+    validate_compose_yaml,
+    validate_required_variables,
+)
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.tool_type import ToolType
 from src.models.user import User

 router = APIRouter(prefix="/tool-types", tags=["tool-types"])


-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    """Fetch a user by ID or raise 401 if not found."""
-    user = await session.get(User, user_id)
-    if user is None:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
-    return user
-
-
 async def _require_admin(user: User) -> None:
    """Check if user has admin privileges.

@@ -37,15 +33,17 @@ class ToolTypeCreate(BaseModel):
    name: str
    display_name: str
    description: str | None = None
-    default_port: int
+    default_port: int = 0
    definition_type: str = "compose"
    compose_template: str | None = None
    dockerfile_template: str | None = None
    build_context: dict | None = None
    readiness_probe: dict | None = None
+    startup_command: str | None = None
    required_variables: list[str] = []
    category: str = "other"
-    interfaces: list[str] = ["web"]
+    interface_type: str = "web"
+    requires_port: bool = True

    @field_validator("definition_type")
    @classmethod
@@ -64,20 +62,7 @@ class ToolTypeCreate(BaseModel):
        if v is None:
            raise ValueError("compose_template is required when definition_type is 'compose'")
        
-        try:
-            parsed = yaml.safe_load(v)
-        except yaml.YAMLError as e:
-            raise ValueError(f"Invalid YAML: {e}")
-        
-        if not isinstance(parsed, dict):
-            raise ValueError("Compose template must be a YAML mapping")
-        
-        if "services" not in parsed:
-            raise ValueError("Compose template must contain 'services' key")
-        
-        if not parsed["services"]:
-            raise ValueError("Compose template must define at least one service")
-        
+        validate_compose_yaml(v)
        return v

    @field_validator("dockerfile_template")
@@ -95,48 +80,22 @@ class ToolTypeCreate(BaseModel):
        
        return v

+    @field_validator("interface_type")
+    @classmethod
+    def validate_interface_type(cls, v: str) -> str:
+        if v not in ("web", "terminal"):
+            raise ValueError("interface_type must be 'web' or 'terminal'")
+        return v
+
    @field_validator("default_port")
    @classmethod
    def validate_default_port(cls, v: int, info) -> int:
+        data = info.data
+        requires_port = data.get("requires_port", True)
+        if not requires_port:
+            return v
        if v <= 0 or v > 65535:
            raise ValueError("Port must be between 1 and 65535")
-        
-        # Get compose_template from the model data
-        data = info.data
-        if data.get("definition_type") != "compose":
-            return v
-        
-        template = data.get("compose_template")
-        if not template:
-            return v
-        
-        try:
-            parsed = yaml.safe_load(template)
-        except yaml.YAMLError:
-            return v
-        
-        # Check if the port is exposed in any service
-        port_str = str(v)
-        port_exposed = False
-        
-        if isinstance(parsed, dict) and "services" in parsed:
-            for service_name, service_config in parsed["services"].items():
-                if isinstance(service_config, dict) and "ports" in service_config:
-                    for port_mapping in service_config["ports"]:
-                        if isinstance(port_mapping, str):
-                            # Format: "8443:8443" or "8443"
-                            if port_str in port_mapping:
-                                port_exposed = True
-                                break
-                        elif isinstance(port_mapping, int) and port_mapping == v:
-                            port_exposed = True
-                            break
-                if port_exposed:
-                    break
-        
-        if not port_exposed:
-            raise ValueError(f"Port {v} is not exposed in the compose template. Add it to the 'ports' section.")
-        
        return v

    @field_validator("required_variables")
@@ -166,6 +125,17 @@ class ToolTypeCreate(BaseModel):
            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
        if self.definition_type == "compose" and self.compose_template is None:
            raise ValueError("compose_template is required when definition_type is 'compose'")
+        
+        # Validate that default_port is exposed in compose template (only if requires_port)
+        if self.requires_port and self.definition_type == "compose" and self.compose_template:
+            try:
+                parsed = validate_compose_yaml(self.compose_template)
+            except ValueError:
+                return self
+            
+            if not check_port_exposed(parsed, self.default_port):
+                raise ValueError(f"Port {self.default_port} is not exposed in the compose template. Add it to the 'ports' section.")
+        
        return self


@@ -178,9 +148,11 @@ class ToolTypeUpdate(BaseModel):
    dockerfile_template: str | None = None
    build_context: dict | None = None
    readiness_probe: dict | None = None
+    startup_command: str | None = None
    required_variables: list[str] | None = None
    category: str | None = None
-    interfaces: list[str] | None = None
+    interface_type: str | None = None
+    requires_port: bool | None = None

    @field_validator("definition_type")
    @classmethod
@@ -191,31 +163,27 @@ class ToolTypeUpdate(BaseModel):
            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
        return v

+    @field_validator("interface_type")
+    @classmethod
+    def validate_interface_type(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v not in ("web", "terminal"):
+            raise ValueError("interface_type must be 'web' or 'terminal'")
+        return v
+
    @field_validator("compose_template")
    @classmethod
    def validate_compose_template(cls, v: str | None, info) -> str | None:
        if v is None:
            return v
-        
+
        data = info.data
        definition_type = data.get("definition_type")
        if definition_type and definition_type != "compose":
            return v
-        
-        try:
-            parsed = yaml.safe_load(v)
-        except yaml.YAMLError as e:
-            raise ValueError(f"Invalid YAML: {e}")
-        
-        if not isinstance(parsed, dict):
-            raise ValueError("Compose template must be a YAML mapping")
-        
-        if "services" not in parsed:
-            raise ValueError("Compose template must contain 'services' key")
-        
-        if not parsed["services"]:
-            raise ValueError("Compose template must define at least one service")
-        
+
+        validate_compose_yaml(v)
        return v

    @field_validator("dockerfile_template")
@@ -243,15 +211,16 @@ class ToolTypeResponse(BaseModel):
    display_name: str
    description: str | None
    category: str
-    interfaces: list[str]
+    interface_type: str
+    requires_port: bool
    default_port: int
    definition_type: str
    compose_template: str | None
    dockerfile_template: str | None
    build_context: dict | None
    readiness_probe: dict | None
+    startup_command: str | None
    required_variables: list[str]
-    is_builtin: bool
    created_by_id: uuid.UUID | None
    created_at: datetime
    updated_at: datetime
@@ -297,10 +266,11 @@ async def create_tool_type(
        dockerfile_template=data.dockerfile_template,
        build_context=data.build_context,
        readiness_probe=data.readiness_probe,
+        startup_command=data.startup_command,
        required_variables=data.required_variables,
        category=data.category,
-        interfaces=data.interfaces,
-        is_builtin=False,
+        interface_type=data.interface_type,
+        requires_port=data.requires_port,
        created_by_id=user.id,
    )
    session.add(tool_type)
@@ -391,13 +361,13 @@ async def update_tool_type(
    if tool_type is None:
        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
    
-    if tool_type.is_builtin:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="cannot modify built-in tool types")
+    # Built-in tool types can now be modified
    
    update_data = data.model_dump(exclude_unset=True)
    
    # Validate port if being updated
-    if "default_port" in update_data:
+    requires_port = update_data.get("requires_port", tool_type.requires_port)
+    if "default_port" in update_data and requires_port:
        new_port = update_data["default_port"]
        if new_port <= 0 or new_port > 65535:
            raise HTTPException(
@@ -411,53 +381,29 @@ async def update_tool_type(
            template = update_data.get("compose_template", tool_type.compose_template)
            if template:
                try:
-                    parsed = yaml.safe_load(template)
-                except yaml.YAMLError:
-                    parsed = None
-                
-                if parsed and isinstance(parsed, dict) and "services" in parsed:
-                    port_str = str(new_port)
-                    port_exposed = False
-                    for service_config in parsed["services"].values():
-                        if isinstance(service_config, dict) and "ports" in service_config:
-                            for port_mapping in service_config["ports"]:
-                                if isinstance(port_mapping, str) and port_str in port_mapping:
-                                    port_exposed = True
-                                    break
-                                elif isinstance(port_mapping, int) and port_mapping == new_port:
-                                    port_exposed = True
-                                    break
-                        if port_exposed:
-                            break
-                    
-                    if not port_exposed:
+                    parsed = validate_compose_yaml(template)
+                    if not check_port_exposed(parsed, new_port):
                        raise HTTPException(
                            status_code=status.HTTP_400_BAD_REQUEST,
                            detail=f"Port {new_port} is not exposed in the compose template"
                        )
-    
+                except ValueError as e:
+                    raise HTTPException(
+                        status_code=status.HTTP_400_BAD_REQUEST,
+                        detail=str(e)
+                    )
+
    # Validate required variables for compose definitions
    definition_type = update_data.get("definition_type", tool_type.definition_type)
    if definition_type == "compose":
        if "required_variables" in update_data and "compose_template" in update_data:
-            template = update_data["compose_template"]
-            for var in update_data["required_variables"]:
-                placeholder = f"{{{{{var}}}}}"
-                if placeholder not in template:
-                    raise HTTPException(
-                        status_code=status.HTTP_400_BAD_REQUEST,
-                        detail=f"Required variable '{var}' not found in compose template"
-                    )
+            validate_required_variables(
+                update_data["compose_template"], update_data["required_variables"]
+            )
        elif "required_variables" in update_data:
            template = tool_type.compose_template
            if template:
-                for var in update_data["required_variables"]:
-                    placeholder = f"{{{{{var}}}}}"
-                    if placeholder not in template:
-                        raise HTTPException(
-                            status_code=status.HTTP_400_BAD_REQUEST,
-                            detail=f"Required variable '{var}' not found in compose template"
-                        )
+                validate_required_variables(template, update_data["required_variables"])
    
    for field, value in update_data.items():
        setattr(tool_type, field, value)
@@ -502,15 +448,9 @@ async def validate_tool_type_template(
            errors.append("Compose template is required")
        else:
            try:
-                parsed = yaml.safe_load(data.compose_template)
-                if not isinstance(parsed, dict):
-                    errors.append("Compose template must be a YAML mapping")
-                elif "services" not in parsed:
-                    errors.append("Compose template must contain 'services' key")
-                elif not parsed["services"]:
-                    errors.append("Compose template must define at least one service")
-            except yaml.YAMLError as e:
-                errors.append(f"Invalid YAML: {e}")
+                validate_compose_yaml(data.compose_template)
+            except ValueError as e:
+                errors.append(str(e))

    elif data.definition_type == "dockerfile":
        if not data.dockerfile_template:
@@ -559,15 +499,9 @@ async def validate_tool_type(
            errors.append("Compose template is empty")
        else:
            try:
-                parsed = yaml.safe_load(tool_type.compose_template)
-                if not isinstance(parsed, dict):
-                    errors.append("Compose template must be a YAML mapping")
-                elif "services" not in parsed:
-                    errors.append("Compose template must contain 'services' key")
-                elif not parsed["services"]:
-                    errors.append("Compose template must define at least one service")
-            except yaml.YAMLError as e:
-                errors.append(f"Invalid YAML: {e}")
+                validate_compose_yaml(tool_type.compose_template)
+            except ValueError as e:
+                errors.append(str(e))
    
    elif tool_type.definition_type == "dockerfile":
        if not tool_type.dockerfile_template:
@@ -609,8 +543,7 @@ async def delete_tool_type(
    if tool_type is None:
        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
    
-    if tool_type.is_builtin:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="cannot delete built-in tool types")
+    # Built-in tool types can now be deleted
    
    await session.delete(tool_type)
    await session.commit()
@@ -0,0 +1,87 @@
+"""Shared validation utilities for tool types."""
+
+import re
+
+import yaml
+from fastapi import HTTPException, status
+
+
+def sanitize_template_vars(template: str) -> str:
+    """Replace template variables like {{VAR}} with placeholders to avoid YAML parsing errors."""
+    return re.sub(r"\{\{[A-Za-z_][A-Za-z0-9_]*\}\}", "__PLACEHOLDER__", template)
+
+
+def validate_compose_yaml(template: str) -> dict:
+    """Validate and parse a compose template.
+
+    Args:
+        template: Raw compose template string.
+
+    Returns:
+        Parsed YAML dict.
+
+    Raises:
+        ValueError: If YAML is invalid or missing required keys.
+    """
+    sanitized = sanitize_template_vars(template)
+
+    try:
+        parsed = yaml.safe_load(sanitized)
+    except yaml.YAMLError as e:
+        raise ValueError(f"Invalid YAML: {e}")
+
+    if not isinstance(parsed, dict):
+        raise ValueError("Compose template must be a YAML mapping")
+
+    if "services" not in parsed:
+        raise ValueError("Compose template must contain 'services' key")
+
+    if not parsed["services"]:
+        raise ValueError("Compose template must define at least one service")
+
+    return parsed
+
+
+def check_port_exposed(parsed: dict, port: int) -> bool:
+    """Check if a port is exposed in a parsed compose template.
+
+    Args:
+        parsed: Parsed compose YAML dict.
+        port: Port number to check.
+
+    Returns:
+        True if port is exposed in any service.
+    """
+    port_str = str(port)
+
+    if not isinstance(parsed, dict) or "services" not in parsed:
+        return False
+
+    for service_config in parsed["services"].values():
+        if isinstance(service_config, dict) and "ports" in service_config:
+            for port_mapping in service_config["ports"]:
+                if isinstance(port_mapping, str) and port_str in port_mapping:
+                    return True
+                elif isinstance(port_mapping, int) and port_mapping == port:
+                    return True
+
+    return False
+
+
+def validate_required_variables(template: str, variables: list[str]) -> None:
+    """Validate that all required variables exist in the template.
+
+    Args:
+        template: Compose template string.
+        variables: List of required variable names.
+
+    Raises:
+        HTTPException: If any variable is not found in the template.
+    """
+    for var in variables:
+        placeholder = f"{{{{{var}}}}}"
+        if placeholder not in template:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail=f"Required variable '{var}' not found in compose template",
+            )
@@ -1,28 +1,19 @@
 import logging
 import uuid

-from fastapi import APIRouter, Depends, HTTPException, status
-
-logger = logging.getLogger(__name__)
+from fastapi import APIRouter, Depends
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession

-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.user import User
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.user_config import UserConfig

+logger = logging.getLogger(__name__)
+
 router = APIRouter(prefix="/users/me", tags=["user-config"])


-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    """Fetch a user by ID or raise 401 if not found."""
-    user = await session.get(User, user_id)
-    if user is None:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
-    return user
-
-
 async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> UserConfig:
    """Get or create user config record.

@@ -111,11 +102,11 @@ async def update_user_config(

    # Merge updates
    update_data = data.model_dump(exclude_unset=True)
-    logger.info("Updating user config for user %s: %s", user_id, update_data)
+    logger.debug("Updating user config for user %s: %s", user_id, update_data)
    # SQLAlchemy JSON doesn't track dict mutations, so we replace the whole dict
    config.config = {**config.config, **update_data}

    await session.commit()
    await session.refresh(config)
-    logger.info("Updated config: %s", config.config)
+    logger.debug("Updated config: %s", config.config)
    return UserConfigResponse.model_validate(config.config)
@@ -5,7 +5,7 @@ from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy.ext.asyncio import AsyncSession

-from src.auth.dependencies import get_current_user_id, get_db_session
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.user import User

 router = APIRouter(prefix="/users", tags=["users"])
@@ -16,14 +16,6 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB


-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    """Fetch a user by ID or raise 401 if not found."""
-    user = await session.get(User, user_id)
-    if user is None:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
-    return user
-
-
 class UserProfileResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)

@@ -7,6 +7,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.session import decode_session_cookie
 from src.config import Settings
 from src.database import SessionLocal
+from src.models.project import Project
 from src.models.user import User


@@ -47,3 +48,39 @@ async def get_current_user(
    if user is None:
        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
    return user
+
+
+async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+    """Fetch a user by ID or raise 401 if not found."""
+    user = await session.get(User, user_id)
+    if user is None:
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
+    return user
+
+
+async def _get_owned_project(
+    project_id: uuid.UUID,
+    user_id: uuid.UUID,
+    session: AsyncSession,
+) -> "Project":
+    """Fetch a project and verify ownership.
+
+    Args:
+        project_id: UUID of the project.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The project if found and owned by the user.
+
+    Raises:
+        HTTPException: 404 if project not found, 403 if user is not the owner.
+    """
+    from src.models.project import Project
+
+    project = await session.get(Project, project_id)
+    if project is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="project not found")
+    if project.owner_id != user_id:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not project owner")
+    return project
@@ -2,7 +2,7 @@ import hmac
 import hashlib
 import json
 import base64
-from datetime import UTC, datetime, timedelta
+from datetime import datetime, timedelta, timezone
 from typing import Any

 from src.config import Settings
@@ -23,7 +23,7 @@ def create_session_cookie(*, settings: Settings, user_id: str) -> str:
    """Create a signed session cookie value."""
    payload = {
        "user_id": user_id,
-        "exp": int((datetime.now(UTC) + timedelta(hours=settings.session_ttl_hours)).timestamp()),
+        "exp": int((datetime.now(timezone.utc) + timedelta(hours=settings.session_ttl_hours)).timestamp()),
    }
    
    header = _base64url_encode(json.dumps({"alg": "HS256", "typ": "session"}).encode())
@@ -65,7 +65,7 @@ def decode_session_cookie(*, settings: Settings, cookie_value: str) -> dict[str,
    payload = json.loads(payload_bytes)
    
    # Check expiry
-    if payload.get("exp", 0) < int(datetime.now(UTC).timestamp()):
+    if payload.get("exp", 0) < int(datetime.now(timezone.utc).timestamp()):
        raise ValueError("session expired")
    
    return payload
@@ -1,4 +1,3 @@
-import json
 import logging
 import os

@@ -7,7 +6,6 @@ from fastapi.exceptions import RequestValidationError
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import JSONResponse
 from fastapi.staticfiles import StaticFiles
-from sqlalchemy import select, text

 from src.api.auth import router as auth_router
 from src.api.dashboard import router as dashboard_router
@@ -18,20 +16,21 @@ from src.api.ssh_keys import router as ssh_keys_router
 from src.api.terminal import router as terminal_router
 from src.api.instance_proxy import router as instance_proxy_router
 from src.api.config_folders import router as config_folders_router
+from src.api.config_profiles import router as config_profiles_router
 from src.api.tool_configs import router as tool_configs_router
+from src.api.tool_definitions import router as tool_definitions_router
 from src.api.tool_instances import router as tool_instances_router
 from src.api.tool_instances import sessions_router
 from src.api.tool_types import router as tool_types_router
 from src.api.user_config import router as user_config_router
 from src.api.users import router as users_router
 from src.config import Settings
-from src.database import SessionLocal, init_database
+from src.database import init_database
 from src.logging_config import (
    ExceptionLoggingMiddleware,
    RequestLoggingMiddleware,
    configure_logging,
 )
-from src.models.tool_type import ToolType

 # Configure logging early
 log_level = os.getenv("LOG_LEVEL", "INFO").upper()
@@ -68,7 +67,9 @@ def _sanitize_validation_errors(errors):
            "type": error.get("type"),
            "loc": error.get("loc"),
            "msg": error.get("msg"),
-            "input": str(error.get("input")) if error.get("input") is not None else None,
+            "input": str(error.get("input"))
+            if error.get("input") is not None
+            else None,
        }
        # Convert ctx to safe format
        ctx = error.get("ctx")
@@ -103,155 +104,6 @@ async def validation_exception_handler(request: Request, exc: RequestValidationE
    )


-async def _table_exists(session, table_name: str) -> bool:
-    """Check if a table exists in the database."""
-    try:
-        result = await session.execute(
-            text("""
-                SELECT EXISTS (
-                    SELECT FROM information_schema.tables
-                    WHERE table_schema = 'public'
-                    AND table_name = :table_name
-                )
-            """),
-            {"table_name": table_name},
-        )
-        return result.scalar() or False
-    except Exception:
-        return False
-
-
-async def seed_builtin_tool_types():
-    async with SessionLocal() as session:
-        # Check if tool_types table exists before attempting to seed
-        if not await _table_exists(session, "tool_types"):
-            logger.warning(
-                "tool_types table does not exist. Skipping seeding. "
-                "Migrations may not have run yet."
-            )
-            return
-
-        builtin_types = [
-            {
-                "name": "code-server",
-                "display_name": "VS Code Server",
-                "description": "VS Code running in the browser via code-server",
-                "category": "editor",
-                "interfaces": ["web"],
-                "compose_template": """version: "3.8"
-services:
-  code-server:
-    image: lscr.io/linuxserver/code-server:latest
-    container_name: {{TOOL_NAME}}
-    environment:
-      - PUID=1000
-      - PGID=1000
-      - TZ=Europe/London
-    volumes:
-      - {{REPO_PATH}}:/config/workspace
-    ports:
-      - "8443:8443"
-    restart: unless-stopped""",
-                "default_port": 8443,
-                "required_variables": ["REPO_PATH", "TOOL_NAME"],
-            },
-            {
-                "name": "jupyter-notebook",
-                "display_name": "Jupyter Notebook",
-                "description": "Jupyter Lab for interactive development",
-                "category": "notebook",
-                "interfaces": ["web"],
-                "default_port": 8888,
-                "compose_template": """version: "3.8"
-services:
-  jupyter:
-    image: jupyter/scipy-notebook:latest
-    container_name: {{TOOL_NAME}}
-    environment:
-      - JUPYTER_ENABLE_LAB=yes
-    volumes:
-      - {{REPO_PATH}}:/home/jovyan/work
-    ports:
-      - "8888:8888"
-    restart: unless-stopped""",
-                "required_variables": ["REPO_PATH", "TOOL_NAME"],
-            },
-            {
-                "name": "opencode",
-                "display_name": "OpenCode",
-                "description": "AI coding assistant - run opencode in terminal",
-                "category": "ai-assistant",
-                "interfaces": ["terminal"],
-                "default_port": 3000,
-                "compose_template": """version: "3.8"
-services:
-  opencode:
-    image: node:20-slim
-    container_name: {{TOOL_NAME}}
-    working_dir: /workspace
-    environment:
-      - HOME=/tmp
-    volumes:
-      - {{REPO_PATH}}:/workspace
-      - opencode_home:/tmp
-    ports:
-      - "3000:3000"
-    command: >
-      sh -c "set -x &&
-             apt-get update && apt-get install -y git ca-certificates &&
-             echo 'Installing opencode...' &&
-             npm install -g opencode-ai 2>&1 || echo 'ERROR: npm install failed' &&
-             which opencode || echo 'ERROR: opencode not in PATH' &&
-             npm bin -g &&
-             ls -la $(npm bin -g) || echo 'ERROR: global bin dir not found' &&
-             echo 'export PATH=\"$(npm bin -g):\$PATH\"' >> /root/.bashrc &&
-             echo 'cd /workspace' >> /root/.bashrc &&
-             echo 'OpenCode installation complete' &&
-             cd /workspace &&
-             exec tail -f /dev/null"
-    stdin_open: true
-    tty: true
-    restart: unless-stopped
-
-volumes:
-  opencode_home:""",
-                "required_variables": ["REPO_PATH", "TOOL_NAME"],
-            },
-        ]
-
-        for tool_data in builtin_types:
-            existing = await session.scalar(select(ToolType).where(ToolType.name == tool_data["name"]))
-            if not existing:
-                tool_type = ToolType(
-                    name=tool_data["name"],
-                    display_name=tool_data["display_name"],
-                    description=tool_data["description"],
-                    category=tool_data["category"],
-                    interfaces=tool_data["interfaces"],
-                    definition_type="compose",
-                    compose_template=tool_data["compose_template"],
-                    required_variables=tool_data["required_variables"],
-                    default_port=tool_data.get("default_port"),
-                    is_builtin=True,
-                )
-                session.add(tool_type)
-                logger.info("Created built-in tool type: %s", tool_data["name"])
-            else:
-                # Update existing built-in tool types to reflect code changes
-                existing.display_name = tool_data["display_name"]
-                existing.description = tool_data["description"]
-                existing.category = tool_data["category"]
-                existing.interfaces = tool_data["interfaces"]
-                existing.definition_type = "compose"
-                existing.compose_template = tool_data["compose_template"]
-                existing.required_variables = tool_data["required_variables"]
-                existing.default_port = tool_data.get("default_port")
-                logger.info("Updated built-in tool type: %s", tool_data["name"])
-
-        await session.commit()
-        logger.info("Built-in tool types seeded successfully.")
-
-
@app.on_event("startup")
 async def on_startup():
    logger.info("Starting up Headquarter API...")
@@ -261,12 +113,12 @@ async def on_startup():
    if not db_ready:
        logger.error("Database initialization failed. Shutting down.")
        import sys
+
        sys.exit(1)

-    # Seed built-in data
-    await seed_builtin_tool_types()
    logger.info("Startup complete.")

+
 app.include_router(health_router)
 app.include_router(auth_router)
 app.include_router(dashboard_router)
@@ -276,7 +128,9 @@ app.include_router(ssh_keys_router)
 app.include_router(git_repositories_router)
 app.include_router(user_config_router)
 app.include_router(tool_types_router)
+app.include_router(tool_definitions_router)
 app.include_router(config_folders_router)
+app.include_router(config_profiles_router)
 app.include_router(tool_instances_router)
 app.include_router(tool_configs_router)
 app.include_router(sessions_router)
@@ -1,11 +1,26 @@
 from src.models.base import Base
 from src.models.config_folder import ConfigFolder
+from src.models.config_profile import ConfigProfile, ConfigProfileInclude
 from src.models.git_repository import GitRepository
 from src.models.project import Project
 from src.models.ssh_key import SSHKey
+from src.models.tool_definition_manifest import ToolDefinitionManifest
 from src.models.tool_instance import ToolInstance
 from src.models.tool_type import ToolType
 from src.models.user import User
 from src.models.user_config import UserConfig

-__all__ = ["Base", "ConfigFolder", "GitRepository", "Project", "SSHKey", "ToolInstance", "ToolType", "User", "UserConfig"]
+__all__ = [
+    "Base",
+    "ConfigFolder",
+    "ConfigProfile",
+    "ConfigProfileInclude",
+    "GitRepository",
+    "Project",
+    "SSHKey",
+    "ToolDefinitionManifest",
+    "ToolInstance",
+    "ToolType",
+    "User",
+    "UserConfig",
+]
@@ -0,0 +1,77 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, JSON, Integer, String, Text, Boolean
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.project import Project
+    from src.models.tool_type import ToolType
+    from src.models.user import User
+
+
+class ConfigProfile(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_profiles"
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id", ondelete="CASCADE"), nullable=False
+    )
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    description: Mapped[str | None] = mapped_column(Text, nullable=True)
+    project_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("projects.id", ondelete="CASCADE"), nullable=True
+    )
+    tool_type_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("tool_types.id", ondelete="CASCADE"), nullable=True
+    )
+    env_vars: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"VAR_NAME": "value", ...}
+    runtime_hints: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"start_command": "...", "working_dir": "...", ...}
+    mounts: Mapped[list] = mapped_column(
+        JSON, default=list, nullable=False
+    )  # [{"target": "/path", "mode": "rw", "files": {"rel/path": "content"}}, ...]
+    files: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"rel/path": "content", ...}
+    git_mounts: Mapped[list] = mapped_column(
+        JSON, default=list, nullable=False
+    )  # [{"remote_url": "https://github.com/user/repo.git", "source_path": ".", "target_path": "/path", "branch": "main"}, ...]
+    is_default: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
+
+    user: Mapped["User"] = relationship()
+    project: Mapped["Project | None"] = relationship()
+    tool_type: Mapped["ToolType | None"] = relationship()
+    includes: Mapped[list["ConfigProfileInclude"]] = relationship(
+        "ConfigProfileInclude",
+        foreign_keys="ConfigProfileInclude.profile_id",
+        order_by="ConfigProfileInclude.order_index",
+        cascade="all, delete-orphan",
+    )
+
+
+class ConfigProfileInclude(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_profile_includes"
+
+    profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    included_profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
+
+    profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[profile_id],
+        back_populates="includes",
+    )
+    included_profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[included_profile_id],
+    )
@@ -10,6 +10,7 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin

 if TYPE_CHECKING:
    from src.models.project import Project
+    from src.models.ssh_key import SSHKey
    from src.models.user import User


@@ -18,11 +19,15 @@ class GitRepository(UUIDPrimaryKeyMixin, TimestampMixin, Base):

    name: Mapped[str] = mapped_column(String(255))
    path: Mapped[str] = mapped_column(String(1024))
-    project_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("projects.id"), nullable=False)
+    project_id: Mapped[uuid.UUID | None] = mapped_column(UUID(), ForeignKey("projects.id"), nullable=True)
    owner_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("users.id"), nullable=False)
    is_mirror: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
    remote_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
    last_push: Mapped[datetime | None] = mapped_column(DateTime(timezone=True), nullable=True)
+    ssh_key_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("ssh_keys.id"), nullable=True
+    )

    project: Mapped["Project"] = relationship(back_populates="repositories")
    owner: Mapped["User"] = relationship()
+    ssh_key: Mapped["SSHKey | None"] = relationship()
@@ -0,0 +1,67 @@
+"""Tool Definition Manifest model."""
+
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import Boolean, ForeignKey, JSON, String, Text
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.user import User
+
+
+class ToolDefinitionManifest(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    """A declarative manifest that compiles to Dockerfile + Compose.
+
+    Can be either:
+    - A base definition (is_base=True) with a FROM image and common packages
+    - A tool definition (is_base=False) that references a base + adds specifics
+    """
+
+    __tablename__ = "tool_definition_manifests"
+
+    name: Mapped[str] = mapped_column(String(64), unique=True, nullable=False)
+    display_name: Mapped[str] = mapped_column(String(128), nullable=False)
+    description: Mapped[str | None] = mapped_column(Text, nullable=True)
+    category: Mapped[str | None] = mapped_column(String(64), nullable=True)
+    interface_type: Mapped[str] = mapped_column(String(16), nullable=False)
+
+    # Base: either a direct image or a reference to another manifest
+    base_image: Mapped[str | None] = mapped_column(String(256), nullable=True)
+    base_definition_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(),
+        ForeignKey("tool_definition_manifests.id"),
+        nullable=True,
+    )
+    base_version: Mapped[str] = mapped_column(
+        String(32), nullable=False, default="latest"
+    )
+
+    # The full manifest JSON
+    manifest: Mapped[dict] = mapped_column(JSON, nullable=False)
+
+    # Caches for quick inspection
+    dockerfile_cache: Mapped[str | None] = mapped_column(Text, nullable=True)
+    compose_cache: Mapped[str | None] = mapped_column(Text, nullable=True)
+
+    # Versioning
+    version: Mapped[str] = mapped_column(String(32), nullable=False, default="v1")
+    is_base: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
+
+    created_by_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(),
+        ForeignKey("users.id"),
+        nullable=True,
+    )
+
+    # Relationships
+    created_by: Mapped["User | None"] = relationship(
+        foreign_keys=[created_by_id],
+    )
+    base_definition: Mapped["ToolDefinitionManifest | None"] = relationship(
+        remote_side="ToolDefinitionManifest.id",
+        foreign_keys=[base_definition_id],
+    )
@@ -2,13 +2,14 @@ import uuid
 from datetime import datetime
 from typing import TYPE_CHECKING

-from sqlalchemy import DateTime, ForeignKey, Integer, String
+from sqlalchemy import DateTime, ForeignKey, Integer, JSON, String
 from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship

 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin

 if TYPE_CHECKING:
+    from src.models.config_profile import ConfigProfile
    from src.models.git_repository import GitRepository
    from src.models.project import Project
    from src.models.tool_type import ToolType
@@ -32,38 +33,35 @@ class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
    owner_id: Mapped[uuid.UUID] = mapped_column(
        UUID(), ForeignKey("users.id"), nullable=False
    )
-    status: Mapped[str] = mapped_column(
-        String(50), nullable=False, default="pending"
-    )
-    container_id: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    container_name: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    compose_path: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    url: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    public_url: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    tunnel_id: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    port: Mapped[int | None] = mapped_column(
-        Integer, nullable=True
-    )
+    status: Mapped[str] = mapped_column(String(50), nullable=False, default="pending")
+    container_id: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    container_name: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    compose_path: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    public_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    tunnel_id: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    port: Mapped[int | None] = mapped_column(Integer, nullable=True)
    last_started_at: Mapped[datetime | None] = mapped_column(
        DateTime(timezone=True), nullable=True
    )
    last_stopped_at: Mapped[datetime | None] = mapped_column(
        DateTime(timezone=True), nullable=True
    )
+    manifest_compiled_at: Mapped[datetime | None] = mapped_column(
+        DateTime(timezone=True), nullable=True
+    )
+    image_tag: Mapped[str | None] = mapped_column(String(256), nullable=True)
+    probe_result: Mapped[dict | None] = mapped_column(JSON, nullable=True)
+    clone_mode: Mapped[str] = mapped_column(String(20), nullable=False, default="mount")
+    branch: Mapped[str | None] = mapped_column(
+        String(255), nullable=True, default="main"
+    )
+    selected_config_profile_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True
+    )

    tool_type: Mapped["ToolType"] = relationship()
    repository: Mapped["GitRepository"] = relationship()
    project: Mapped["Project"] = relationship()
    owner: Mapped["User"] = relationship()
+    selected_config_profile: Mapped["ConfigProfile | None"] = relationship()
@@ -8,6 +8,7 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin

 if TYPE_CHECKING:
+    from src.models.tool_definition_manifest import ToolDefinitionManifest
    from src.models.user import User


@@ -18,23 +19,36 @@ class ToolType(UUIDPrimaryKeyMixin, TimestampMixin, Base):
    display_name: Mapped[str] = mapped_column(String(255), nullable=False)
    description: Mapped[str | None] = mapped_column(Text, nullable=True)
    category: Mapped[str] = mapped_column(String(50), nullable=False, default="other")
-    interfaces: Mapped[list[str]] = mapped_column(JSON, default=list, nullable=False)
+    interface_type: Mapped[str] = mapped_column(
+        String(20), nullable=False, default="web"
+    )
+    requires_port: Mapped[bool] = mapped_column(Boolean, default=True, nullable=False)
    default_port: Mapped[int] = mapped_column(nullable=False)
    definition_type: Mapped[str] = mapped_column(
-        String(20), nullable=False, default="compose"
-    )  # "compose" or "dockerfile"
+        String(16), nullable=False, default="legacy"
+    )  # "legacy" | "manifest"
+    manifest_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(),
+        ForeignKey("tool_definition_manifests.id"),
+        nullable=True,
+    )
    compose_template: Mapped[str | None] = mapped_column(Text, nullable=True)
    dockerfile_template: Mapped[str | None] = mapped_column(Text, nullable=True)
    build_context: Mapped[dict | None] = mapped_column(
        JSON, default=dict, nullable=True
    )
    readiness_probe: Mapped[dict | None] = mapped_column(JSON, nullable=True)
-    required_variables: Mapped[list[str]] = mapped_column(JSON, default=list, nullable=False)
-    is_builtin: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
+    startup_command: Mapped[str | None] = mapped_column(Text, nullable=True)
+    required_variables: Mapped[list[str]] = mapped_column(
+        JSON, default=list, nullable=False
+    )
    created_by_id: Mapped[uuid.UUID | None] = mapped_column(
        UUID(),
        ForeignKey("users.id"),
        nullable=True,
    )

+    manifest: Mapped["ToolDefinitionManifest | None"] = relationship(
+        foreign_keys=[manifest_id],
+    )
    created_by: Mapped["User | None"] = relationship()
@@ -0,0 +1,97 @@
+"""Clone service for repository cloning and dirty state checking."""
+
+import logging
+import os
+import subprocess
+from pathlib import Path
+
+logger = logging.getLogger(__name__)
+
+
+def clone_repository(
+    remote_url: str,
+    ssh_key_path: str | None,
+    instance_dir: str,
+    branch: str = "main",
+) -> str:
+    """Clone a git repository into the instance directory.
+
+    Args:
+        remote_url: Git remote URL (SSH or HTTPS)
+        ssh_key_path: Path to SSH private key for authentication (optional)
+        instance_dir: Path to instance directory
+        branch: Branch to clone (default: main)
+
+    Returns:
+        Path to the cloned repository
+    """
+    clone_path = Path(instance_dir) / "repo-clone"
+    clone_path.mkdir(parents=True, exist_ok=True)
+
+    env = os.environ.copy()
+    if ssh_key_path:
+        # Use SSH key for cloning
+        env["GIT_SSH_COMMAND"] = f"ssh -i {ssh_key_path} -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
+
+    cmd = [
+        "git",
+        "clone",
+        "--branch", branch,
+        "--single-branch",
+        remote_url,
+        str(clone_path),
+    ]
+
+    logger.debug("Cloning repository %s (branch: %s) into %s", remote_url, branch, clone_path)
+    result = subprocess.run(
+        cmd,
+        capture_output=True,
+        text=True,
+        env=env,
+        timeout=300,
+    )
+
+    if result.returncode != 0:
+        logger.error("Git clone failed: %s", result.stderr)
+        raise RuntimeError(f"Failed to clone repository: {result.stderr}")
+
+    logger.debug("Successfully cloned repository into %s", clone_path)
+    return str(clone_path)
+
+
+def check_dirty_state(clone_path: str) -> tuple[bool, list[str]]:
+    """Check for uncommitted changes in a cloned repository.
+
+    Args:
+        clone_path: Path to the cloned repository
+
+    Returns:
+        Tuple of (is_dirty, list_of_changed_files)
+    """
+    result = subprocess.run(
+        ["git", "-C", clone_path, "status", "--short"],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode != 0:
+        logger.warning("Failed to check git status: %s", result.stderr)
+        return False, []
+
+    changed_files = [line.strip() for line in result.stdout.split("\n") if line.strip()]
+    is_dirty = len(changed_files) > 0
+
+    return is_dirty, changed_files
+
+
+def remove_clone_directory(instance_dir: str) -> None:
+    """Remove the cloned repository from the instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+    """
+    clone_path = Path(instance_dir) / "repo-clone"
+    if clone_path.exists():
+        import shutil
+        shutil.rmtree(clone_path)
+        logger.debug("Removed clone directory: %s", clone_path)
@@ -0,0 +1,484 @@
+"""Config profile resolver service.
+
+Provides recursive ordered include resolution with deterministic merge rules
+and cycle protection.
+"""
+
+import logging
+import uuid
+from dataclasses import dataclass, field
+from typing import Any
+
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+
+logger = logging.getLogger(__name__)
+
+
+class ConfigProfileCycleError(Exception):
+    """Raised when a cycle is detected in profile includes."""
+
+    pass
+
+
+class ConfigProfileNotFoundError(Exception):
+    """Raised when a referenced profile is not found."""
+
+    pass
+
+
+@dataclass
+class ResolvedMount:
+    """A resolved mount with merged files and final mode."""
+
+    target: str
+    mode: str
+    files: dict[str, str] = field(default_factory=dict)
+    overridden_files: dict[str, str] = field(default_factory=dict)
+
+
+@dataclass
+class ResolvedProfile:
+    """The fully resolved output of a config profile."""
+
+    profile_id: uuid.UUID
+    profile_name: str
+    env_vars: dict[str, str] = field(default_factory=dict)
+    runtime_hints: dict[str, Any] = field(default_factory=dict)
+    mounts: dict[str, ResolvedMount] = field(default_factory=dict)
+    git_mounts: list[dict[str, Any]] = field(default_factory=list)
+    files: dict[str, str] = field(default_factory=dict)
+    env_overrides: dict[str, str] = field(default_factory=dict)
+    hint_overrides: dict[str, str] = field(default_factory=dict)
+    file_overrides: dict[str, str] = field(default_factory=dict)
+    mount_overrides: dict[str, str] = field(default_factory=dict)
+    included_profiles: list[dict[str, Any]] = field(default_factory=list)
+
+
+def _detect_cycle(profile_id: uuid.UUID, visited: set[uuid.UUID], path: list[uuid.UUID]) -> bool:
+    """Detect if adding profile_id to path would create a cycle.
+
+    Args:
+        profile_id: The profile ID to check.
+        visited: Set of already-visited profile IDs in current resolution.
+        path: Current resolution path for error reporting.
+
+    Returns:
+        True if a cycle would be created.
+    """
+    if profile_id in visited:
+        return True
+    return False
+
+
+def _merge_env_vars(
+    base: dict[str, str],
+    overlay: dict[str, str],
+    overrides: dict[str, str],
+    source_name: str,
+) -> dict[str, str]:
+    """Merge env vars, tracking overrides.
+
+    Later values replace earlier values.
+    """
+    result = dict(base)
+    for key, value in overlay.items():
+        if key in result and result[key] != value:
+            overrides[key] = source_name
+        result[key] = value
+    return result
+
+
+def _merge_runtime_hints(
+    base: dict[str, Any],
+    overlay: dict[str, Any],
+    overrides: dict[str, str],
+    source_name: str,
+) -> dict[str, Any]:
+    """Merge runtime hints, tracking overrides.
+
+    Later values replace earlier values.
+    """
+    result = dict(base)
+    for key, value in overlay.items():
+        if key in result and result[key] != value:
+            overrides[key] = source_name
+        result[key] = value
+    return result
+
+
+def _merge_files(
+    base: dict[str, str],
+    overlay: dict[str, str],
+    overrides: dict[str, str],
+    source_name: str,
+) -> dict[str, str]:
+    """Merge file maps, tracking overrides.
+
+    Later relative file paths win.
+    """
+    result = dict(base)
+    for path, content in overlay.items():
+        if path in result and result[path] != content:
+            overrides[path] = source_name
+        result[path] = content
+    return result
+
+
+def _merge_mounts(
+    base: dict[str, ResolvedMount],
+    overlay: list[dict[str, Any]],
+    overrides: dict[str, str],
+    source_name: str,
+) -> dict[str, ResolvedMount]:
+    """Merge mounts, tracking overrides.
+
+    Mounts with the same target path have their file maps merged and later
+    relative file paths win. Mode conflicts: later layer wins.
+    """
+    result = dict(base)
+    for mount_data in overlay:
+        target = mount_data["target"]
+        mode = mount_data.get("mode", "rw")
+        files = mount_data.get("files", {})
+
+        if target in result:
+            existing = result[target]
+            merged_files = dict(existing.files)
+            file_overrides = dict(existing.overridden_files)
+            for rel_path, content in files.items():
+                if rel_path in merged_files and merged_files[rel_path] != content:
+                    file_overrides[rel_path] = source_name
+                merged_files[rel_path] = content
+            if existing.mode != mode:
+                overrides[target] = source_name
+            result[target] = ResolvedMount(
+                target=target,
+                mode=mode,
+                files=merged_files,
+                overridden_files=file_overrides,
+            )
+        else:
+            result[target] = ResolvedMount(
+                target=target,
+                mode=mode,
+                files=dict(files),
+            )
+    return result
+
+
+def _merge_git_mounts(
+    base: list[dict[str, Any]],
+    overlay: list[dict[str, Any]],
+    source_name: str,
+) -> list[dict[str, Any]]:
+    """Merge git mounts from included profiles.
+
+    Later mounts override earlier ones with the same remote_url + target_path combo.
+    """
+    result = list(base)
+    # Build lookup by (remote_url, target_path)
+    seen = {(m["remote_url"], m["target_path"]): i for i, m in enumerate(result)}
+    for mount in overlay:
+        key = (mount["remote_url"], mount["target_path"])
+        if key in seen:
+            result[seen[key]] = dict(mount)
+        else:
+            seen[key] = len(result)
+            result.append(dict(mount))
+    return result
+
+
+async def _resolve_profile_recursive(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+    visited: set[uuid.UUID],
+    path: list[uuid.UUID],
+) -> ResolvedProfile:
+    """Recursively resolve a profile and its includes.
+
+    Args:
+        session: Database session.
+        profile_id: Profile ID to resolve.
+        visited: Set of already-visited profile IDs in current resolution chain.
+        path: Current resolution path for error reporting.
+
+    Returns:
+        ResolvedProfile with all includes merged.
+
+    Raises:
+        ConfigProfileCycleError: If a cycle is detected.
+        ConfigProfileNotFoundError: If the profile is not found.
+    """
+    if _detect_cycle(profile_id, visited, path):
+        cycle_path = " -> ".join(str(p) for p in path + [profile_id])
+        raise ConfigProfileCycleError(f"Cycle detected in profile includes: {cycle_path}")
+
+    profile = await session.get(ConfigProfile, profile_id)
+    if profile is None:
+        raise ConfigProfileNotFoundError(f"Config profile not found: {profile_id}")
+
+    new_visited = visited | {profile_id}
+    new_path = path + [profile_id]
+
+    result = ResolvedProfile(
+        profile_id=profile.id,
+        profile_name=profile.name,
+    )
+
+    # Resolve includes in order
+    include_query = (
+        select(ConfigProfileInclude)
+        .where(ConfigProfileInclude.profile_id == profile_id)
+        .order_by(ConfigProfileInclude.order_index)
+    )
+    include_result = await session.execute(include_query)
+    includes = include_result.scalars().all()
+
+    for include in includes:
+        included = await _resolve_profile_recursive(
+            session, include.included_profile_id, new_visited, new_path
+        )
+        result.included_profiles.append({
+            "id": str(included.profile_id),
+            "name": included.profile_name,
+        })
+
+        result.env_vars = _merge_env_vars(
+            result.env_vars, included.env_vars, result.env_overrides, included.profile_name
+        )
+        result.runtime_hints = _merge_runtime_hints(
+            result.runtime_hints,
+            included.runtime_hints,
+            result.hint_overrides,
+            included.profile_name,
+        )
+        result.files = _merge_files(
+            result.files, included.files, result.file_overrides, included.profile_name
+        )
+        result.mounts = _merge_mounts(
+            result.mounts,
+            [
+                {"target": m.target, "mode": m.mode, "files": m.files}
+                for m in included.mounts.values()
+            ],
+            result.mount_overrides,
+            included.profile_name,
+        )
+        result.git_mounts = _merge_git_mounts(
+            result.git_mounts, included.git_mounts, included.profile_name
+        )
+
+    # Apply the profile's own settings (selected profile overrides includes)
+    result.env_vars = _merge_env_vars(
+        result.env_vars,
+        profile.env_vars or {},
+        result.env_overrides,
+        profile.name,
+    )
+    result.runtime_hints = _merge_runtime_hints(
+        result.runtime_hints,
+        profile.runtime_hints or {},
+        result.hint_overrides,
+        profile.name,
+    )
+    result.files = _merge_files(
+        result.files,
+        profile.files or {},
+        result.file_overrides,
+        profile.name,
+    )
+    result.mounts = _merge_mounts(
+        result.mounts,
+        profile.mounts or [],
+        result.mount_overrides,
+        profile.name,
+    )
+    result.git_mounts = _merge_git_mounts(
+        result.git_mounts,
+        profile.git_mounts or [],
+        profile.name,
+    )
+    return result
+
+
+async def resolve_profile(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+) -> ResolvedProfile:
+    """Resolve a config profile with all includes.
+
+    Args:
+        session: Database session.
+        profile_id: Profile ID to resolve.
+
+    Returns:
+        ResolvedProfile with merged env vars, runtime hints, mounts, and files.
+
+    Raises:
+        ConfigProfileCycleError: If a cycle is detected in includes.
+        ConfigProfileNotFoundError: If the profile is not found.
+    """
+    return await _resolve_profile_recursive(session, profile_id, set(), [])
+
+
+async def check_include_cycle(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+    new_include_id: uuid.UUID | None = None,
+) -> list[uuid.UUID] | None:
+    """Check if adding an include would create a cycle.
+
+    Used at save time to validate include relationships before persisting.
+
+    Args:
+        session: Database session.
+        profile_id: The profile that would receive the new include.
+        new_include_id: Optional new profile to include. If None, checks existing includes.
+
+    Returns:
+        The cycle path as a list of UUIDs if a cycle exists, otherwise None.
+    """
+
+    async def _check_from(
+        current_id: uuid.UUID,
+        target_id: uuid.UUID,
+        visited: set[uuid.UUID],
+        path: list[uuid.UUID],
+    ) -> list[uuid.UUID] | None:
+        if current_id in visited:
+            if current_id == target_id:
+                return path + [current_id]
+            return None
+        if current_id == target_id and path:
+            return path + [current_id]
+
+        new_visited = visited | {current_id}
+        new_path = path + [current_id]
+
+        include_query = (
+            select(ConfigProfileInclude)
+            .where(ConfigProfileInclude.profile_id == current_id)
+            .order_by(ConfigProfileInclude.order_index)
+        )
+        include_result = await session.execute(include_query)
+        includes = include_result.scalars().all()
+
+        for include in includes:
+            cycle = await _check_from(
+                include.included_profile_id, target_id, new_visited, new_path
+            )
+            if cycle is not None:
+                return cycle
+        return None
+
+    # Check if new_include_id can reach profile_id (would create cycle)
+    if new_include_id is not None:
+        cycle = await _check_from(new_include_id, profile_id, set(), [])
+        if cycle is not None:
+            return cycle
+
+    # Also check existing includes for cycles
+    cycle = await _check_from(profile_id, profile_id, set(), [])
+    if cycle is not None and len(cycle) > 1:
+        return cycle
+
+    return None
+
+
+def apply_resolved_profile(
+    instance_dir: str,
+    resolved: ResolvedProfile,
+) -> tuple[dict[str, str], dict[str, str], list[dict], dict[str, Any]]:
+    """Apply a resolved profile to an instance directory.
+
+    Stages files, writes env vars, and prepares mount volumes.
+
+    Args:
+        instance_dir: Path to the instance directory.
+        resolved: The resolved profile.
+
+    Returns:
+        Tuple of (env_vars, files, volume_mounts, runtime_hints).
+        env_vars: Merged environment variables.
+        files: Relative file paths to content for the instance.
+        volume_mounts: List of Docker volume mount dicts.
+        runtime_hints: Extracted runtime hints.
+    """
+    from pathlib import Path
+
+    instance_path = Path(instance_dir)
+    env_vars = dict(resolved.env_vars)
+    files = dict(resolved.files)
+    volume_mounts = []
+
+    # Write profile files to instance directory
+    for file_path, content in files.items():
+        full_path = instance_path / file_path
+        try:
+            full_path.resolve().relative_to(instance_path.resolve())
+        except ValueError:
+            logger.warning("Profile file path escapes instance directory: %s", file_path)
+            continue
+        full_path.parent.mkdir(parents=True, exist_ok=True)
+        full_path.write_text(content)
+
+    # Stage mount files and prepare volume mounts
+    for mount in resolved.mounts.values():
+        mount_dir = instance_path / "mounts" / mount.target.lstrip("/").replace("/", "_")
+        mount_dir.mkdir(parents=True, exist_ok=True)
+
+        for file_path, content in mount.files.items():
+            full_path = mount_dir / file_path
+            try:
+                full_path.resolve().relative_to(mount_dir.resolve())
+            except ValueError:
+                logger.warning("Mount file path escapes mount directory: %s", file_path)
+                continue
+            full_path.parent.mkdir(parents=True, exist_ok=True)
+            full_path.write_text(content)
+
+        volume_mounts.append({
+            "source": str(mount_dir),
+            "target": mount.target,
+            "type": "bind",
+        })
+
+    return env_vars, files, volume_mounts, resolved.runtime_hints
+
+
+def resolved_profile_to_dict(resolved: ResolvedProfile) -> dict[str, Any]:
+    """Convert a ResolvedProfile to a plain dict for serialization.
+
+    Args:
+        resolved: The resolved profile.
+
+    Returns:
+        Dict with env_vars, runtime_hints, mounts, files, and metadata.
+    """
+    return {
+        "profile_id": str(resolved.profile_id),
+        "profile_name": resolved.profile_name,
+        "env_vars": resolved.env_vars,
+        "runtime_hints": resolved.runtime_hints,
+        "mounts": [
+            {
+                "target": m.target,
+                "mode": m.mode,
+                "files": m.files,
+                "overridden_files": m.overridden_files,
+            }
+            for m in resolved.mounts.values()
+        ],
+        "files": resolved.files,
+        "overrides": {
+            "env_vars": resolved.env_overrides,
+            "runtime_hints": resolved.hint_overrides,
+            "files": resolved.file_overrides,
+            "mounts": resolved.mount_overrides,
+        },
+        "git_mounts": resolved.git_mounts,
+        "included_profiles": resolved.included_profiles,
+    }
@@ -1,7 +1,9 @@
 """Docker service for managing tool instances."""

 import os
+import re
 import subprocess
+import time
 from pathlib import Path
 from typing import Any

@@ -35,6 +37,7 @@ def ensure_instance_directory(instance_id: str, base_path: str | None = None) ->
    """
    if base_path is None:
        from src.config import Settings
+
        base_path = Settings().instance_base_path
    instance_dir = Path(base_path) / instance_id
    instance_dir.mkdir(parents=True, exist_ok=True)
@@ -87,64 +90,11 @@ def write_config_files(instance_dir: str, files: dict[str, str]) -> None:
            full_path.resolve().relative_to(instance_path.resolve())
        except ValueError:
            raise ValueError(f"File path '{file_path}' escapes instance directory")
-        
+
        full_path.parent.mkdir(parents=True, exist_ok=True)
        full_path.write_text(content)


-def write_config_folder_files(instance_dir: str, folders: list, project_id: str | None = None) -> list[dict]:
-    """Write config folder files to the instance directory and return volume mounts.
-
-    Args:
-        instance_dir: Path to instance directory
-        folders: List of ConfigFolder objects
-        project_id: Optional project ID for applying overrides
-
-    Returns:
-        List of volume mount dicts [{"source": "...", "target": "...", "type": "..."}]
-    """
-    instance_path = Path(instance_dir)
-    volume_mounts = []
-
-    for folder in folders:
-        # Determine mount path (with project override if applicable)
-        mount_path = folder.mount_path
-        files = folder.files.copy()
-        
-        if project_id and folder.project_overrides:
-            override = folder.project_overrides.get(str(project_id))
-            if override:
-                if override.get("mount_path"):
-                    mount_path = override["mount_path"]
-                if override.get("files"):
-                    files.update(override["files"])
-        
-        # Write files to instance directory
-        folder_dir = instance_path / "volumes" / folder.name
-        folder_dir.mkdir(parents=True, exist_ok=True)
-        
-        for file_path, content in files.items():
-            # Security: ensure path doesn't escape folder_dir
-            full_path = folder_dir / file_path
-            try:
-                full_path.resolve().relative_to(folder_dir.resolve())
-            except ValueError:
-                logger.warning("Config folder file path escapes directory: %s", file_path)
-                continue
-            
-            full_path.parent.mkdir(parents=True, exist_ok=True)
-            full_path.write_text(content)
-        
-        # Add volume mount
-        volume_mounts.append({
-            "source": str(folder_dir),
-            "target": mount_path,
-            "type": "bind",
-        })
-    
-    return volume_mounts
-
-
 def execute_compose_command(
    compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
 ) -> tuple[int, str, str]:
@@ -162,7 +112,7 @@ def execute_compose_command(
    instance_dir = Path(compose_path).parent

    cmd = ["docker", "compose", "-f", compose_path]
-    
+
    if env_file:
        cmd.extend(["--env-file", env_file])

@@ -189,14 +139,17 @@ def execute_compose_command(
 def get_container_id(instance_name: str) -> str | None:
    """Get the container ID for a compose service.

+    Searches all containers including stopped/exited ones.
+
    Args:
        instance_name: The service name in compose

    Returns:
        Container ID or None if not found
    """
+    # Docker container names are lowercase internally; normalize to ensure match
    result = subprocess.run(
-        ["docker", "ps", "-q", "--filter", f"name={instance_name}"],
+        ["docker", "ps", "-a", "-q", "--filter", f"name={instance_name.lower()}"],
        capture_output=True,
        text=True,
    )
@@ -209,14 +162,25 @@ def get_container_id(instance_name: str) -> str | None:
 def get_container_name(instance_name: str) -> str | None:
    """Get the full container name for a compose service.

+    Searches all containers including stopped/exited ones.
+
    Args:
        instance_name: The service name in compose

    Returns:
        Container name or None if not found
    """
+    # Docker container names are lowercase internally; normalize to ensure match
    result = subprocess.run(
-        ["docker", "ps", "--format", "{{.Names}}", "--filter", f"name={instance_name}"],
+        [
+            "docker",
+            "ps",
+            "-a",
+            "--format",
+            "{{.Names}}",
+            "--filter",
+            f"name={instance_name.lower()}",
+        ],
        capture_output=True,
        text=True,
    )
@@ -226,7 +190,9 @@ def get_container_name(instance_name: str) -> str | None:
    return None


-def connect_container_to_network(container_name: str, network_name: str = "backend") -> bool:
+def connect_container_to_network(
+    container_name: str, network_name: str = "backend"
+) -> bool:
    """Connect a Docker container to an existing network.

    Args:
@@ -244,24 +210,95 @@ def connect_container_to_network(container_name: str, network_name: str = "backe
    return result.returncode == 0


-def get_container_status(container_id: str) -> str:
+def get_container_status(container_id: str) -> dict[str, Any]:
    """Get the status of a Docker container.

    Args:
        container_id: Docker container ID

    Returns:
-        Container status string (running, exited, etc.)
+        Dict with 'status' (running, exited, restarting, not_found),
+        'exit_code' (int or None), and 'health' (health status or None)
    """
    result = subprocess.run(
-        ["docker", "inspect", "-f", "{{.State.Status}}", container_id],
+        [
+            "docker",
+            "inspect",
+            "-f",
+            "{{.State.Status}}|{{.State.ExitCode}}|{{if .State.Health}}{{.State.Health.Status}}{{else}}none{{end}}",
+            container_id,
+        ],
        capture_output=True,
        text=True,
    )

-    if result.returncode == 0:
-        return result.stdout.strip()
-    return "unknown"
+    if result.returncode != 0:
+        return {"status": "not_found", "exit_code": None, "health": None}
+
+    parts = result.stdout.strip().split("|")
+    status = parts[0] if parts else "unknown"
+    exit_code = int(parts[1]) if len(parts) > 1 and parts[1].isdigit() else None
+    health = parts[2] if len(parts) > 2 and parts[2] != "none" else None
+
+    return {"status": status, "exit_code": exit_code, "health": health}
+
+
+def wait_for_container_running(
+    container_id: str, timeout: int = 30, interval: float = 2.0
+) -> dict[str, Any]:
+    """Wait for a container to reach the running state.
+
+    Polls docker inspect until the container status is "running" or timeout.
+
+    Args:
+        container_id: Docker container ID
+        timeout: Maximum seconds to wait
+        interval: Seconds between polls
+
+    Returns:
+        Dict with 'success' (bool), 'status' (str), 'exit_code' (int or None),
+        and 'waited_seconds' (float)
+    """
+
+    start_time = time.time()
+
+    while time.time() - start_time < timeout:
+        info = get_container_status(container_id)
+
+        if info["status"] == "running":
+            return {
+                "success": True,
+                "status": "running",
+                "exit_code": None,
+                "waited_seconds": time.time() - start_time,
+            }
+
+        if info["status"] == "exited":
+            return {
+                "success": False,
+                "status": "exited",
+                "exit_code": info["exit_code"],
+                "waited_seconds": time.time() - start_time,
+            }
+
+        if info["status"] == "not_found":
+            return {
+                "success": False,
+                "status": "not_found",
+                "exit_code": None,
+                "waited_seconds": time.time() - start_time,
+            }
+
+        time.sleep(interval)
+
+    # Timeout reached
+    info = get_container_status(container_id)
+    return {
+        "success": False,
+        "status": info["status"],
+        "exit_code": info["exit_code"],
+        "waited_seconds": time.time() - start_time,
+    }


 def get_container_logs(container_id: str, tail: int = 100) -> str:
@@ -305,11 +342,6 @@ def find_free_port(start: int = 10000, end: int = 20000) -> int:
    raise RuntimeError(f"No free port found in range {start}-{end}")


-import subprocess
-import time
-import re
-
-
 def start_cloudflared_tunnel(
    container_name: str, port: int, timeout: int = 30
 ) -> dict[str, str]:
@@ -327,8 +359,6 @@ def start_cloudflared_tunnel(
        Dict with 'url' (the public tunnel URL) and 'pid' (process ID)
    """
    import subprocess
-    import time
-    import re
    import logging

    logger = logging.getLogger(__name__)
@@ -337,18 +367,29 @@ def start_cloudflared_tunnel(
    logger.info("Checking connectivity to %s:%d...", container_name, port)
    for attempt in range(10):
        check = subprocess.run(
-            ["curl", "-s", "-o", "/dev/null", "-w", "%{http_code}", 
-             f"http://{container_name}:{port}"],
+            [
+                "curl",
+                "-s",
+                "-o",
+                "/dev/null",
+                "-w",
+                "%{http_code}",
+                f"http://{container_name}:{port}",
+            ],
            capture_output=True,
            text=True,
            timeout=5,
        )
-        logger.info("Connectivity check %d: http_code=%s", attempt + 1, check.stdout.strip())
+        logger.info(
+            "Connectivity check %d: http_code=%s", attempt + 1, check.stdout.strip()
+        )
        if check.returncode == 0:
            break
        time.sleep(1)
    else:
-        logger.warning("Container %s:%d not responding to curl checks", container_name, port)
+        logger.warning(
+            "Container %s:%d not responding to curl checks", container_name, port
+        )

    # Run cloudflared in background, capture output
    logger.info("Starting cloudflared tunnel to http://%s:%d", container_name, port)
@@ -364,9 +405,15 @@ def start_cloudflared_tunnel(
    start_time = time.time()
    url = None

+    if proc.stdout is None:
+        proc.terminate()
+        proc.wait(timeout=5)
+        raise RuntimeError("Failed to capture cloudflared output")
+
    while time.time() - start_time < timeout:
        # Read available output
        import select
+
        readable, _, _ = select.select([proc.stdout], [], [], 1.0)
        if readable:
            line = proc.stdout.readline()
@@ -393,7 +440,6 @@ def stop_cloudflared_tunnel(pid: str) -> None:
    Args:
        pid: Process ID of the cloudflared tunnel
    """
-    import os
    import signal

    try:
@@ -424,33 +470,87 @@ def recreate_tunnel(


 def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
-    """Check if a tunnel URL is healthy.
+    """Check if a tunnel URL is healthy with smart error classification.

    Args:
        url: The tunnel URL to check
        timeout: Request timeout in seconds

    Returns:
-        Dict with 'healthy' (bool) and 'status_code' (int or None)
+        Dict with 'tunnel_status' (healthy, unreachable, error_response, not_applicable),
+        'status_code' (int or None), 'healthy' (bool), and 'error' (str or None)
    """
    import subprocess

    try:
        result = subprocess.run(
-            ["curl", "-s", "-o", "/dev/null", "-w", "%{http_code}",
-             "--max-time", str(timeout), url],
+            [
+                "curl",
+                "-s",
+                "-o",
+                "/dev/null",
+                "-w",
+                "%{http_code}",
+                "--max-time",
+                str(timeout),
+                url,
+            ],
            capture_output=True,
            text=True,
            timeout=timeout + 5,
        )
        status_code = int(result.stdout.strip())
+
+        if 200 <= status_code < 400:
+            return {
+                "tunnel_status": "healthy",
+                "status_code": status_code,
+                "healthy": True,
+                "error": None,
+            }
+        elif status_code in (502, 503, 504):
+            # Application error, not tunnel error
+            return {
+                "tunnel_status": "error_response",
+                "status_code": status_code,
+                "healthy": False,
+                "error": f"Application returned HTTP {status_code}",
+            }
+        else:
+            return {
+                "tunnel_status": "error_response",
+                "status_code": status_code,
+                "healthy": False,
+                "error": f"HTTP {status_code}",
+            }
+    except subprocess.TimeoutExpired:
        return {
-            "healthy": 200 <= status_code < 400,
-            "status_code": status_code,
-        }
-    except (ValueError, subprocess.TimeoutExpired, Exception) as e:
-        return {
-            "healthy": False,
+            "tunnel_status": "unreachable",
            "status_code": None,
+            "healthy": False,
+            "error": "Tunnel request timed out",
+        }
+    except (ValueError, Exception) as e:
+        error_str = str(e).lower()
+        # Classify connection errors
+        if any(
+            err in error_str
+            for err in [
+                "connection refused",
+                "econnrefused",
+                "could not resolve",
+                "nodename",
+            ]
+        ):
+            return {
+                "tunnel_status": "unreachable",
+                "status_code": None,
+                "healthy": False,
+                "error": f"Tunnel unreachable: {e}",
+            }
+        return {
+            "tunnel_status": "unreachable",
+            "status_code": None,
+            "healthy": False,
            "error": str(e),
        }
@@ -18,13 +18,12 @@ def build_image(instance_dir: str, dockerfile: str, tag: str, build_context: dic
    Returns:
        Tuple of (returncode, stdout, stderr)
    """
-    import os
    from pathlib import Path

    # Write Dockerfile
    dockerfile_path = Path(instance_dir) / "Dockerfile"
    dockerfile_path.write_text(dockerfile)
-    logger.info("Wrote Dockerfile to %s", dockerfile_path)
+    logger.debug("Wrote Dockerfile to %s", dockerfile_path)

    # Write build context files
    if build_context:
@@ -39,10 +38,10 @@ def build_image(instance_dir: str, dockerfile: str, tag: str, build_context: dic
            
            full_path.parent.mkdir(parents=True, exist_ok=True)
            full_path.write_text(content)
-            logger.info("Wrote build context file: %s", full_path)
+            logger.debug("Wrote build context file: %s", full_path)

    # Build image
-    logger.info("Building Docker image with tag: %s", tag)
+    logger.debug("Building Docker image with tag: %s", tag)
    cmd = [
        "docker", "build",
        "-t", tag,
@@ -57,7 +56,7 @@ def build_image(instance_dir: str, dockerfile: str, tag: str, build_context: dic
            text=True,
            timeout=300,  # 5 minute timeout for builds
        )
-        logger.info("Docker build completed: returncode=%d", result.returncode)
+        logger.debug("Docker build completed: returncode=%d", result.returncode)
        if result.returncode != 0:
            logger.error("Docker build failed: %s", result.stderr[:1000])
        return result.returncode, result.stdout, result.stderr
@@ -0,0 +1,412 @@
+"""Manifest compiler: transforms ToolDefinitionManifest into Dockerfile + Compose."""
+
+import hashlib
+import json
+import shlex
+from copy import deepcopy
+from typing import Any
+
+import yaml
+
+
+def resolve_base(manifest: dict) -> dict:
+    """Merge a base definition into a tool manifest.
+
+    If the manifest has base_definition_id, the base manifest is loaded
+    and merged. Tool-specific values override base values.
+
+    Args:
+        manifest: The tool manifest JSON (may reference a base)
+
+    Returns:
+        A fully resolved manifest with base values merged in.
+    """
+    result = deepcopy(manifest)
+
+    base_definition_id = result.pop("base_definition_id", None)
+    base_version = result.pop("base_version", "latest")
+
+    if base_definition_id:
+        # This will be provided by the caller (they have the DB session)
+        # For now, we assume the manifest has been pre-resolved
+        # or the caller provides the base manifest separately.
+        pass
+
+    return result
+
+
+def deep_merge(base: dict, override: dict) -> dict:
+    """Deep merge two manifests. Arrays are concatenated; dicts are merged.
+
+    Args:
+        base: The base manifest.
+        override: The tool-specific overrides.
+
+    Returns:
+        Merged manifest.
+    """
+    merged = deepcopy(base)
+
+    for key, value in override.items():
+        if key == "mounts" and isinstance(value, list):
+            # Concatenate mount arrays
+            existing = merged.get("mounts", [])
+            merged["mounts"] = existing + deepcopy(value)
+        elif key == "scripts" and isinstance(value, dict):
+            # Merge script categories
+            if "scripts" not in merged:
+                merged["scripts"] = {}
+            for script_key, script_value in value.items():
+                existing = merged["scripts"].get(script_key, [])
+                merged["scripts"][script_key] = existing + deepcopy(script_value)
+        elif key == "packages" and isinstance(value, dict):
+            # Union package arrays
+            if "packages" not in merged:
+                merged["packages"] = {}
+            for pkg_key, pkg_value in value.items():
+                if (
+                    pkg_key in merged["packages"]
+                    and isinstance(merged["packages"][pkg_key], list)
+                    and isinstance(pkg_value, list)
+                ):
+                    merged["packages"][pkg_key] = merged["packages"][
+                        pkg_key
+                    ] + deepcopy(pkg_value)
+                else:
+                    merged["packages"][pkg_key] = deepcopy(pkg_value)
+        elif key == "env" and isinstance(value, dict):
+            # Dict merge: override wins on key conflict
+            if "env" not in merged:
+                merged["env"] = {}
+            merged["env"].update(deepcopy(value))
+        elif (
+            isinstance(value, dict) and key in merged and isinstance(merged[key], dict)
+        ):
+            # Generic dict merge
+            merged[key] = {**merged[key], **deepcopy(value)}
+        else:
+            # Override entirely
+            merged[key] = deepcopy(value)
+
+    return merged
+
+
+def compile_dockerfile(manifest: dict) -> str:
+    """Compile a resolved manifest into a Dockerfile string.
+
+    Args:
+        manifest: Fully resolved manifest JSON.
+
+    Returns:
+        Dockerfile content.
+    """
+    lines: list[str] = []
+
+    # FROM
+    base_image = manifest.get("base_image", "ubuntu:24.04")
+    lines.append(f"FROM {base_image}")
+    lines.append("")
+
+    # Build-time environment
+    env = manifest.get("env", {})
+    for key, value in env.items():
+        lines.append(f"ENV {key}={shlex.quote(value)}")
+    if env:
+        lines.append("")
+
+    # System packages (apt)
+    apt_packages = manifest.get("packages", {}).get("apt", [])
+    if apt_packages:
+        lines.append("RUN apt-get update && apt-get install -y \\\\")
+        for pkg in apt_packages[:-1]:
+            lines.append(f"    {pkg} \\\\")
+        lines.append(f"    {apt_packages[-1]} \\\\")
+        lines.append("    && rm -rf /var/lib/apt/lists/*")
+        lines.append("")
+
+    # Node.js
+    node = manifest.get("packages", {}).get("node")
+    if node:
+        version = node.get("version", "20")
+        lines.append(
+            f"RUN curl -fsSL https://deb.nodesource.com/setup_{version}.x | bash - && \\\\"
+        )
+        lines.append("    apt-get install -y nodejs && \\\\")
+        lines.append("    rm -rf /var/lib/apt/lists/*")
+        lines.append("")
+
+    # NPM global packages
+    npm_packages = manifest.get("packages", {}).get("npm_global", [])
+    if npm_packages:
+        pkg_list = " ".join(shlex.quote(p) for p in npm_packages)
+        lines.append(f"RUN npm install -g {pkg_list}")
+        lines.append("")
+
+    # Pip packages
+    pip_packages = manifest.get("packages", {}).get("pip", [])
+    if pip_packages:
+        pkg_list = " ".join(shlex.quote(p) for p in pip_packages)
+        lines.append(f"RUN pip install {pkg_list}")
+        lines.append("")
+
+    # User creation
+    user = manifest.get("user")
+    if user:
+        name = user["name"]
+        uid = user["uid"]
+        gid = user["gid"]
+        create_home = "-m " if user.get("create_home", True) else ""
+        shell = user.get("shell", "/bin/bash")
+        lines.append(f"RUN groupadd -g {gid} {name} && \\\\")
+        lines.append(f"    useradd -u {uid} -g {gid} {create_home}-s {shell} {name}")
+        lines.append("")
+
+    # Build scripts
+    build_scripts = manifest.get("scripts", {}).get("build", [])
+    for script in build_scripts:
+        # Normalize multi-line scripts into single RUN command
+        stripped_lines = [
+            line.strip() for line in script.strip().split("\n") if line.strip()
+        ]
+        if stripped_lines:
+            normalized = " && ".join(stripped_lines)
+            lines.append(f"RUN {normalized}")
+    if build_scripts:
+        lines.append("")
+
+    # Create mount target directories
+    mounts = manifest.get("mounts", [])
+    if mounts:
+        dirs = [mount["target"] for mount in mounts]
+        dir_str = " ".join(dirs)
+        lines.append(f"RUN mkdir -p {dir_str}")
+        if user:
+            lines.append(f"RUN chown -R {user['name']}:{user['name']} {dir_str}")
+        lines.append("")
+
+    # Entrypoint for startup scripts
+    startup_scripts = manifest.get("scripts", {}).get("startup", [])
+    if startup_scripts:
+        lines.append(
+            "COPY .headquarter/entrypoint.sh /usr/local/bin/headquarter-entrypoint"
+        )
+        lines.append("RUN chmod +x /usr/local/bin/headquarter-entrypoint")
+        lines.append("")
+
+    # Switch to runtime user
+    if user:
+        lines.append(f"USER {user['name']}")
+        lines.append(f"WORKDIR /home/{user['name']}")
+        lines.append("")
+
+    # Entrypoint and CMD
+    runtime = manifest.get("runtime", {})
+    if startup_scripts:
+        lines.append('ENTRYPOINT ["/usr/local/bin/headquarter-entrypoint"]')
+
+    command = runtime.get("command", ["/bin/bash"])
+    cmd_json = json.dumps(command)
+    lines.append(f"CMD {cmd_json}")
+
+    return "\n".join(lines)
+
+
+def compile_entrypoint(manifest: dict) -> str:
+    """Generate the startup entrypoint script from startup scripts.
+
+    Args:
+        manifest: Fully resolved manifest JSON.
+
+    Returns:
+        Shell script content.
+    """
+    lines = ["#!/bin/bash", "set -e", ""]
+
+    startup_scripts = manifest.get("scripts", {}).get("startup", [])
+    for script in startup_scripts:
+        lines.append(script)
+        lines.append("")
+
+    lines.append('exec "$@"')
+    return "\n".join(lines)
+
+
+def compile_compose(manifest: dict, variables: dict[str, Any]) -> str:
+    """Compile a resolved manifest into a Docker Compose string.
+
+    Args:
+        manifest: Fully resolved manifest JSON.
+        variables: Resolved values: IMAGE_TAG, INSTANCE_NAME, REPO_PATH, etc.
+
+    Returns:
+        Docker Compose YAML content.
+    """
+    runtime = manifest.get("runtime", {})
+    user = manifest.get("user")
+    interface_type = manifest["interface_type"]
+
+    service: dict[str, Any] = {
+        "image": variables["IMAGE_TAG"],
+        "container_name": variables["INSTANCE_NAME"],
+        "restart": "unless-stopped",
+    }
+
+    # Terminal-specific fields
+    if runtime.get("stdin_open", False):
+        service["stdin_open"] = True
+    if runtime.get("tty", False):
+        service["tty"] = True
+    if runtime.get("working_dir"):
+        service["working_dir"] = runtime["working_dir"]
+
+    # User override
+    if user:
+        service["user"] = f"{user['uid']}:{user['gid']}"
+
+    # Ports for web tools
+    default_port = manifest.get("default_port")
+    if interface_type == "web" and default_port:
+        service["ports"] = [f"{variables['TOOL_PORT']}:{default_port}"]
+
+    # Environment
+    env = manifest.get("env", {})
+    if env:
+        service["environment"] = dict(env)
+
+    # Merge extra env from config
+    extra_env = variables.get("EXTRA_ENV", {})
+    if extra_env:
+        if "environment" not in service:
+            service["environment"] = {}
+        service["environment"].update(extra_env)
+
+    # Volumes from mount schema
+    volumes = []
+    for mount in manifest.get("mounts", []):
+        source = resolve_mount_source(mount, variables)
+        if not source:
+            continue
+        target = mount["target"]
+        readonly = ":ro" if mount.get("readonly", False) else ""
+        volumes.append(f"{source}:{target}{readonly}")
+
+    # Append extra volumes from tool config / config profile
+    for vol in variables.get("EXTRA_VOLUMES", []):
+        vol_str = f"{vol['source']}:{vol['target']}"
+        if vol.get("readonly"):
+            vol_str += ":ro"
+        volumes.append(vol_str)
+
+    if volumes:
+        service["volumes"] = volumes
+
+    compose = {"services": {"app": service}}
+    return yaml.dump(compose, default_flow_style=False)
+
+
+def resolve_mount_source(mount: dict, variables: dict[str, Any]) -> str:
+    """Resolve a mount's source_type to an actual host path.
+
+    Args:
+        mount: Mount definition from manifest.
+        variables: Resolved variables dict.
+
+    Returns:
+        Host path string, or empty string if unresolved.
+    """
+    source_type = mount.get("source_type", "host_path")
+
+    if source_type == "repo":
+        return variables.get("REPO_PATH", "")
+    elif source_type == "ssh_key":
+        return variables.get("SSH_PATH", "")
+    elif source_type == "instance":
+        instance_dir = variables.get("INSTANCE_DIR", "")
+        mount_name = mount.get("name", "unknown")
+        return f"{instance_dir}/mounts/{mount_name}"
+    elif source_type == "git_mount":
+        ref = mount.get("git_mount_ref", "default")
+        return variables.get(f"GIT_MOUNT_{ref}", "")
+    elif source_type == "host_path":
+        return mount.get("source", "")
+
+    return ""
+
+
+def compute_image_tag(tool_name: str, manifest: dict) -> str:
+    """Compute a deterministic image tag from manifest content.
+
+    Args:
+        tool_name: Human-readable tool name.
+        manifest: Fully resolved manifest JSON.
+
+    Returns:
+        Docker image tag string.
+    """
+    # Canonicalize: sort keys, stable JSON
+    canonical = json.dumps(manifest, sort_keys=True, separators=(",", ":"))
+    hash_suffix = hashlib.sha256(canonical.encode()).hexdigest()[:8]
+    safe_name = tool_name.lower().replace(" ", "-").replace("_", "-")
+    return f"headquarter/{safe_name}-{hash_suffix}:latest"
+
+
+def merge_with_config(
+    manifest: dict, tool_configs: list[dict], profile: dict | None = None
+) -> dict:
+    """Merge ToolConfig and ConfigProfile overrides into a manifest.
+
+    Args:
+        manifest: Base manifest from tool definition.
+        tool_configs: List of ToolConfig records.
+        profile: Resolved ConfigProfile (optional).
+
+    Returns:
+        Manifest with overrides applied.
+    """
+    result = deepcopy(manifest)
+
+    # Apply ToolConfigs
+    extra_env: dict[str, str] = {}
+    extra_volumes: list[dict] = []
+
+    for config in tool_configs:
+        if config.get("config_type") == "env":
+            extra_env[config["key"]] = config["value"]
+        elif config.get("config_type") == "file" and config.get("file_path"):
+            # Files are handled outside the manifest (written to instance dir)
+            pass
+        if config.get("port_override"):
+            result["default_port"] = config["port_override"]
+        if config.get("start_command"):
+            result["runtime"] = result.get("runtime", {})
+            result["runtime"]["command"] = config["start_command"].split()
+        if config.get("working_directory"):
+            result["runtime"] = result.get("runtime", {})
+            result["runtime"]["working_dir"] = config["working_directory"]
+        if config.get("environment_variables"):
+            extra_env.update(config["environment_variables"])
+        if config.get("volumes"):
+            extra_volumes.extend(config["volumes"])
+
+    # Apply ConfigProfile
+    if profile:
+        if profile.get("environment_variables"):
+            extra_env.update(profile["environment_variables"])
+        if profile.get("mounts"):
+            extra_volumes.extend(profile["mounts"])
+        # Profile hints override everything
+        hints = profile.get("hints", {})
+        if hints.get("start_command"):
+            result["runtime"] = result.get("runtime", {})
+            result["runtime"]["command"] = hints["start_command"].split()
+        if hints.get("working_directory"):
+            result["runtime"] = result.get("runtime", {})
+            result["runtime"]["working_dir"] = hints["working_directory"]
+        if hints.get("port_override"):
+            result["default_port"] = hints["port_override"]
+
+    # Store merged extras for the compose compiler
+    result["_extra_env"] = extra_env
+    result["_extra_volumes"] = extra_volumes
+
+    return result
@@ -0,0 +1,164 @@
+"""Permission fixer: applies mount permission policies post-start."""
+
+import logging
+import subprocess
+from typing import Any
+
+logger = logging.getLogger(__name__)
+
+
+def apply_mount_permissions(
+    container_id: str,
+    mounts: list[dict],
+    timeout: int = 10,
+) -> list[dict[str, Any]]:
+    """Apply permission policies to mounted directories in a running container.
+
+    Runs `chown`, `chmod`, and file-mode fixes for each mount that declares
+    an owner, mode, or file_mode. Requires the container to have a root user.
+
+    Args:
+        container_id: Docker container ID or name.
+        mounts: List of mount definitions from the manifest.
+        timeout: Max seconds per docker exec command.
+
+    Returns:
+        List of result dicts: [{mount_name, success, error}]
+    """
+    results = []
+
+    for mount in mounts:
+        name = mount.get("name", "unknown")
+        target = mount["target"]
+        owner = mount.get("owner")
+        mode = mount.get("mode")
+        file_mode = mount.get("file_mode")
+
+        result: dict[str, Any] = {
+            "mount_name": name,
+            "success": True,
+            "error": None,
+        }
+
+        # Skip if no permission policy defined
+        if not owner and not mode and not file_mode:
+            results.append(result)
+            continue
+
+        try:
+            if owner:
+                _run_in_container(
+                    container_id,
+                    ["chown", "-R", f"{owner}:{owner}", target],
+                    timeout,
+                )
+                logger.debug(
+                    "Applied owner %s to %s in container %s",
+                    owner,
+                    target,
+                    container_id,
+                )
+
+            if mode and result["success"]:
+                _run_in_container(
+                    container_id,
+                    ["chmod", mode, target],
+                    timeout,
+                )
+                logger.debug(
+                    "Applied mode %s to %s in container %s",
+                    mode,
+                    target,
+                    container_id,
+                )
+
+            if file_mode and result["success"]:
+                _run_in_container(
+                    container_id,
+                    [
+                        "sh",
+                        "-c",
+                        f"find {target} -type f -exec chmod {file_mode} {{}} +",
+                    ],
+                    timeout,
+                )
+                logger.debug(
+                    "Applied file_mode %s to files in %s in container %s",
+                    file_mode,
+                    target,
+                    container_id,
+                )
+
+        except PermissionFixError as exc:
+            result["success"] = False
+            result["error"] = str(exc)
+            logger.warning(
+                "Permission fix failed for mount %s (target=%s): %s",
+                name,
+                target,
+                exc,
+            )
+
+        results.append(result)
+
+    return results
+
+
+class PermissionFixError(Exception):
+    """Raised when a permission fix command fails."""
+
+    pass
+
+
+def _run_in_container(
+    container_id: str,
+    command: list[str],
+    timeout: int,
+) -> None:
+    """Run a command inside a container as root.
+
+    Args:
+        container_id: Docker container ID or name.
+        command: Command + args to execute.
+        timeout: Max seconds to wait.
+
+    Raises:
+        PermissionFixError: If the command fails or times out.
+    """
+    cmd = ["docker", "exec", "--user", "root", container_id] + command
+
+    try:
+        result = subprocess.run(
+            cmd,
+            capture_output=True,
+            text=True,
+            timeout=timeout,
+        )
+    except subprocess.TimeoutExpired:
+        raise PermissionFixError(
+            f"Command timed out after {timeout}s: {' '.join(command)}"
+        )
+    except FileNotFoundError:
+        raise PermissionFixError(f"Docker command not found: {' '.join(command)}")
+
+    if result.returncode != 0:
+        raise PermissionFixError(
+            f"Command failed (rc={result.returncode}): {result.stderr.strip()}"
+        )
+
+
+def check_root_user_available(container_id: str, timeout: int = 5) -> bool:
+    """Check if the container has a root user we can exec as.
+
+    Args:
+        container_id: Docker container ID or name.
+        timeout: Max seconds to wait.
+
+    Returns:
+        True if root user exists and is usable.
+    """
+    try:
+        _run_in_container(container_id, ["id", "root"], timeout)
+        return True
+    except PermissionFixError:
+        return False
@@ -0,0 +1,73 @@
+"""SSH key service utilities for preparing keys for container use."""
+
+import os
+from pathlib import Path
+
+from cryptography.fernet import Fernet
+
+from src.config import Settings
+
+
+def _get_fernet() -> Fernet:
+    """Generate a valid Fernet key from the session secret."""
+    import base64
+    import hashlib
+
+    settings = Settings()
+    key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
+    key = base64.urlsafe_b64encode(key_bytes)
+    return Fernet(key)
+
+
+def prepare_ssh_key_files(instance_dir: str, ssh_key) -> str:
+    """Decrypt and write SSH key files to instance directory for container mounting.
+
+    Args:
+        instance_dir: Path to instance directory
+        ssh_key: SSHKey model instance with encrypted private key
+
+    Returns:
+        Path to the .ssh directory
+    """
+    ssh_dir = Path(instance_dir) / ".ssh"
+    ssh_dir.mkdir(parents=True, exist_ok=True)
+
+    # Decrypt private key
+    fernet = _get_fernet()
+    private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
+
+    # Write private key with restricted permissions
+    private_key_path = ssh_dir / "id_ed25519"
+    private_key_path.write_text(private_key)
+    os.chmod(private_key_path, 0o600)
+
+    # Write public key
+    public_key_path = ssh_dir / "id_ed25519.pub"
+    public_key_path.write_text(ssh_key.public_key)
+    os.chmod(public_key_path, 0o644)
+
+    # Write SSH config
+    config_path = ssh_dir / "config"
+    config_content = """Host *
+    StrictHostKeyChecking no
+    UserKnownHostsFile /dev/null
+    IdentityFile ~/.ssh/id_ed25519
+    IdentitiesOnly yes
+"""
+    config_path.write_text(config_content)
+    os.chmod(config_path, 0o644)
+
+    return str(ssh_dir)
+
+
+def cleanup_ssh_key_files(instance_dir: str) -> None:
+    """Remove temporary SSH key files from instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+    """
+    ssh_dir = Path(instance_dir) / ".ssh"
+    if ssh_dir.exists():
+        for file_path in ssh_dir.iterdir():
+            file_path.unlink()
+        ssh_dir.rmdir()
@@ -1,88 +1,150 @@
 """Terminal session manager for WebSocket connections."""

 import asyncio
+import logging
 import uuid
-from typing import Any

 from fastapi import WebSocket

 from src.services.terminal_session import TerminalSession

+logger = logging.getLogger(__name__)
+

 class TerminalManager:
-    """Manages active terminal sessions."""
+    """Manages active terminal sessions with persistence support."""

    def __init__(self) -> None:
+        # Track sessions by instance_id for persistence
        self._sessions: dict[str, TerminalSession] = {}
+        self._idle_check_task: asyncio.Task | None = None
+        self._start_idle_check()

-    async def create_session(
+    def _start_idle_check(self) -> None:
+        """Start the idle timeout background task."""
+        if self._idle_check_task is not None and not self._idle_check_task.done():
+            return
+        try:
+            loop = asyncio.get_running_loop()
+            self._idle_check_task = loop.create_task(self._idle_check_loop())
+        except RuntimeError:
+            # No event loop running yet, will be started lazily
+            pass
+
+    async def _idle_check_loop(self) -> None:
+        """Periodically check for idle sessions and clean them up."""
+        while True:
+            try:
+                await asyncio.sleep(60)  # Check every minute
+                await self._cleanup_idle_sessions()
+            except Exception as exc:
+                logger.error("Error in idle check loop: %s", exc)
+
+    async def _cleanup_idle_sessions(self) -> None:
+        """Clean up sessions that have been idle for too long."""
+        idle_sessions = []
+        for instance_id, session in list(self._sessions.items()):
+            if session.is_idle():
+                idle_sessions.append(instance_id)
+        
+        for instance_id in idle_sessions:
+            logger.info("Cleaning up idle terminal session for instance %s", instance_id)
+            session = self._sessions.pop(instance_id, None)
+            if session:
+                await session.close()
+
+    async def get_or_create_session(
        self,
        instance_id: uuid.UUID,
        container_id: str,
-        websocket: WebSocket,
+        startup_command: str | None = None,
    ) -> TerminalSession:
-        """Create a new terminal session."""
+        """Get existing session or create a new one."""
+        # Ensure idle check is running (lazy start)
+        self._start_idle_check()
+        
+        instance_id_str = str(instance_id)
+        
+        # Check for existing session
+        if instance_id_str in self._sessions:
+            session = self._sessions[instance_id_str]
+            
+            # Check if session is still alive
+            if session.is_alive():
+                logger.debug("Reattaching to existing terminal session for instance %s", instance_id)
+                return session
+            else:
+                # Session died, clean it up
+                logger.debug("Existing session for instance %s is dead, cleaning up", instance_id)
+                await session.close()
+                del self._sessions[instance_id_str]
+        
+        # Create new session
+        logger.info("Creating new terminal session for instance %s", instance_id)
        session_id = str(uuid.uuid4())
-        session = TerminalSession(session_id, instance_id, container_id)
-        await session.start()
-        self._sessions[session_id] = session
-
-        # Start background tasks for I/O streaming
-        asyncio.create_task(self._read_loop(session, websocket))
-        asyncio.create_task(self._write_loop(session, websocket))
-
+        session = TerminalSession(session_id, instance_id, container_id, startup_command=startup_command)
+        await session.start(startup_command=startup_command)
+        self._sessions[instance_id_str] = session
+        
        return session

-    async def _read_loop(self, session: TerminalSession, websocket: WebSocket) -> None:
-        """Read output from the container and send to WebSocket."""
-        try:
-            while session.is_alive() and not session._closed:
-                data = await session.read_output()
-                if data:
-                    await websocket.send_bytes(data)
-                else:
-                    await asyncio.sleep(0.01)
-        except Exception:
-            pass
-        finally:
-            await self._cleanup_session(session)
+    async def attach_websocket(
+        self,
+        session: TerminalSession,
+        websocket: WebSocket,
+    ) -> None:
+        """Attach a WebSocket to an existing session."""
+        # Handle concurrent connections - close existing ones
+        if session.has_websockets():
+            logger.debug("Closing existing WebSocket connections for instance %s", session.instance_id)
+            for ws in list(session._websockets):
+                try:
+                    await ws.close(code=4000, reason="New connection established")
+                except Exception:
+                    pass
+            session._websockets.clear()
+        
+        # Attach new WebSocket
+        session.attach_websocket(websocket)
+        
+        # Replay buffer
+        buffer = session.get_buffer()
+        if buffer:
+            try:
+                await websocket.send_bytes(buffer)
+            except Exception:
+                pass

-    async def _write_loop(self, session: TerminalSession, websocket: WebSocket) -> None:
-        """Read input from WebSocket and send to container."""
-        try:
-            while session.is_alive() and not session._closed:
-                message = await websocket.receive()
-                if message["type"] == "websocket.receive":
-                    if "bytes" in message:
-                        await session.write_input(message["bytes"])
-                    elif "text" in message:
-                        text = message["text"]
-                        if text.startswith("{"):
-                            # Control message (JSON)
-                            import json
-                            try:
-                                ctrl = json.loads(text)
-                                if ctrl.get("type") == "resize":
-                                    await session.resize(
-                                        ctrl.get("cols", 80),
-                                        ctrl.get("rows", 24),
-                                    )
-                            except json.JSONDecodeError:
-                                pass
-                        else:
-                            await session.write_input(text.encode("utf-8"))
-                elif message["type"] == "websocket.disconnect":
-                    break
-        except Exception:
-            pass
-        finally:
-            await self._cleanup_session(session)
+    async def detach_websocket(
+        self,
+        session: TerminalSession,
+        websocket: WebSocket,
+    ) -> None:
+        """Detach a WebSocket from a session."""
+        session.detach_websocket(websocket)

-    async def _cleanup_session(self, session: TerminalSession) -> None:
-        """Clean up a session."""
-        if session.session_id in self._sessions:
-            del self._sessions[session.session_id]
-        await session.close()
+    async def reset_session(
+        self,
+        instance_id: uuid.UUID,
+        container_id: str,
+        startup_command: str | None = None,
+    ) -> TerminalSession:
+        """Reset a session by killing it and creating a new one."""
+        instance_id_str = str(instance_id)
+        
+        # Close existing session if any
+        if instance_id_str in self._sessions:
+            logger.debug("Resetting terminal session for instance %s", instance_id)
+            old_session = self._sessions.pop(instance_id_str)
+            await old_session.close()
+        
+        # Create new session
+        session_id = str(uuid.uuid4())
+        session = TerminalSession(session_id, instance_id, container_id, startup_command=startup_command)
+        await session.start(startup_command=startup_command)
+        self._sessions[instance_id_str] = session
+        
+        return session

    async def close_all(self) -> None:
        """Close all active sessions."""
@@ -90,6 +152,9 @@ class TerminalManager:
        self._sessions.clear()
        for session in sessions:
            await session.close()
+        
+        if self._idle_check_task and not self._idle_check_task.done():
+            self._idle_check_task.cancel()


 # Global terminal manager instance
@@ -1,34 +1,73 @@
 """Terminal session management for tool instances."""

 import asyncio
+import logging
 import os
 import pty
 import select
+import signal
 import struct
 import fcntl
+import time
 import uuid
+from collections import deque
 from typing import Any

+logger = logging.getLogger(__name__)
+

 class TerminalSession:
-    """Manages a single terminal session connected to a docker container."""
+    """Manages a single terminal session connected to a docker container.
+    
+    Supports persistent sessions that survive WebSocket disconnections.
+    Multiple WebSocket connections can attach/detach from the same session.
+    """

-    def __init__(self, session_id: str, instance_id: uuid.UUID, container_id: str) -> None:
+    # Circular buffer size (10KB)
+    BUFFER_SIZE = 10 * 1024
+    
+    # Idle timeout in seconds (30 minutes)
+    IDLE_TIMEOUT = 30 * 60
+
+    def __init__(self, session_id: str, instance_id: uuid.UUID, container_id: str, startup_command: str | None = None) -> None:
        self.session_id = session_id
        self.instance_id = instance_id
        self.container_id = container_id
+        self.startup_command = startup_command
        self.process: asyncio.subprocess.Process | None = None
        self._closed = False
        self._master_fd: int | None = None
        self._slave_fd: int | None = None
+        
+        # Circular buffer for output replay
+        self._output_buffer: deque[bytes] = deque(maxlen=self.BUFFER_SIZE)
+        self._buffer_size = 0
+        
+        # WebSocket connections
+        self._websockets: set[Any] = set()
+        
+        # Activity tracking
+        self.last_activity = time.time()
+        
+        # Terminal size
+        self._cols = 80
+        self._rows = 24

-    async def start(self) -> None:
+    async def start(self, startup_command: str | None = None) -> None:
        """Start the docker exec process with a shell using a PTY."""
        # Create a pseudo-terminal on the host
        self._master_fd, self._slave_fd = pty.openpty()
        
        # Set the terminal size initially
-        self._set_terminal_size(80, 24)
+        self._set_terminal_size(self._cols, self._rows)
+        logger.debug(f"Starting terminal session {self.session_id} for container {self.container_id} with initial size {self._cols}x{self._rows}")
+        
+        # Build the shell command
+        if startup_command:
+            shell_cmd = f'bash -c "{startup_command}" || true; exec bash -il'
+            logger.debug(f"Using startup command for session {self.session_id}: {startup_command}")
+        else:
+            shell_cmd = "bash -il"
        
        # Start docker exec with the slave fd as stdin/stdout/stderr
        # Using -it because the slave fd IS a TTY
@@ -40,7 +79,8 @@ class TerminalSession:
            "TERM=xterm",
            self.container_id,
            "bash",
-            "-il",
+            "-c",
+            shell_cmd,
            stdin=self._slave_fd,
            stdout=self._slave_fd,
            stderr=self._slave_fd,
@@ -49,46 +89,103 @@ class TerminalSession:
        # Close slave fd in parent process
        os.close(self._slave_fd)
        self._slave_fd = None
+        
+        self.last_activity = time.time()

    def _set_terminal_size(self, cols: int, rows: int) -> None:
        """Set the terminal size using TIOCSWINSZ."""
        if self._master_fd is None:
+            logger.warning("Cannot resize: master_fd is None (session not started)")
            return
        # TIOCSWINSZ = 0x5414 on Linux
        TIOCSWINSZ = 0x5414
        size = struct.pack('HHHH', rows, cols, 0, 0)
        try:
            fcntl.ioctl(self._master_fd, TIOCSWINSZ, size)
-        except (OSError, IOError):
-            pass
+            logger.debug(f"Resized PTY to {cols}x{rows} (fd={self._master_fd})")
+        except (OSError, IOError) as e:
+            logger.error(f"Failed to resize PTY: {e}")

    async def read_output(self) -> bytes:
-        """Read output from the PTY master."""
+        """Read output from the PTY master and store in buffer."""
        if self._master_fd is None or self._closed:
            return b""
        try:
            # Use select to check if data is available
            readable, _, _ = select.select([self._master_fd], [], [], 0.1)
            if readable:
-                return os.read(self._master_fd, 4096)
+                data = os.read(self._master_fd, 4096)
+                if data:
+                    self._add_to_buffer(data)
+                    self.last_activity = time.time()
+                return data
            return b""
        except (OSError, IOError, ValueError):
            return b""

+    def _add_to_buffer(self, data: bytes) -> None:
+        """Add data to circular buffer, maintaining size limit."""
+        self._output_buffer.append(data)
+        self._buffer_size += len(data)
+        
+        # Trim if exceeds max size
+        while self._buffer_size > self.BUFFER_SIZE and self._output_buffer:
+            removed = self._output_buffer.popleft()
+            self._buffer_size -= len(removed)
+
+    def get_buffer(self) -> bytes:
+        """Get buffered output for replay."""
+        return b"".join(self._output_buffer)
+
    async def write_input(self, data: bytes) -> None:
        """Write input to the PTY master."""
        if self._master_fd is None or self._closed:
            return
        try:
            os.write(self._master_fd, data)
+            self.last_activity = time.time()
        except (OSError, IOError):
            pass

    async def resize(self, cols: int, rows: int) -> None:
        """Resize the terminal."""
        if self._closed:
+            logger.warning("Cannot resize: session is closed")
            return
+        
+        # Only resize if dimensions actually changed
+        if cols == self._cols and rows == self._rows:
+            return
+            
+        self._cols = cols
+        self._rows = rows
+        logger.debug(f"resize() called for session {self.session_id}: {cols}x{rows}")
        self._set_terminal_size(cols, rows)
+        
+        # Docker exec -it creates its own PTY inside the container,
+        # so host PTY resize doesn't propagate to the container shell.
+        # Send SIGWINCH to the docker exec process on the host.
+        # Docker exec forwards signals to the container process, which should
+        # cause the container's shell to re-read its terminal size.
+        if self.process and self.process.pid:
+            try:
+                os.kill(self.process.pid, signal.SIGWINCH)
+                logger.debug(f"Sent SIGWINCH to docker exec process {self.process.pid} for session {self.session_id}")
+            except ProcessLookupError:
+                logger.warning(f"docker exec process {self.process.pid} not found for session {self.session_id}")
+            except Exception as e:
+                logger.warning(f"Failed to send SIGWINCH: {e}")
+
+    async def reset(self) -> None:
+        """Reset the session by killing the process and clearing state."""
+        await self.close()
+        self._closed = False
+        self._output_buffer.clear()
+        self._buffer_size = 0
+        self._websockets.clear()
+        self.process = None
+        self._master_fd = None
+        self._slave_fd = None

    async def close(self) -> None:
        """Close the session and cleanup."""
@@ -115,3 +212,35 @@ class TerminalSession:
        if self.process is None:
            return False
        return self.process.returncode is None
+
+    def is_idle(self) -> bool:
+        """Check if the session has been idle for too long."""
+        if self._websockets:
+            return False
+        return time.time() - self.last_activity > self.IDLE_TIMEOUT
+
+    def attach_websocket(self, websocket: Any) -> None:
+        """Attach a WebSocket to this session."""
+        self._websockets.add(websocket)
+        self.last_activity = time.time()
+
+    def detach_websocket(self, websocket: Any) -> None:
+        """Detach a WebSocket from this session."""
+        self._websockets.discard(websocket)
+
+    def has_websockets(self) -> bool:
+        """Check if any WebSockets are attached."""
+        return len(self._websockets) > 0
+
+    async def send_to_all(self, data: bytes) -> None:
+        """Send data to all attached WebSockets."""
+        dead_sockets = set()
+        for ws in self._websockets:
+            try:
+                await ws.send_bytes(data)
+            except Exception:
+                dead_sockets.add(ws)
+        
+        # Clean up dead sockets
+        for ws in dead_sockets:
+            self._websockets.discard(ws)
@@ -2,7 +2,6 @@

 import subprocess
 from dataclasses import dataclass, field
-from typing import Any


 def _run_git_command(repo_path: str, *args: str) -> str:
@@ -124,7 +123,15 @@ def create_branch(repo_path: str, name: str, base_branch: str = "HEAD") -> None:
    try:
        _run_git_command(repo_path, "rev-parse", "--verify", "HEAD^{commit}")
    except RuntimeError:
-        _run_git_command(repo_path, "checkout", "--orphan", name)
+        # No commits yet - empty repository
+        try:
+            _run_git_command(repo_path, "checkout", "--orphan", name)
+        except RuntimeError as e:
+            if "work tree" in str(e).lower():
+                # Bare repository - use symbolic-ref instead
+                _run_git_command(repo_path, "symbolic-ref", "HEAD", f"refs/heads/{name}")
+                return
+            raise
        return

    _run_git_command(repo_path, "branch", name, base_branch)
@@ -155,7 +162,14 @@ def checkout_branch(repo_path: str, name: str) -> None:
    Raises:
        RuntimeError: If checkout fails
    """
-    _run_git_command(repo_path, "checkout", name)
+    try:
+        _run_git_command(repo_path, "checkout", name)
+    except RuntimeError as e:
+        if "work tree" in str(e).lower():
+            # Bare repository - use symbolic-ref instead
+            _run_git_command(repo_path, "symbolic-ref", "HEAD", f"refs/heads/{name}")
+            return
+        raise


 def commit_changes(
@@ -290,6 +304,10 @@ def get_current_branch(repo_path: str) -> str:
        Current branch name
    """
    try:
-        return _run_git_command(repo_path, "rev-parse", "--abbrev-ref", "HEAD").strip()
+        branch = _run_git_command(repo_path, "rev-parse", "--abbrev-ref", "HEAD").strip()
+        if branch != "HEAD":
+            return branch
    except RuntimeError:
-        return _run_git_command(repo_path, "symbolic-ref", "--short", "HEAD").strip()
+        pass
+
+    return _run_git_command(repo_path, "symbolic-ref", "--short", "HEAD").strip()
@@ -289,19 +289,37 @@ def list_branches(repo_path: str) -> tuple[list[BranchInfo], str]:
    branches: list[BranchInfo] = []
    default_branch = "main"

+    # Get list of remote names to properly filter remote tracking branches
+    try:
+        remote_output = _run_git_command(repo_path, "remote")
+        remote_names = {r.strip() for r in remote_output.strip().split("\n") if r.strip()}
+    except RuntimeError:
+        remote_names = set()
+
    for line in output.strip().split("\n"):
        if not line:
            continue

        branch_name = line.strip()
-        # Skip remote tracking branches (they start with remotes/)
-        if branch_name.startswith("remotes/"):
-            # Extract just the branch name part
-            parts = branch_name.split("/", 2)
-            if len(parts) >= 3:
-                branch_name = parts[2]
-            else:
-                continue
+        
+        # Skip detached HEAD pointer
+        if branch_name == "HEAD":
+            continue
+            
+        # Skip remote tracking branches - they appear as "origin/branch-name"
+        # Check if first part is a remote name
+        if "/" in branch_name:
+            first_part = branch_name.split("/", 1)[0]
+            if first_part in remote_names:
+                # Extract just the branch name part (after "origin/")
+                branch_name = branch_name.split("/", 1)[1]
+            elif branch_name.startswith("remotes/"):
+                # Handle "remotes/origin/branch-name" format
+                parts = branch_name.split("/", 2)
+                if len(parts) >= 3:
+                    branch_name = parts[2]
+                else:
+                    continue

        # Skip duplicates
        if any(b.name == branch_name for b in branches):
@@ -8,16 +8,14 @@ from unittest.mock import patch
 import pytest
 import pytest_asyncio
 from fastapi.testclient import TestClient
-from sqlalchemy import create_engine, text
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
-from sqlalchemy.orm import sessionmaker

 # Set test environment BEFORE importing app modules
 os.environ["APP_ENV"] = "testing"
 os.environ["SECRET_KEY"] = "test-secret-key-for-testing-only-do-not-use-in-production"
 os.environ["DATABASE_URL"] = "sqlite+aiosqlite:///:memory:"

-from src.config import Settings, build_database_url
+from src.config import Settings
 from src.models.base import Base
 from src.main import app
 from src.auth.dependencies import get_db_session
@@ -47,10 +45,8 @@ def test_client() -> Generator[TestClient, None, None]:
    app.dependency_overrides[get_db_session] = override_get_db_session
    
    # Patch startup events to prevent PostgreSQL connection attempts
-    with patch("src.main.init_database") as mock_init, \
-         patch("src.main.seed_builtin_tool_types") as mock_seed:
+    with patch("src.main.init_database") as mock_init:
        mock_init.return_value = True
-        mock_seed.return_value = None
        
        try:
            with TestClient(app) as client:
@@ -61,6 +57,31 @@ def test_client() -> Generator[TestClient, None, None]:
            asyncio.run(engine.dispose())


+@pytest_asyncio.fixture
+async def db_session(test_client) -> AsyncGenerator[AsyncSession, None]:
+    """Provide an async database session for unit tests."""
+    # Get the override function from the test_client fixture
+    override_fn = app.dependency_overrides.get(get_db_session)
+    if override_fn:
+        gen = override_fn()
+        session = await gen.asend(None)
+        try:
+            yield session
+        finally:
+            await gen.aclose()
+    else:
+        # Fallback: create a new engine and session
+        engine = create_async_engine(
+            "sqlite+aiosqlite:///:memory:",
+            connect_args={"check_same_thread": False},
+        )
+        async with engine.begin() as conn:
+            await conn.run_sync(Base.metadata.create_all)
+        async with async_sessionmaker(engine, expire_on_commit=False)() as session:
+            yield session
+        await engine.dispose()
+
+
@pytest.fixture
 def authenticated_client(test_client) -> Generator[TestClient, None, None]:
    """Provide an authenticated test client with a test user."""
@@ -110,6 +131,65 @@ def authenticated_client(test_client) -> Generator[TestClient, None, None]:
    yield test_client


+@pytest.fixture
+def test_project_and_repo(authenticated_client) -> tuple[str, str]:
+    """Create a project and repository directly in the database."""
+    import uuid
+    from src.models.project import Project
+    from src.models.git_repository import GitRepository
+    
+    project_id = uuid.uuid4()
+    repo_id = uuid.uuid4()
+    user_id = None
+    
+    # Get user ID from session
+    async def get_user_id():
+        nonlocal user_id
+        from src.auth.session import decode_session_cookie
+        settings = Settings()
+        session_cookie = authenticated_client.cookies.get("session")
+        if session_cookie:
+            session = decode_session_cookie(settings=settings, cookie_value=session_cookie)
+            if session:
+                user_id = uuid.UUID(session["user_id"])
+    
+    asyncio.run(get_user_id())
+    
+    if not user_id:
+        raise RuntimeError("Could not get user ID from authenticated client")
+    
+    async def create_project_and_repo():
+        override_fn = app.dependency_overrides.get(get_db_session)
+        if override_fn:
+            gen = override_fn()
+            session = await gen.asend(None)
+            try:
+                project = Project(
+                    id=project_id,
+                    name="test-project",
+                    description="Test project",
+                    owner_id=user_id,
+                )
+                session.add(project)
+                
+                repo = GitRepository(
+                    id=repo_id,
+                    name="test-repo",
+                    path="/tmp/test-repo",
+                    project_id=project_id,
+                    owner_id=user_id,
+                    remote_url="https://github.com/test/repo.git",
+                )
+                session.add(repo)
+                await session.commit()
+            finally:
+                await gen.aclose()
+    
+    asyncio.run(create_project_and_repo())
+    
+    return str(project_id), str(repo_id)
+
+
@pytest.fixture
 def admin_client(test_client) -> Generator[TestClient, None, None]:
    """Provide an authenticated test client with an admin user."""
@@ -0,0 +1,453 @@
+import uuid
+import pytest
+from fastapi.testclient import TestClient
+
+
+@pytest.mark.integration
+class TestConfigProfilesAPI:
+    """Integration tests for config profiles API."""
+
+    def test_list_config_profiles_requires_authentication(self, test_client: TestClient) -> None:
+        """Test that listing config profiles requires authentication."""
+        response = test_client.get("/config-profiles")
+        assert response.status_code == 401
+
+    def test_list_config_profiles_returns_user_profiles(self, authenticated_client: TestClient) -> None:
+        """Test that authenticated users can list their profiles."""
+        response = authenticated_client.get("/config-profiles")
+        assert response.status_code == 200
+        data = response.json()
+        assert isinstance(data, list)
+
+    def test_create_config_profile_successfully(self, authenticated_client: TestClient) -> None:
+        """Test creating a config profile."""
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "test-profile",
+                "description": "Test profile",
+                "env_vars": {"VAR": "value"},
+                "runtime_hints": {"start_command": "npm start"},
+                "mounts": [{"target": "/app", "mode": "rw", "files": {}}],
+                "files": {"test.txt": "hello"},
+            },
+        )
+        assert response.status_code == 201
+        data = response.json()
+        assert data["name"] == "test-profile"
+        assert data["env_vars"] == {"VAR": "value"}
+        assert data["files"] == {"test.txt": "hello"}
+        assert data["mounts"][0]["target"] == "/app"
+
+    def test_create_config_profile_duplicate_name(self, authenticated_client: TestClient) -> None:
+        """Test that duplicate profile names are rejected."""
+        # Create first profile
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "duplicate-profile",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        assert response.status_code == 201
+
+        # Try to create second with same name
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "duplicate-profile",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        assert response.status_code == 409
+
+    def test_create_config_profile_exceeds_size_limit(self, authenticated_client: TestClient) -> None:
+        """Test that profiles exceeding 10MB are rejected."""
+        large_content = "x" * (11 * 1024 * 1024)  # 11MB
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "large-profile",
+                "env_vars": {},
+                "files": {"large.txt": large_content},
+            },
+        )
+        assert response.status_code == 413
+
+    def test_create_config_profile_invalid_file_path(self, authenticated_client: TestClient) -> None:
+        """Test that invalid file paths are rejected."""
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "bad-profile",
+                "env_vars": {},
+                "files": {"../../../etc/passwd": "malicious"},
+            },
+        )
+        assert response.status_code == 422
+
+    def test_create_config_profile_invalid_mount_target(self, authenticated_client: TestClient) -> None:
+        """Test that invalid mount targets are rejected."""
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "bad-mount-profile",
+                "env_vars": {},
+                "files": {},
+                "mounts": [{"target": "relative/path", "mode": "rw", "files": {}}],
+            },
+        )
+        assert response.status_code == 422
+
+    def test_get_config_profile_by_id(self, authenticated_client: TestClient) -> None:
+        """Test getting a config profile by ID."""
+        # Create profile first
+        create_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "get-test",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        profile_id = create_response.json()["id"]
+
+        # Get it back
+        response = authenticated_client.get(f"/config-profiles/{profile_id}")
+        assert response.status_code == 200
+        data = response.json()
+        assert data["name"] == "get-test"
+
+    def test_get_config_profile_not_found(self, authenticated_client: TestClient) -> None:
+        """Test getting a non-existent profile."""
+        response = authenticated_client.get(f"/config-profiles/{uuid.uuid4()}")
+        assert response.status_code == 404
+
+    def test_update_config_profile_successfully(self, authenticated_client: TestClient) -> None:
+        """Test updating a config profile."""
+        # Create profile first
+        create_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "update-test",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        profile_id = create_response.json()["id"]
+
+        # Update it
+        response = authenticated_client.put(
+            f"/config-profiles/{profile_id}",
+            json={
+                "name": "updated-name",
+                "env_vars": {"NEW_VAR": "new_value"},
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["name"] == "updated-name"
+        assert data["env_vars"] == {"NEW_VAR": "new_value"}
+
+    def test_delete_config_profile_successfully(self, authenticated_client: TestClient) -> None:
+        """Test deleting a config profile."""
+        # Create profile first
+        create_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "delete-test",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        profile_id = create_response.json()["id"]
+
+        # Delete it
+        response = authenticated_client.delete(f"/config-profiles/{profile_id}")
+        assert response.status_code == 204
+
+        # Verify it's gone
+        get_response = authenticated_client.get(f"/config-profiles/{profile_id}")
+        assert get_response.status_code == 404
+
+    def test_update_profile_includes_successfully(self, authenticated_client: TestClient) -> None:
+        """Test updating profile includes."""
+        # Create base profile
+        base_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "base-profile",
+                "env_vars": {"BASE_VAR": "base_value"},
+                "files": {},
+            },
+        )
+        base_id = base_response.json()["id"]
+
+        # Create child profile
+        child_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "child-profile",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        child_id = child_response.json()["id"]
+
+        # Update includes
+        response = authenticated_client.put(
+            f"/config-profiles/{child_id}/includes",
+            json={"includes": [base_id]},
+        )
+        assert response.status_code == 200
+        data = response.json()
+        print(f"Response data: {data}")
+        print(f"Includes: {data.get('includes', 'NO INCLUDES KEY')}")
+        assert len(data["includes"]) == 1, f"Expected 1 include, got {len(data.get('includes', []))}: {data.get('includes', [])}"
+        assert data["includes"][0]["included_profile_id"] == base_id
+
+    def test_update_profile_includes_cycle_detection(self, authenticated_client: TestClient) -> None:
+        """Test that include cycles are detected."""
+        # Create profile A
+        a_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "profile-a",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        a_id = a_response.json()["id"]
+
+        # Create profile B
+        b_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "profile-b",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        b_id = b_response.json()["id"]
+
+        # Make B include A
+        authenticated_client.put(
+            f"/config-profiles/{b_id}/includes",
+            json={"includes": [a_id]},
+        )
+
+        # Try to make A include B (would create cycle)
+        response = authenticated_client.put(
+            f"/config-profiles/{a_id}/includes",
+            json={"includes": [b_id]},
+        )
+        assert response.status_code == 400
+
+    def test_preview_config_profile_successfully(self, authenticated_client: TestClient) -> None:
+        """Test previewing a resolved config profile."""
+        # Create base profile
+        base_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "preview-base",
+                "env_vars": {"BASE_VAR": "base"},
+                "files": {},
+            },
+        )
+        base_id = base_response.json()["id"]
+
+        # Create child profile
+        child_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "preview-child",
+                "env_vars": {"CHILD_VAR": "child"},
+                "files": {},
+            },
+        )
+        child_id = child_response.json()["id"]
+
+        # Make child include base
+        authenticated_client.put(
+            f"/config-profiles/{child_id}/includes",
+            json={"includes": [base_id]},
+        )
+
+        # Preview child
+        response = authenticated_client.get(f"/config-profiles/{child_id}/preview")
+        assert response.status_code == 200
+        data = response.json()
+        assert data["profile_name"] == "preview-child"
+        assert data["env_vars"]["BASE_VAR"] == "base"
+        assert data["env_vars"]["CHILD_VAR"] == "child"
+        assert len(data["included_profiles"]) == 1
+
+    def test_resolve_default_profile(self, authenticated_client: TestClient) -> None:
+        """Test resolving default profile for project/tool."""
+        # Create a global default profile (no project/tool scoping)
+        authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "default-profile",
+                "env_vars": {},
+                "files": {},
+                "is_default": True,
+            },
+        )
+
+        # Resolve default with random project/tool (should fall back to global)
+        project_id = str(uuid.uuid4())
+        tool_type_id = str(uuid.uuid4())
+        response = authenticated_client.get(
+            "/config-profiles/defaults/resolve",
+            params={"project_id": project_id, "tool_type_id": tool_type_id},
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["profile_name"] == "default-profile"
+
+    def test_resolve_default_profile_no_match(self, authenticated_client: TestClient) -> None:
+        """Test resolving default profile when no profiles exist."""
+        project_id = str(uuid.uuid4())
+        tool_type_id = str(uuid.uuid4())
+
+        response = authenticated_client.get(
+            "/config-profiles/defaults/resolve",
+            params={"project_id": project_id, "tool_type_id": tool_type_id},
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["profile_id"] is None
+
+    def test_create_config_profile_with_git_mounts(self, authenticated_client: TestClient, test_project_and_repo) -> None:
+        """Test creating a config profile with git mounts."""
+        _project_id, repo_id = test_project_and_repo
+
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "git-mount-profile",
+                "env_vars": {},
+                "files": {},
+                "git_mounts": [
+                    {
+                        "remote_url": "https://github.com/user/repo.git",
+                        "source_path": ".",
+                        "target_path": "/app",
+                        "branch": "main",
+                    }
+                ],
+            },
+        )
+        assert response.status_code == 201
+        data = response.json()
+        assert data["name"] == "git-mount-profile"
+        assert len(data["git_mounts"]) == 1
+        assert data["git_mounts"][0]["target_path"] == "/app"
+        assert data["git_mounts"][0]["branch"] == "main"
+
+    def test_update_config_profile_git_mounts(self, authenticated_client: TestClient, test_project_and_repo) -> None:
+        """Test updating git mounts on a config profile."""
+        _project_id, repo_id = test_project_and_repo
+
+        # Create profile first
+        create_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "update-git-mounts",
+                "env_vars": {},
+                "files": {},
+            },
+        )
+        profile_id = create_response.json()["id"]
+
+        # Update with git mounts
+        response = authenticated_client.put(
+            f"/config-profiles/{profile_id}",
+            json={
+                "git_mounts": [
+                    {
+                        "remote_url": "https://github.com/user/repo.git",
+                        "source_path": "config",
+                        "target_path": "/config",
+                    }
+                ],
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert len(data["git_mounts"]) == 1
+        assert data["git_mounts"][0]["source_path"] == "config"
+
+    def test_create_config_profile_invalid_git_mount_source_path(self, authenticated_client: TestClient, test_project_and_repo) -> None:
+        """Test that invalid git mount source paths are rejected."""
+        _project_id, repo_id = test_project_and_repo
+
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "bad-git-mount",
+                "env_vars": {},
+                "files": {},
+                "git_mounts": [
+                    {
+                        "remote_url": "https://github.com/user/repo.git",
+                        "source_path": "/absolute/path",
+                        "target_path": "/app",
+                    }
+                ],
+            },
+        )
+        assert response.status_code == 422
+
+    def test_create_config_profile_invalid_git_mount_target_path_traversal(self, authenticated_client: TestClient, test_project_and_repo) -> None:
+        """Test that git mount target paths with traversal are rejected."""
+        _project_id, repo_id = test_project_and_repo
+
+        response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "bad-git-mount-target",
+                "env_vars": {},
+                "files": {},
+                "git_mounts": [
+                    {
+                        "remote_url": "https://github.com/user/repo.git",
+                        "source_path": ".",
+                        "target_path": "../../../etc/passwd",
+                    }
+                ],
+            },
+        )
+        assert response.status_code == 422
+
+    def test_preview_config_profile_with_git_mounts(self, authenticated_client: TestClient, test_project_and_repo) -> None:
+        """Test previewing a profile with git mounts."""
+        _project_id, repo_id = test_project_and_repo
+
+        # Create profile with git mounts
+        create_response = authenticated_client.post(
+            "/config-profiles",
+            json={
+                "name": "preview-git-mounts",
+                "env_vars": {},
+                "files": {},
+                "git_mounts": [
+                    {
+                        "remote_url": "https://github.com/user/repo.git",
+                        "source_path": ".",
+                        "target_path": "/app",
+                    }
+                ],
+            },
+        )
+        profile_id = create_response.json()["id"]
+
+        # Preview
+        response = authenticated_client.get(f"/config-profiles/{profile_id}/preview")
+        assert response.status_code == 200
+        data = response.json()
+        assert len(data["git_mounts"]) == 1
+        assert data["git_mounts"][0]["remote_url"] == "https://github.com/user/repo.git"
@@ -70,6 +70,20 @@ def test_get_current_branch_handles_unborn_main() -> None:
        assert get_current_branch(tmpdir) == "main"


+def test_create_branch_on_bare_repo_with_no_commits() -> None:
+    with tempfile.TemporaryDirectory() as tmpdir:
+        os.system(f"git init --bare {tmpdir}/bare.git >/dev/null 2>&1")
+        create_branch(f"{tmpdir}/bare.git", "main")
+        assert get_current_branch(f"{tmpdir}/bare.git") == "main"
+
+
+def test_checkout_branch_on_bare_repo_with_no_commits() -> None:
+    with tempfile.TemporaryDirectory() as tmpdir:
+        os.system(f"git init --bare {tmpdir}/bare.git >/dev/null 2>&1")
+        checkout_branch(f"{tmpdir}/bare.git", "main")
+        assert get_current_branch(f"{tmpdir}/bare.git") == "main"
+
+
 class TestBranchOperations:
    """Tests for branch management functions."""

@@ -82,28 +82,6 @@ def test_repository_and_user_config_relationships_are_registered() -> None:
    assert UserConfig.user.property.mapper.class_ is User


-@pytest.mark.integration
-
-def test_refresh_token_table_has_required_columns_and_relationships() -> None:
-    columns = RefreshToken.__table__.columns
-    user_fk = next(iter(RefreshToken.__table__.c.user_id.foreign_keys))
-
-    assert set(columns.keys()) == {
-        "id",
-        "user_id",
-        "token_hash",
-        "expires_at",
-        "revoked_at",
-        "user_agent",
-        "ip_address",
-        "created_at",
-    }
-    assert columns["token_hash"].unique is True
-    assert columns["revoked_at"].nullable is True
-    assert user_fk.target_fullname == "users.id"
-    assert RefreshToken.user.property.mapper.class_ is User
-
-
@pytest.mark.asyncio
@pytest.mark.integration

@@ -3,6 +3,7 @@ from datetime import UTC, datetime, timedelta
 import asyncio

 import pytest
+from fastapi.testclient import TestClient
 from sqlalchemy import text
 from sqlalchemy.ext.asyncio import create_async_engine, async_sessionmaker

@@ -1,4 +1,3 @@
-import uuid
 import pytest
 from fastapi.testclient import TestClient

@@ -98,7 +98,6 @@ def _insert_tool_type(
    name: str,
    display_name: str,
    compose_template: str,
-    is_builtin: bool = False,
    created_by_id: str | None = None,
 ) -> None:
    async def _run() -> None:
@@ -120,7 +119,6 @@ def _insert_tool_type(
                description="A test tool type",
                compose_template=compose_template,
                required_variables=["REPO_PATH", "TOOL_NAME"],
-                is_builtin=is_builtin,
                created_by_id=uuid.UUID(created_by_id) if created_by_id else None,
            )
            await session.merge(tool_type)
@@ -234,7 +232,6 @@ def test_create_tool_type_successfully() -> None:
    assert data["name"] == "my-custom-tool"
    assert data["display_name"] == "My Custom Tool"
    assert data["description"] == "A custom development tool"
-    assert data["is_builtin"] == False
    assert data["created_by_id"] == user_id
    assert "id" in data

@@ -376,28 +373,7 @@ def test_update_tool_type_not_found() -> None:
    assert response.status_code == 404


-@pytest.mark.integration
-def test_update_builtin_tool_type_fails() -> None:
-    _prepare_test_db()
-    user_id = "11111111-1111-1111-1111-111111111111"
-    tool_type_id = "aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa"
-    _insert_user(user_id)
-    _insert_tool_type(
-        tool_type_id,
-        "builtin-tool",
-        "Built-in Tool",
-        "version: '3.8'\nservices:\n  app:\n    image: builtin",
-        is_builtin=True,
-    )
-    
-    app = _load_app()
-    client = TestClient(app)
-    client.cookies.set("access_token", _mint_token(user_id))

-    payload = {"display_name": "Updated"}
-    response = client.put(f"/tool-types/{tool_type_id}", json=payload)
-    
-    assert response.status_code == 403


@pytest.mark.integration
@@ -442,53 +418,4 @@ def test_delete_tool_type_not_found() -> None:
    assert response.status_code == 404


-@pytest.mark.integration
-def test_delete_builtin_tool_type_fails() -> None:
-    _prepare_test_db()
-    user_id = "11111111-1111-1111-1111-111111111111"
-    tool_type_id = "aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa"
-    _insert_user(user_id)
-    _insert_tool_type(
-        tool_type_id,
-        "builtin-tool",
-        "Built-in Tool",
-        "version: '3.8'\nservices:\n  app:\n    image: builtin",
-        is_builtin=True,
-    )
-    
-    app = _load_app()
-    client = TestClient(app)
-    client.cookies.set("access_token", _mint_token(user_id))

-    response = client.delete(f"/tool-types/{tool_type_id}")
-    
-    assert response.status_code == 403
-
-
-@pytest.mark.integration
-def test_builtin_tool_types_seeded_on_startup() -> None:
-    _prepare_test_db()
-    user_id = "11111111-1111-1111-1111-111111111111"
-    _insert_user(user_id)
-    
-    # Load app triggers startup event which seeds built-in types
-    app = _load_app()
-    client = TestClient(app)
-    client.cookies.set("access_token", _mint_token(user_id))
-
-    response = client.get("/tool-types")
-    
-    assert response.status_code == 200
-    data = response.json()
-    
-    # Check that built-in types exist
-    builtin_names = [t["name"] for t in data if t["is_builtin"]]
-    assert "code-server" in builtin_names
-    assert "jupyter-notebook" in builtin_names
-    
-    # Verify built-in types have correct attributes
-    code_server = next((t for t in data if t["name"] == "code-server"), None)
-    assert code_server is not None
-    assert code_server["display_name"] == "VS Code Server"
-    assert "services" in code_server["compose_template"]
-    assert code_server["required_variables"] == ["REPO_PATH", "TOOL_NAME"]
@@ -1,4 +1,3 @@
-import uuid
 import pytest
 from fastapi.testclient import TestClient

@@ -39,7 +38,7 @@ class TestToolTypesAPIExtended:
                "interfaces": ["web"],
                "default_port": 8080,
                "definition_type": "compose",
-                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx\n    ports:\n      - '8080:8080'",
                "readiness_probe": {
                    "command": "curl -f http://localhost:8080",
                    "timeout": 30,
@@ -92,7 +91,7 @@ class TestToolTypesAPIExtended:
                "display_name": "Update Test Tool",
                "default_port": 8080,
                "definition_type": "compose",
-                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx\n    ports:\n      - '8080:8080'",
                "required_variables": [],
            },
        )
@@ -167,7 +166,7 @@ class TestToolTypesAPIExtended:
                "interfaces": ["web", "terminal"],
                "default_port": 8443,
                "definition_type": "compose",
-                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: code-server\n    volumes:\n      - \"{{REPO_PATH}}:/workspace\"",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: code-server\n    ports:\n      - '8443:8443'\n    volumes:\n      - \"{{REPO_PATH}}:/workspace\"",
                "readiness_probe": {
                    "command": "curl -f http://localhost:8443",
                    "timeout": 30,
@@ -186,3 +185,114 @@ class TestToolTypesAPIExtended:
        assert data["category"] == "editor"
        assert data["interfaces"] == ["web", "terminal"]
        assert "readiness_probe" in data
+
+    def test_create_tool_type_without_port_fails(self, authenticated_client: TestClient) -> None:
+        """Test that creating a tool type without default_port fails validation."""
+        response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "no-port-tool",
+                "display_name": "No Port Tool",
+                "category": "utility",
+                "interfaces": ["web"],
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx\n    ports:\n      - '8080:8080'",
+                "required_variables": [],
+            },
+        )
+        assert response.status_code == 422
+        data = response.json()
+        assert "default_port" in str(data)
+
+    def test_create_tool_type_with_port_mismatch_fails(self, authenticated_client: TestClient) -> None:
+        """Test that port mismatch between default_port and compose template fails."""
+        response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "port-mismatch-tool",
+                "display_name": "Port Mismatch Tool",
+                "category": "utility",
+                "interfaces": ["web"],
+                "default_port": 9999,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: nginx\n    ports:\n      - '8080:8080'",
+                "required_variables": [],
+            },
+        )
+        assert response.status_code == 422
+        _ = response.json()
+
+    def test_create_tool_type_with_startup_command(self, authenticated_client: TestClient) -> None:
+        """Test creating a tool type with startup_command."""
+        response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "startup-tool",
+                "display_name": "Startup Tool",
+                "category": "utility",
+                "interface_type": "terminal",
+                "requires_port": False,
+                "default_port": 0,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: alpine",
+                "startup_command": "cd /workspace && ls",
+                "required_variables": [],
+            },
+        )
+        assert response.status_code == 201
+        data = response.json()
+        assert data["startup_command"] == "cd /workspace && ls"
+        assert data["interface_type"] == "terminal"
+
+    def test_update_tool_type_startup_command(self, authenticated_client: TestClient) -> None:
+        """Test updating a tool type's startup_command."""
+        # Create tool type first
+        create_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "update-startup-tool",
+                "display_name": "Update Startup Tool",
+                "interface_type": "terminal",
+                "requires_port": False,
+                "default_port": 0,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: alpine",
+                "required_variables": [],
+            },
+        )
+        tool_id = create_response.json()["id"]
+
+        # Update with startup_command
+        response = authenticated_client.put(
+            f"/tool-types/{tool_id}",
+            json={
+                "startup_command": "source /etc/profile",
+            },
+        )
+        assert response.status_code == 200
+        data = response.json()
+        assert data["startup_command"] == "source /etc/profile"
+
+    def test_get_tool_type_returns_startup_command(self, authenticated_client: TestClient) -> None:
+        """Test that GET returns startup_command."""
+        create_response = authenticated_client.post(
+            "/tool-types",
+            json={
+                "name": "get-startup-tool",
+                "display_name": "Get Startup Tool",
+                "interface_type": "terminal",
+                "requires_port": False,
+                "default_port": 0,
+                "definition_type": "compose",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: alpine",
+                "startup_command": "echo hello",
+                "required_variables": [],
+            },
+        )
+        tool_id = create_response.json()["id"]
+
+        response = authenticated_client.get(f"/tool-types/{tool_id}")
+        assert response.status_code == 200
+        data = response.json()
+        assert data["startup_command"] == "echo hello"
+        assert "Port 9999 is not exposed" in str(data)
@@ -0,0 +1,485 @@
+import uuid
+import pytest
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.services.config_profile_resolver import (
+    ConfigProfileCycleError,
+    ConfigProfileNotFoundError,
+    check_include_cycle,
+    resolve_profile,
+    _merge_env_vars,
+    _merge_files,
+    _merge_mounts,
+    _merge_runtime_hints,
+    _merge_git_mounts,
+)
+
+
+class TestMergeFunctions:
+    """Unit tests for merge helper functions."""
+
+    def test_merge_env_vars_basic(self) -> None:
+        """Test basic env var merging."""
+        result = _merge_env_vars(
+            {"A": "1", "B": "2"},
+            {"B": "3", "C": "4"},
+            {},
+            "source",
+        )
+        assert result == {"A": "1", "B": "3", "C": "4"}
+
+    def test_merge_env_vars_tracks_overrides(self) -> None:
+        """Test that env var overrides are tracked."""
+        overrides = {}
+        _merge_env_vars(
+            {"A": "1"},
+            {"A": "2"},
+            overrides,
+            "source",
+        )
+        assert overrides == {"A": "source"}
+
+    def test_merge_runtime_hints_basic(self) -> None:
+        """Test basic runtime hint merging."""
+        result = _merge_runtime_hints(
+            {"command": "old"},
+            {"command": "new", "port": 8080},
+            {},
+            "source",
+        )
+        assert result == {"command": "new", "port": 8080}
+
+    def test_merge_files_basic(self) -> None:
+        """Test basic file merging."""
+        result = _merge_files(
+            {"a.txt": "old"},
+            {"a.txt": "new", "b.txt": "content"},
+            {},
+            "source",
+        )
+        assert result == {"a.txt": "new", "b.txt": "content"}
+
+    def test_merge_mounts_basic(self) -> None:
+        """Test basic mount merging."""
+        result = _merge_mounts(
+            {},
+            [{"target": "/app", "mode": "rw", "files": {"a.txt": "content"}}],
+            {},
+            "source",
+        )
+        assert "/app" in result
+        assert result["/app"].mode == "rw"
+        assert result["/app"].files == {"a.txt": "content"}
+
+    def test_merge_mounts_file_override(self) -> None:
+        """Test mount file map merging with overrides."""
+        from src.services.config_profile_resolver import ResolvedMount
+        result = _merge_mounts(
+            {"/app": ResolvedMount(target="/app", mode="rw", files={"a.txt": "old"})},
+            [{"target": "/app", "mode": "rw", "files": {"a.txt": "new"}}],
+            {},
+            "source",
+        )
+        assert result["/app"].files == {"a.txt": "new"}
+
+    def test_merge_mounts_mode_conflict(self) -> None:
+        """Test that mount mode conflicts are resolved (later wins)."""
+        from src.services.config_profile_resolver import ResolvedMount
+        overrides = {}
+        result = _merge_mounts(
+            {"/app": ResolvedMount(target="/app", mode="rw", files={})},
+            [{"target": "/app", "mode": "ro", "files": {}}],
+            overrides,
+            "source",
+        )
+        assert result["/app"].mode == "ro"
+        assert overrides == {"/app": "source"}
+
+    def test_merge_git_mounts_basic(self) -> None:
+        """Test basic git mount merging."""
+        result = _merge_git_mounts(
+            [],
+            [{"remote_url": "https://github.com/user/repo1.git", "source_path": ".", "target_path": "/app"}],
+            "source",
+        )
+        assert len(result) == 1
+        assert result[0]["remote_url"] == "https://github.com/user/repo1.git"
+        assert result[0]["target_path"] == "/app"
+
+    def test_merge_git_mounts_override_same_repo_target(self) -> None:
+        """Test that git mounts with same repo+target override."""
+        result = _merge_git_mounts(
+            [{"remote_url": "https://github.com/user/repo1.git", "source_path": ".", "target_path": "/app", "branch": "main"}],
+            [{"remote_url": "https://github.com/user/repo1.git", "source_path": "src", "target_path": "/app", "branch": "dev"}],
+            "source",
+        )
+        assert len(result) == 1
+        assert result[0]["source_path"] == "src"
+        assert result[0]["branch"] == "dev"
+
+    def test_merge_git_mounts_different_targets(self) -> None:
+        """Test that git mounts with different targets are preserved."""
+        result = _merge_git_mounts(
+            [{"remote_url": "https://github.com/user/repo1.git", "source_path": ".", "target_path": "/app"}],
+            [{"remote_url": "https://github.com/user/repo2.git", "source_path": ".", "target_path": "/config"}],
+            "source",
+        )
+        assert len(result) == 2
+        targets = {m["target_path"] for m in result}
+        assert targets == {"/app", "/config"}
+
+
+class TestResolveProfile:
+    """Unit tests for profile resolution."""
+
+    @pytest.mark.asyncio
+    async def test_resolve_simple_profile(self, db_session: AsyncSession) -> None:
+        """Test resolving a profile with no includes."""
+        user_id = uuid.uuid4()
+        profile = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="simple",
+            env_vars={"VAR": "value"},
+            runtime_hints={"command": "run"},
+            files={"test.txt": "content"},
+            mounts=[{"target": "/app", "mode": "rw", "files": {}}],
+        )
+        db_session.add(profile)
+        await db_session.commit()
+
+        result = await resolve_profile(db_session, profile.id)
+        assert result.profile_name == "simple"
+        assert result.env_vars == {"VAR": "value"}
+        assert result.runtime_hints == {"command": "run"}
+        assert result.files == {"test.txt": "content"}
+
+    @pytest.mark.asyncio
+    async def test_resolve_profile_with_includes(self, db_session: AsyncSession) -> None:
+        """Test resolving a profile that includes another."""
+        user_id = uuid.uuid4()
+
+        # Create base profile
+        base = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="base",
+            env_vars={"BASE_VAR": "base_value"},
+            files={},
+        )
+        db_session.add(base)
+
+        # Create child profile
+        child = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="child",
+            env_vars={"CHILD_VAR": "child_value"},
+            files={},
+        )
+        db_session.add(child)
+        await db_session.commit()
+
+        # Create include relationship
+        include = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=child.id,
+            included_profile_id=base.id,
+            order_index=0,
+        )
+        db_session.add(include)
+        await db_session.commit()
+
+        result = await resolve_profile(db_session, child.id)
+        assert result.env_vars == {
+            "BASE_VAR": "base_value",
+            "CHILD_VAR": "child_value",
+        }
+        assert len(result.included_profiles) == 1
+        assert result.included_profiles[0]["name"] == "base"
+
+    @pytest.mark.asyncio
+    async def test_resolve_profile_child_overrides_parent(self, db_session: AsyncSession) -> None:
+        """Test that child profile values override parent values."""
+        user_id = uuid.uuid4()
+
+        base = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="base",
+            env_vars={"VAR": "base"},
+            files={},
+        )
+        db_session.add(base)
+
+        child = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="child",
+            env_vars={"VAR": "child"},
+            files={},
+        )
+        db_session.add(child)
+        await db_session.commit()
+
+        include = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=child.id,
+            included_profile_id=base.id,
+            order_index=0,
+        )
+        db_session.add(include)
+        await db_session.commit()
+
+        result = await resolve_profile(db_session, child.id)
+        assert result.env_vars == {"VAR": "child"}
+        assert result.env_overrides == {"VAR": "child"}
+
+    @pytest.mark.asyncio
+    async def test_resolve_profile_cycle_detection(self, db_session: AsyncSession) -> None:
+        """Test that cycles are detected during resolution."""
+        user_id = uuid.uuid4()
+
+        profile_a = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="a",
+            env_vars={},
+            files={},
+        )
+        db_session.add(profile_a)
+
+        profile_b = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="b",
+            env_vars={},
+            files={},
+        )
+        db_session.add(profile_b)
+        await db_session.commit()
+
+        # A includes B
+        include_ab = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=profile_a.id,
+            included_profile_id=profile_b.id,
+            order_index=0,
+        )
+        db_session.add(include_ab)
+
+        # B includes A (creates cycle)
+        include_ba = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=profile_b.id,
+            included_profile_id=profile_a.id,
+            order_index=0,
+        )
+        db_session.add(include_ba)
+        await db_session.commit()
+
+        with pytest.raises(ConfigProfileCycleError):
+            await resolve_profile(db_session, profile_a.id)
+
+    @pytest.mark.asyncio
+    async def test_resolve_profile_with_git_mounts(self, db_session: AsyncSession) -> None:
+        """Test resolving a profile with git mounts."""
+        user_id = uuid.uuid4()
+        
+        profile = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="with-git-mounts",
+            env_vars={},
+            files={},
+            git_mounts=[
+                {"remote_url": "https://github.com/user/repo1.git", "source_path": ".", "target_path": "/app"},
+            ],
+        )
+        db_session.add(profile)
+        await db_session.commit()
+        
+        result = await resolve_profile(db_session, profile.id)
+        assert len(result.git_mounts) == 1
+        assert result.git_mounts[0]["remote_url"] == "https://github.com/user/repo1.git"
+        assert result.git_mounts[0]["target_path"] == "/app"
+    
+    @pytest.mark.asyncio
+    async def test_resolve_profile_with_git_mount_includes(self, db_session: AsyncSession) -> None:
+        """Test resolving a profile that includes another with git mounts."""
+        user_id = uuid.uuid4()
+        
+        # Create base profile with git mount
+        base = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="base",
+            env_vars={},
+            files={},
+            git_mounts=[
+                {"remote_url": "https://github.com/user/repo1.git", "source_path": ".", "target_path": "/app"},
+            ],
+        )
+        db_session.add(base)
+        
+        # Create child profile with its own git mount
+        child = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="child",
+            env_vars={},
+            files={},
+            git_mounts=[
+                {"remote_url": "https://github.com/user/repo2.git", "source_path": "config", "target_path": "/config"},
+            ],
+        )
+        db_session.add(child)
+        await db_session.commit()
+        
+        # Create include relationship
+        include = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=child.id,
+            included_profile_id=base.id,
+            order_index=0,
+        )
+        db_session.add(include)
+        await db_session.commit()
+        
+        result = await resolve_profile(db_session, child.id)
+        assert len(result.git_mounts) == 2
+        targets = {m["target_path"] for m in result.git_mounts}
+        assert targets == {"/app", "/config"}
+
+    @pytest.mark.asyncio
+    async def test_resolve_profile_not_found(self, db_session: AsyncSession) -> None:
+        """Test resolving a non-existent profile."""
+        with pytest.raises(ConfigProfileNotFoundError):
+            await resolve_profile(db_session, uuid.uuid4())
+
+
+class TestCheckIncludeCycle:
+    """Unit tests for include cycle checking."""
+
+    @pytest.mark.asyncio
+    async def test_check_no_cycle(self, db_session: AsyncSession) -> None:
+        """Test checking when no cycle exists."""
+        user_id = uuid.uuid4()
+
+        profile_a = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="a",
+            env_vars={},
+            files={},
+        )
+        db_session.add(profile_a)
+
+        profile_b = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="b",
+            env_vars={},
+            files={},
+        )
+        db_session.add(profile_b)
+        await db_session.commit()
+
+        # A includes B
+        include = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=profile_a.id,
+            included_profile_id=profile_b.id,
+            order_index=0,
+        )
+        db_session.add(include)
+        await db_session.commit()
+
+        result = await check_include_cycle(db_session, profile_a.id)
+        assert result is None
+
+    @pytest.mark.asyncio
+    async def test_check_detects_cycle(self, db_session: AsyncSession) -> None:
+        """Test detecting an existing cycle."""
+        user_id = uuid.uuid4()
+
+        profile_a = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="a",
+            env_vars={},
+            files={},
+        )
+        db_session.add(profile_a)
+
+        profile_b = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="b",
+            env_vars={},
+            files={},
+        )
+        db_session.add(profile_b)
+        await db_session.commit()
+
+        # A includes B
+        include_ab = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=profile_a.id,
+            included_profile_id=profile_b.id,
+            order_index=0,
+        )
+        db_session.add(include_ab)
+
+        # B includes A
+        include_ba = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=profile_b.id,
+            included_profile_id=profile_a.id,
+            order_index=0,
+        )
+        db_session.add(include_ba)
+        await db_session.commit()
+
+        result = await check_include_cycle(db_session, profile_a.id)
+        assert result is not None
+        assert len(result) > 1
+
+    @pytest.mark.asyncio
+    async def test_check_would_create_cycle(self, db_session: AsyncSession) -> None:
+        """Test detecting a cycle that would be created."""
+        user_id = uuid.uuid4()
+
+        profile_a = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="a",
+            env_vars={},
+            files={},
+        )
+        db_session.add(profile_a)
+
+        profile_b = ConfigProfile(
+            id=uuid.uuid4(),
+            user_id=user_id,
+            name="b",
+            env_vars={},
+            files={},
+        )
+        db_session.add(profile_b)
+        await db_session.commit()
+
+        # A includes B
+        include = ConfigProfileInclude(
+            id=uuid.uuid4(),
+            profile_id=profile_a.id,
+            included_profile_id=profile_b.id,
+            order_index=0,
+        )
+        db_session.add(include)
+        await db_session.commit()
+
+        # Check if adding B includes A would create cycle
+        result = await check_include_cycle(db_session, profile_b.id, profile_a.id)
+        assert result is not None
@@ -0,0 +1,52 @@
+"""Unit tests for docker service utilities."""
+
+from unittest.mock import MagicMock, patch
+
+from src.services.docker import get_container_id, get_container_name
+
+
+class TestGetContainerId:
+    """Tests for get_container_id."""
+
+    @patch("subprocess.run")
+    def test_lowercases_name_for_filter(self, mock_run) -> None:
+        """Docker ps name filter is case-sensitive; we must lowercase."""
+        mock_run.return_value = MagicMock(returncode=0, stdout="abc123\n")
+
+        result = get_container_id("MyContainer-ABC")
+
+        assert result == "abc123"
+        call_args = mock_run.call_args[0][0]
+        # The filter must use lowercase
+        assert "name=mycontainer-abc" in call_args
+
+    @patch("subprocess.run")
+    def test_returns_none_when_not_found(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="")
+
+        result = get_container_id("missing")
+
+        assert result is None
+
+
+class TestGetContainerName:
+    """Tests for get_container_name."""
+
+    @patch("subprocess.run")
+    def test_lowercases_name_for_filter(self, mock_run) -> None:
+        """Docker ps name filter is case-sensitive; we must lowercase."""
+        mock_run.return_value = MagicMock(returncode=0, stdout="mycontainer-abc\n")
+
+        result = get_container_name("MyContainer-ABC")
+
+        assert result == "mycontainer-abc"
+        call_args = mock_run.call_args[0][0]
+        assert "name=mycontainer-abc" in call_args
+
+    @patch("subprocess.run")
+    def test_returns_none_when_not_found(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="")
+
+        result = get_container_name("missing")
+
+        assert result is None
@@ -0,0 +1,124 @@
+"""Unit tests for git mount resolution in tool instances."""
+
+import os
+from pathlib import Path
+
+import pytest
+
+from src.api.tool_instances import (
+    _checkout_branch,
+    _expand_glob_source,
+    _resolve_single_git_mount,
+)
+
+
+class TestExpandGlobSource:
+    """Unit tests for glob pattern expansion."""
+
+    def test_no_glob_single_file(self, tmp_path: Path) -> None:
+        """Test non-glob path returns single file."""
+        test_file = tmp_path / "test.txt"
+        test_file.write_text("content")
+        
+        result = _expand_glob_source(str(test_file), str(tmp_path))
+        assert len(result) == 1
+        assert result[0] == str(test_file)
+
+    def test_no_glob_missing_file(self, tmp_path: Path) -> None:
+        """Test non-glob missing file returns empty list."""
+        missing_file = tmp_path / "missing.txt"
+        
+        result = _expand_glob_source(str(missing_file), str(tmp_path))
+        assert len(result) == 0
+
+    def test_glob_pattern(self, tmp_path: Path) -> None:
+        """Test glob pattern matches files."""
+        (tmp_path / "file1.txt").write_text("content1")
+        (tmp_path / "file2.txt").write_text("content2")
+        (tmp_path / "other.py").write_text("code")
+        
+        result = _expand_glob_source(str(tmp_path / "*.txt"), str(tmp_path))
+        assert len(result) == 2
+        assert all(f.endswith(".txt") for f in result)
+
+    def test_glob_recursive(self, tmp_path: Path) -> None:
+        """Test recursive glob pattern."""
+        subdir = tmp_path / "subdir"
+        subdir.mkdir()
+        (subdir / "nested.txt").write_text("content")
+        
+        result = _expand_glob_source(str(tmp_path / "**" / "*.txt"), str(tmp_path))
+        assert len(result) == 1
+        assert "nested.txt" in result[0]
+
+    def test_glob_limit_enforced(self, tmp_path: Path) -> None:
+        """Test that glob matches are limited to prevent abuse."""
+        # Create more than 100 files
+        for i in range(105):
+            (tmp_path / f"file{i}.txt").write_text("content")
+        
+        result = _expand_glob_source(str(tmp_path / "*.txt"), str(tmp_path))
+        assert len(result) == 100  # MAX_GLOB_MATCHES limit
+
+    def test_glob_escapes_repo(self, tmp_path: Path) -> None:
+        """Test that glob results outside repo are filtered."""
+        other_dir = tmp_path.parent / "other"
+        other_dir.mkdir(exist_ok=True)
+        (other_dir / "outside.txt").write_text("content")
+        
+        result = _expand_glob_source(str(tmp_path.parent / "*" / "*.txt"), str(tmp_path))
+        # Should only include files within tmp_path, not other_dir
+        assert all(r.startswith(str(tmp_path)) for r in result)
+
+
+class TestCheckoutBranch:
+    """Unit tests for branch checkout."""
+
+    def test_checkout_existing_branch(self, tmp_path: Path) -> None:
+        """Test checking out an existing branch."""
+        # Initialize git repo
+        os.system(f"cd {tmp_path} && git init && git config user.email 'test@test.com' && git config user.name 'Test'")
+        (tmp_path / "file.txt").write_text("content")
+        os.system(f"cd {tmp_path} && git add . && git commit -m 'initial'")
+        os.system(f"cd {tmp_path} && git branch feature")
+        
+        _checkout_branch(str(tmp_path), "feature")
+        
+        # Verify we're on feature branch
+        result = os.popen(f"cd {tmp_path} && git branch --show-current").read().strip()
+        assert result == "feature"
+
+    def test_checkout_nonexistent_branch(self, tmp_path: Path) -> None:
+        """Test checking out a non-existent branch returns False."""
+        os.system(f"cd {tmp_path} && git init && git config user.email 'test@test.com' && git config user.name 'Test'")
+        (tmp_path / "file.txt").write_text("content")
+        os.system(f"cd {tmp_path} && git add . && git commit -m 'initial'")
+        
+        result = _checkout_branch(str(tmp_path), "nonexistent")
+        assert result is False
+
+
+class TestResolveSingleGitMount:
+    """Unit tests for resolving a single git mount."""
+
+    @pytest.mark.asyncio
+    async def test_resolve_missing_remote_url(self, db_session) -> None:
+        """Test that missing remote_url returns empty list."""
+        git_mount = {
+            "source_path": ".",
+            "target_path": "/app",
+        }
+        
+        result = await _resolve_single_git_mount(db_session, git_mount)
+        assert result == []
+
+    @pytest.mark.asyncio
+    async def test_resolve_missing_target_path(self, db_session) -> None:
+        """Test that missing target path returns empty list."""
+        git_mount = {
+            "remote_url": "https://github.com/user/repo.git",
+            "source_path": ".",
+        }
+        
+        result = await _resolve_single_git_mount(db_session, git_mount)
+        assert result == []
@@ -1,6 +1,5 @@
 """Tests for git URL parsing utilities."""

-import pytest

 from src.utils.git_url_parser import extract_base_repo_url, is_valid_clone_url, parse_git_url

@@ -0,0 +1,315 @@
+"""Unit tests for the manifest compiler."""
+
+import pytest
+
+from src.services.manifest_compiler import (
+    compile_compose,
+    compile_dockerfile,
+    compile_entrypoint,
+    compute_image_tag,
+    deep_merge,
+    merge_with_config,
+    resolve_base,
+)
+
+
+class TestResolveBase:
+    """Tests for resolve_base."""
+
+    def test_returns_manifest_unchanged_when_no_base(self) -> None:
+        manifest = {"name": "test", "base_image": "ubuntu:24.04"}
+        result = resolve_base(manifest)
+        assert result["name"] == "test"
+        assert "base_definition_id" not in result
+
+
+class TestDeepMerge:
+    """Tests for deep_merge."""
+
+    def test_packages_are_unioned(self) -> None:
+        base = {"packages": {"apt": ["curl", "git"]}}
+        override = {"packages": {"apt": ["neovim"]}}
+        result = deep_merge(base, override)
+        assert result["packages"]["apt"] == ["curl", "git", "neovim"]
+
+    def test_node_version_overrides(self) -> None:
+        base = {"packages": {"node": {"version": "18"}}}
+        override = {"packages": {"node": {"version": "20"}}}
+        result = deep_merge(base, override)
+        assert result["packages"]["node"]["version"] == "20"
+
+    def test_env_is_merged_with_override_winning(self) -> None:
+        base = {"env": {"FOO": "base", "BAR": "base"}}
+        override = {"env": {"FOO": "override"}}
+        result = deep_merge(base, override)
+        assert result["env"]["FOO"] == "override"
+        assert result["env"]["BAR"] == "base"
+
+    def test_build_scripts_are_concatenated(self) -> None:
+        base = {"scripts": {"build": ["echo base"]}}
+        override = {"scripts": {"build": ["echo override"]}}
+        result = deep_merge(base, override)
+        assert result["scripts"]["build"] == ["echo base", "echo override"]
+
+    def test_mounts_are_concatenated(self) -> None:
+        base = {"mounts": [{"name": "base-mount", "target": "/base"}]}
+        override = {"mounts": [{"name": "tool-mount", "target": "/tool"}]}
+        result = deep_merge(base, override)
+        assert len(result["mounts"]) == 2
+
+    def test_user_is_overridden_entirely(self) -> None:
+        base = {"user": {"name": "base", "uid": 1000}}
+        override = {"user": {"name": "tool", "uid": 1001}}
+        result = deep_merge(base, override)
+        assert result["user"]["name"] == "tool"
+        assert result["user"]["uid"] == 1001
+
+
+class TestCompileDockerfile:
+    """Tests for compile_dockerfile."""
+
+    def test_includes_from(self) -> None:
+        manifest = {"base_image": "ubuntu:24.04", "name": "test"}
+        df = compile_dockerfile(manifest)
+        assert "FROM ubuntu:24.04" in df
+
+    def test_installs_apt_packages(self) -> None:
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "name": "test",
+            "packages": {"apt": ["curl", "git"]},
+        }
+        df = compile_dockerfile(manifest)
+        assert "apt-get install -y" in df
+        assert "curl" in df
+        assert "git" in df
+        assert "rm -rf /var/lib/apt/lists/*" in df
+
+    def test_installs_node(self) -> None:
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "name": "test",
+            "packages": {"node": {"version": "20"}},
+        }
+        df = compile_dockerfile(manifest)
+        assert "nodesource.com/setup_20.x" in df
+
+    def test_installs_npm_global(self) -> None:
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "name": "test",
+            "packages": {"npm_global": ["@scope/pkg"]},
+        }
+        df = compile_dockerfile(manifest)
+        assert "npm install -g @scope/pkg" in df
+
+    def test_creates_user(self) -> None:
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "name": "test",
+            "user": {"name": "dev", "uid": 1001, "gid": 1001},
+        }
+        df = compile_dockerfile(manifest)
+        assert "groupadd -g 1001 dev" in df
+        assert "useradd -u 1001 -g 1001" in df
+        assert "USER dev" in df
+
+    def test_build_scripts_as_run_commands(self) -> None:
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "name": "test",
+            "scripts": {"build": ["echo hello", "echo world"]},
+        }
+        df = compile_dockerfile(manifest)
+        assert "RUN echo hello" in df
+        assert "RUN echo world" in df
+
+    def test_creates_mount_directories(self) -> None:
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "name": "test",
+            "user": {"name": "dev", "uid": 1001, "gid": 1001},
+            "mounts": [
+                {"name": "ws", "target": "/workspace"},
+                {"name": "cfg", "target": "/config"},
+            ],
+        }
+        df = compile_dockerfile(manifest)
+        assert "mkdir -p /workspace /config" in df
+        assert "chown -R dev:dev /workspace /config" in df
+
+    def test_entrypoint_for_startup_scripts(self) -> None:
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "name": "test",
+            "scripts": {"startup": ["echo start"]},
+        }
+        df = compile_dockerfile(manifest)
+        assert 'ENTRYPOINT ["/usr/local/bin/headquarter-entrypoint"]' in df
+
+    def test_cmd_from_runtime(self) -> None:
+        manifest = {
+            "base_image": "ubuntu:24.04",
+            "name": "test",
+            "runtime": {"command": ["/bin/bash", "-il"]},
+        }
+        df = compile_dockerfile(manifest)
+        assert 'CMD ["/bin/bash", "-il"]' in df
+
+    def test_default_cmd_when_no_runtime(self) -> None:
+        manifest = {"base_image": "ubuntu:24.04", "name": "test"}
+        df = compile_dockerfile(manifest)
+        assert 'CMD ["/bin/bash"]' in df
+
+
+class TestCompileEntrypoint:
+    """Tests for compile_entrypoint."""
+
+    def test_includes_shebang_and_set_e(self) -> None:
+        manifest = {"scripts": {"startup": ["echo hello"]}}
+        ep = compile_entrypoint(manifest)
+        assert "#!/bin/bash" in ep
+        assert "set -e" in ep
+
+    def test_includes_startup_scripts(self) -> None:
+        manifest = {"scripts": {"startup": ["echo hello", "echo world"]}}
+        ep = compile_entrypoint(manifest)
+        assert "echo hello" in ep
+        assert "echo world" in ep
+
+    def test_ends_with_exec(self) -> None:
+        manifest: dict = {"scripts": {"startup": []}}
+        ep = compile_entrypoint(manifest)
+        assert 'exec "$@"' in ep
+
+
+class TestCompileCompose:
+    """Tests for compile_compose."""
+
+    def test_includes_image_and_container_name(self) -> None:
+        manifest = {"name": "test", "interface_type": "terminal"}
+        vars_dict = {"IMAGE_TAG": "test:v1", "INSTANCE_NAME": "test-1"}
+        compose = compile_compose(manifest, vars_dict)
+        assert "image: test:v1" in compose
+        assert "container_name: test-1" in compose
+
+    def test_terminal_fields(self) -> None:
+        manifest = {
+            "name": "test",
+            "interface_type": "terminal",
+            "runtime": {"stdin_open": True, "tty": True, "working_dir": "/workspace"},
+        }
+        compose = compile_compose(manifest, {"IMAGE_TAG": "t", "INSTANCE_NAME": "n"})
+        assert "stdin_open: true" in compose
+        assert "tty: true" in compose
+        assert "working_dir: /workspace" in compose
+
+    def test_web_ports(self) -> None:
+        manifest = {
+            "name": "test",
+            "interface_type": "web",
+            "default_port": 8080,
+        }
+        compose = compile_compose(
+            manifest, {"IMAGE_TAG": "t", "INSTANCE_NAME": "n", "TOOL_PORT": "3000"}
+        )
+        assert "3000:8080" in compose
+
+    def test_user_override(self) -> None:
+        manifest = {
+            "name": "test",
+            "interface_type": "terminal",
+            "user": {"uid": 1001, "gid": 1001},
+        }
+        compose = compile_compose(manifest, {"IMAGE_TAG": "t", "INSTANCE_NAME": "n"})
+        assert "user: 1001:1001" in compose
+
+    def test_mounts_resolved(self) -> None:
+        manifest = {
+            "name": "test",
+            "interface_type": "terminal",
+            "mounts": [
+                {"name": "ws", "target": "/workspace", "source_type": "repo"},
+                {
+                    "name": "ssh",
+                    "target": "/home/user/.ssh",
+                    "source_type": "ssh_key",
+                    "readonly": True,
+                },
+            ],
+        }
+        compose = compile_compose(
+            manifest,
+            {
+                "IMAGE_TAG": "t",
+                "INSTANCE_NAME": "n",
+                "REPO_PATH": "/repos/myrepo",
+                "SSH_PATH": "/keys/ssh",
+            },
+        )
+        assert "/repos/myrepo:/workspace" in compose
+        assert "/keys/ssh:/home/user/.ssh:ro" in compose
+
+    def test_extra_volumes_appended(self) -> None:
+        manifest = {"name": "test", "interface_type": "terminal"}
+        compose = compile_compose(
+            manifest,
+            {
+                "IMAGE_TAG": "t",
+                "INSTANCE_NAME": "n",
+                "EXTRA_VOLUMES": [{"source": "/host/x", "target": "/container/x"}],
+            },
+        )
+        assert "/host/x:/container/x" in compose
+
+
+class TestComputeImageTag:
+    """Tests for compute_image_tag."""
+
+    def test_is_deterministic(self) -> None:
+        manifest = {"name": "test", "packages": {"apt": ["curl"]}}
+        tag1 = compute_image_tag("My Tool", manifest)
+        tag2 = compute_image_tag("My Tool", manifest)
+        assert tag1 == tag2
+
+    def test_changes_with_content(self) -> None:
+        manifest1 = {"name": "test", "packages": {"apt": ["curl"]}}
+        manifest2 = {"name": "test", "packages": {"apt": ["wget"]}}
+        tag1 = compute_image_tag("test", manifest1)
+        tag2 = compute_image_tag("test", manifest2)
+        assert tag1 != tag2
+
+    def test_lowercases_name(self) -> None:
+        manifest = {"name": "test"}
+        tag = compute_image_tag("My Tool", manifest)
+        assert "my-tool" in tag
+
+    def test_valid_docker_reference(self) -> None:
+        manifest = {"name": "test"}
+        tag = compute_image_tag("test", manifest)
+        assert tag.startswith("headquarter/test-")
+        assert tag.endswith(":latest")
+
+
+class TestMergeWithConfig:
+    """Tests for merge_with_config."""
+
+    def test_applies_tool_config_env(self) -> None:
+        manifest = {"name": "test"}
+        configs = [
+            {"config_type": "env", "key": "FOO", "value": "bar"},
+        ]
+        result = merge_with_config(manifest, configs)
+        assert result["_extra_env"]["FOO"] == "bar"
+
+    def test_applies_port_override(self) -> None:
+        manifest = {"name": "test", "default_port": 8080}
+        configs = [{"port_override": 3000}]
+        result = merge_with_config(manifest, configs)
+        assert result["default_port"] == 3000
+
+    def test_applies_start_command(self) -> None:
+        manifest = {"name": "test", "runtime": {"command": ["/bin/bash"]}}
+        configs = [{"start_command": "/bin/sh"}]
+        result = merge_with_config(manifest, configs)
+        assert result["runtime"]["command"] == ["/bin/sh"]
@@ -0,0 +1,145 @@
+"""Unit tests for the permission fixer."""
+
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from src.services.permission_fixer import (
+    PermissionFixError,
+    apply_mount_permissions,
+    check_root_user_available,
+    _run_in_container,
+)
+
+
+class TestApplyMountPermissions:
+    """Tests for apply_mount_permissions."""
+
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_applies_chown_when_owner_declared(self, mock_run) -> None:
+        mounts = [
+            {"name": "workspace", "target": "/workspace", "owner": "user"},
+        ]
+        results = apply_mount_permissions("abc123", mounts)
+
+        assert len(results) == 1
+        assert results[0]["mount_name"] == "workspace"
+        assert results[0]["success"] is True
+        mock_run.assert_called_once()
+        args = mock_run.call_args[0]
+        assert args[0] == "abc123"
+        assert args[1] == ["chown", "-R", "user:user", "/workspace"]
+
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_applies_chmod_when_mode_declared(self, mock_run) -> None:
+        mounts = [
+            {"name": "ssh", "target": "/home/user/.ssh", "mode": "0700"},
+        ]
+        results = apply_mount_permissions("abc123", mounts)
+
+        assert results[0]["success"] is True
+        # Only chmod called (no owner, so no chown)
+        assert mock_run.call_count == 1
+        chmod_call = mock_run.call_args_list[0]
+        assert chmod_call[0][1] == ["chmod", "0700", "/home/user/.ssh"]
+
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_applies_file_mode_when_declared(self, mock_run) -> None:
+        mounts = [
+            {
+                "name": "ssh",
+                "target": "/home/user/.ssh",
+                "file_mode": "0600",
+            },
+        ]
+        results = apply_mount_permissions("abc123", mounts)
+
+        assert results[0]["success"] is True
+        # Only file_mode called (no owner, no mode)
+        assert mock_run.call_count == 1
+        file_mode_call = mock_run.call_args_list[0]
+        assert file_mode_call[0][1][0] == "sh"
+        assert (
+            "find /home/user/.ssh -type f -exec chmod 0600" in file_mode_call[0][1][2]
+        )
+
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_skips_mount_with_no_policy(self, mock_run) -> None:
+        mounts = [
+            {"name": "workspace", "target": "/workspace", "writable": True},
+        ]
+        results = apply_mount_permissions("abc123", mounts)
+
+        assert len(results) == 1
+        assert results[0]["success"] is True
+        mock_run.assert_not_called()
+
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_reports_failure_on_command_error(self, mock_run) -> None:
+        mock_run.side_effect = PermissionFixError("chown failed")
+
+        mounts = [
+            {"name": "workspace", "target": "/workspace", "owner": "user"},
+        ]
+        results = apply_mount_permissions("abc123", mounts)
+
+        assert results[0]["success"] is False
+        assert "chown failed" in results[0]["error"]
+
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_stops_on_first_failure(self, mock_run) -> None:
+        """If chown fails, chmod and file_mode should not run."""
+        mock_run.side_effect = PermissionFixError("chown failed")
+
+        mounts = [
+            {
+                "name": "workspace",
+                "target": "/workspace",
+                "owner": "user",
+                "mode": "0755",
+                "file_mode": "0644",
+            },
+        ]
+        results = apply_mount_permissions("abc123", mounts)
+
+        assert results[0]["success"] is False
+        assert mock_run.call_count == 1  # Only chown attempted
+
+
+class TestRunInContainer:
+    """Tests for _run_in_container."""
+
+    @patch("subprocess.run")
+    def test_success(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stderr="")
+        _run_in_container("abc123", ["echo", "hello"], 10)
+        mock_run.assert_called_once()
+        cmd = mock_run.call_args[0][0]
+        assert cmd == ["docker", "exec", "--user", "root", "abc123", "echo", "hello"]
+
+    @patch("subprocess.run")
+    def test_failure_raises(self, mock_run) -> None:
+        mock_run.return_value = MagicMock(returncode=1, stderr="permission denied")
+        with pytest.raises(PermissionFixError, match="permission denied"):
+            _run_in_container("abc123", ["chown", "x"], 10)
+
+    @patch("subprocess.run")
+    def test_timeout_raises(self, mock_run) -> None:
+        import subprocess
+
+        mock_run.side_effect = subprocess.TimeoutExpired(cmd=["docker"], timeout=10)
+        with pytest.raises(PermissionFixError, match="timed out"):
+            _run_in_container("abc123", ["chown", "x"], 10)
+
+
+class TestCheckRootUserAvailable:
+    """Tests for check_root_user_available."""
+
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_returns_true_when_root_exists(self, mock_run) -> None:
+        assert check_root_user_available("abc123") is True
+
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_returns_false_when_root_missing(self, mock_run) -> None:
+        mock_run.side_effect = PermissionFixError("no such user")
+        assert check_root_user_available("abc123") is False
@@ -1,9 +1,7 @@
 """Unit tests for readiness probe service."""

-import asyncio
 from unittest.mock import MagicMock, patch

-import pytest

 from src.services.readiness_probe import execute_probe

@@ -0,0 +1,179 @@
+"""Tests for session creation with branch selection and new branch creation."""
+
+import os
+import subprocess
+import tempfile
+
+
+from src.api.tool_instances import CreateInstanceRequest
+
+
+class TestCreateInstanceRequest:
+    """Tests for CreateInstanceRequest model."""
+
+    def test_default_values(self):
+        """Test default values for CreateInstanceRequest."""
+        request = CreateInstanceRequest(tool_type_id="123")
+        assert request.clone_mode == "mount"
+        assert request.branch == "main"
+        assert request.new_branch is None
+        assert request.display_name is None
+
+    def test_clone_mode_with_branch(self):
+        """Test CreateInstanceRequest with clone mode and branch."""
+        request = CreateInstanceRequest(
+            tool_type_id="123",
+            clone_mode="clone",
+            branch="dev",
+        )
+        assert request.clone_mode == "clone"
+        assert request.branch == "dev"
+
+    def test_new_branch_field(self):
+        """Test CreateInstanceRequest with new_branch field."""
+        request = CreateInstanceRequest(
+            tool_type_id="123",
+            clone_mode="clone",
+            branch="main",
+            new_branch="feature/test",
+        )
+        assert request.new_branch == "feature/test"
+
+
+class TestBranchCreationInClone:
+    """Tests for branch creation logic in clone process."""
+
+    def test_create_local_branch_success(self):
+        """Test successful local branch creation."""
+        with tempfile.TemporaryDirectory() as tmpdir:
+            # Initialize repo
+            subprocess.run(
+                ["git", "init", tmpdir],
+                capture_output=True,
+                check=True,
+            )
+            subprocess.run(
+                ["git", "-C", tmpdir, "config", "user.email", "test@test.com"],
+                capture_output=True,
+                check=True,
+            )
+            subprocess.run(
+                ["git", "-C", tmpdir, "config", "user.name", "Test User"],
+                capture_output=True,
+                check=True,
+            )
+            
+            # Create initial commit
+            readme = os.path.join(tmpdir, "README.md")
+            with open(readme, "w") as f:
+                f.write("# Test\n")
+            subprocess.run(
+                ["git", "-C", tmpdir, "add", "README.md"],
+                capture_output=True,
+                check=True,
+            )
+            subprocess.run(
+                ["git", "-C", tmpdir, "commit", "-m", "Initial commit"],
+                capture_output=True,
+                check=True,
+            )
+            
+            # Create new branch
+            result = subprocess.run(
+                ["git", "-C", tmpdir, "checkout", "-b", "feature/new-branch"],
+                capture_output=True,
+                text=True,
+            )
+            
+            assert result.returncode == 0
+            
+            # Verify branch exists
+            branches_result = subprocess.run(
+                ["git", "-C", tmpdir, "branch", "--show-current"],
+                capture_output=True,
+                text=True,
+            )
+            assert branches_result.stdout.strip() == "feature/new-branch"
+
+    def test_create_local_branch_invalid_name(self):
+        """Test local branch creation with invalid name fails."""
+        with tempfile.TemporaryDirectory() as tmpdir:
+            # Initialize repo
+            subprocess.run(
+                ["git", "init", tmpdir],
+                capture_output=True,
+                check=True,
+            )
+            subprocess.run(
+                ["git", "-C", tmpdir, "config", "user.email", "test@test.com"],
+                capture_output=True,
+                check=True,
+            )
+            subprocess.run(
+                ["git", "-C", tmpdir, "config", "user.name", "Test User"],
+                capture_output=True,
+                check=True,
+            )
+            
+            # Create initial commit
+            readme = os.path.join(tmpdir, "README.md")
+            with open(readme, "w") as f:
+                f.write("# Test\n")
+            subprocess.run(
+                ["git", "-C", tmpdir, "add", "README.md"],
+                capture_output=True,
+                check=True,
+            )
+            subprocess.run(
+                ["git", "-C", tmpdir, "commit", "-m", "Initial commit"],
+                capture_output=True,
+                check=True,
+            )
+            
+            # Try to create branch with invalid name (contains spaces)
+            result = subprocess.run(
+                ["git", "-C", tmpdir, "checkout", "-b", "invalid branch name"],
+                capture_output=True,
+                text=True,
+            )
+            
+            # Git accepts branch names with spaces but it's not recommended
+            # This test verifies the command structure
+            assert result.returncode == 0 or "fatal" in result.stderr
+
+
+class TestCreateInstanceAPI:
+    """Tests for create instance API endpoint with branch options."""
+
+    def test_create_instance_request_validation(self):
+        """Test that CreateInstanceRequest validates correctly."""
+        # Valid request with new_branch
+        request = CreateInstanceRequest(
+            tool_type_id="550e8400-e29b-41d4-a716-446655440000",
+            clone_mode="clone",
+            branch="main",
+            new_branch="feature/test",
+        )
+        assert request.new_branch == "feature/test"
+        
+        # Valid request without new_branch
+        request2 = CreateInstanceRequest(
+            tool_type_id="550e8400-e29b-41d4-a716-446655440000",
+            clone_mode="clone",
+            branch="dev",
+        )
+        assert request2.new_branch is None
+
+    def test_create_instance_with_new_branch_sets_instance_branch(self):
+        """Test that instance branch is set to new_branch when provided."""
+        # This tests the logic: data.new_branch if data.new_branch else data.branch
+        new_branch = "feature/test"
+        base_branch = "main"
+        
+        # Simulate the logic from create_instance
+        stored_branch = new_branch if new_branch else base_branch
+        assert stored_branch == "feature/test"
+        
+        # Without new_branch
+        stored_branch2 = None if None else base_branch
+        assert stored_branch2 == "main"
@@ -0,0 +1,804 @@
+"""Unit tests for legacy tool instance fallback paths.
+
+Verifies that tool types with definition_type "dockerfile", "compose",
+and "legacy" continue to use the original startup flow after the
+manifest-based flow was introduced.
+"""
+
+import os
+import uuid
+from datetime import datetime
+from unittest.mock import AsyncMock, MagicMock, patch
+
+import pytest
+
+from src.api.tool_instances import create_instance, start_instance
+from src.models.git_repository import GitRepository
+from src.models.tool_instance import ToolInstance
+from src.models.tool_type import ToolType
+from src.models.ssh_key import SSHKey
+from src.models.user import User
+
+
+@pytest.fixture
+def fake_user_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def fake_project_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def fake_repo_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def fake_tool_type_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def fake_instance_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def mock_session(fake_user_id, fake_project_id, fake_repo_id, fake_tool_type_id):
+    """Return an async SQLAlchemy session with basic mocks."""
+    session = AsyncMock()
+
+    user = User(id=fake_user_id, email="test@example.com")
+    project = MagicMock()
+    project.id = fake_project_id
+    repo = GitRepository(
+        id=fake_repo_id,
+        project_id=fake_project_id,
+        name="test-repo",
+        path="/data/repos/test-repo",
+        remote_url=None,
+        ssh_key_id=None,
+    )
+
+    async def _get(model, pk):
+        if model is User and pk == fake_user_id:
+            return user
+        if model is GitRepository and pk == fake_repo_id:
+            return repo
+        return None
+
+    def _add(instance):
+        if getattr(instance, "created_at", None) is None:
+            instance.created_at = datetime.now()
+        if getattr(instance, "updated_at", None) is None:
+            instance.updated_at = datetime.now()
+
+    session.get.side_effect = _get
+    session.add = MagicMock(side_effect=_add)
+    session.execute.return_value = MagicMock(scalars=MagicMock(return_value=MagicMock(all=MagicMock(return_value=[]))))
+    return session
+
+
+class TestCreateInstanceDockerfileLegacy:
+    """Legacy dockerfile definition type in create_instance."""
+
+    @patch("src.api.tool_instances.ensure_instance_directory")
+    @patch("src.api.tool_instances.find_free_port")
+    @patch("src.api.tool_instances.build_image")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_builds_from_dockerfile_template(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_write_compose,
+        mock_build_image,
+        mock_find_port,
+        mock_ensure_dir,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'dockerfile', build_image is called with the template."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_find_port.return_value = 12345
+        mock_ensure_dir.return_value = "/data/instances/test-instance"
+        mock_build_image.return_value = (0, "built", "")
+
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-df-tool",
+            display_name="Legacy DF Tool",
+            default_port=8080,
+            definition_type="dockerfile",
+            dockerfile_template="FROM python:3.11\nRUN echo hi",
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        data = MagicMock()
+        data.tool_type_id = str(fake_tool_type_id)
+        data.display_name = None
+        data.clone_mode = "mount"
+        data.branch = None
+        data.new_branch = None
+        data.config_profile_id = None
+
+        result = await create_instance(
+            project_id=fake_project_id,
+            repo_id=fake_repo_id,
+            data=data,
+            user_id=fake_user_id,
+            session=mock_session,
+        )
+
+        assert result["status"] == "pending"
+        mock_build_image.assert_called_once()
+        call_kwargs = mock_build_image.call_args.kwargs
+        assert call_kwargs["dockerfile"] == "FROM python:3.11\nRUN echo hi"
+        mock_write_compose.assert_called_once()
+
+    @patch("src.api.tool_instances.ensure_instance_directory")
+    @patch("src.api.tool_instances.find_free_port")
+    @patch("src.api.tool_instances.build_image")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_dockerfile_build_failure_raises_500(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_write_compose,
+        mock_build_image,
+        mock_find_port,
+        mock_ensure_dir,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_tool_type_id,
+    ) -> None:
+        """Failed dockerfile build should raise HTTP 500."""
+        from fastapi import HTTPException
+
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_find_port.return_value = 12345
+        mock_ensure_dir.return_value = "/data/instances/test-instance"
+        mock_build_image.return_value = (1, "", "build failed")
+
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-df-tool",
+            display_name="Legacy DF Tool",
+            default_port=8080,
+            definition_type="dockerfile",
+            dockerfile_template="FROM invalid",
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        data = MagicMock()
+        data.tool_type_id = str(fake_tool_type_id)
+        data.display_name = None
+        data.clone_mode = "mount"
+        data.branch = None
+        data.new_branch = None
+        data.config_profile_id = None
+
+        with pytest.raises(HTTPException) as exc_info:
+            await create_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                data=data,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert exc_info.value.status_code == 500
+        assert "Failed to build Docker image" in exc_info.value.detail
+
+
+class TestCreateInstanceComposeLegacy:
+    """Legacy compose definition type in create_instance."""
+
+    @patch("src.api.tool_instances.ensure_instance_directory")
+    @patch("src.api.tool_instances.find_free_port")
+    @patch("src.api.tool_instances.render_compose_template")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_renders_compose_template(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_write_compose,
+        mock_render_compose,
+        mock_find_port,
+        mock_ensure_dir,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'compose', render_compose_template is called."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_find_port.return_value = 12345
+        mock_ensure_dir.return_value = "/data/instances/test-instance"
+        mock_render_compose.return_value = "services:\n  app:\n    image: nginx"
+
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-compose-tool",
+            display_name="Legacy Compose Tool",
+            default_port=80,
+            definition_type="compose",
+            dockerfile_template=None,
+            compose_template="services:\n  app:\n    image: nginx\n    ports:\n      - ${TOOL_PORT}:80",
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        data = MagicMock()
+        data.tool_type_id = str(fake_tool_type_id)
+        data.display_name = None
+        data.clone_mode = "mount"
+        data.branch = None
+        data.new_branch = None
+        data.config_profile_id = None
+
+        result = await create_instance(
+            project_id=fake_project_id,
+            repo_id=fake_repo_id,
+            data=data,
+            user_id=fake_user_id,
+            session=mock_session,
+        )
+
+        assert result["status"] == "pending"
+        mock_render_compose.assert_called_once()
+        args = mock_render_compose.call_args[0]
+        assert "services:" in args[0]
+        mock_write_compose.assert_called_once()
+
+
+class TestCreateInstanceManifestNotCalledForLegacy:
+    """Ensure manifest compiler is never invoked for legacy types."""
+
+    @patch("src.api.tool_instances.ensure_instance_directory")
+    @patch("src.api.tool_instances.find_free_port")
+    @patch("src.api.tool_instances.build_image")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_dockerfile_does_not_call_manifest_compiler(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_prepare_manifest,
+        mock_write_compose,
+        mock_build_image,
+        mock_find_port,
+        mock_ensure_dir,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_tool_type_id,
+    ) -> None:
+        """Legacy dockerfile type must not trigger manifest compilation."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_find_port.return_value = 12345
+        mock_ensure_dir.return_value = "/data/instances/test-instance"
+        mock_build_image.return_value = (0, "built", "")
+
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-df",
+            display_name="Legacy",
+            default_port=8080,
+            definition_type="dockerfile",
+            dockerfile_template="FROM alpine",
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        data = MagicMock()
+        data.tool_type_id = str(fake_tool_type_id)
+        data.display_name = None
+        data.clone_mode = "mount"
+        data.branch = None
+        data.new_branch = None
+        data.config_profile_id = None
+
+        await create_instance(
+            project_id=fake_project_id,
+            repo_id=fake_repo_id,
+            data=data,
+            user_id=fake_user_id,
+            session=mock_session,
+        )
+
+        mock_prepare_manifest.assert_not_called()
+
+
+class TestStartInstanceLegacyFallback:
+    """Legacy paths in start_instance must NOT call manifest compiler."""
+
+    @patch("src.api.tool_instances.wait_for_container_running")
+    @patch("src.api.tool_instances.execute_compose_command")
+    @patch("src.api.tool_instances.get_container_id")
+    @patch("src.api.tool_instances.get_container_name")
+    @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._sanitize_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_legacy_type_skips_manifest_flow(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_prepare_manifest,
+        mock_sanitize,
+        mock_connect_network,
+        mock_get_container_name,
+        mock_get_container_id,
+        mock_execute_compose,
+        mock_wait_container,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_instance_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'legacy', start_instance uses old flow."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_execute_compose.return_value = (0, "started", "")
+        mock_get_container_id.return_value = "abc123"
+        mock_get_container_name.return_value = "test-container"
+        mock_connect_network.return_value = True
+        mock_wait_container.return_value = {"success": True, "status": "running", "waited_seconds": 0.5}
+
+        instance = ToolInstance(
+            id=fake_instance_id,
+            name="legacy-instance",
+            repository_id=fake_repo_id,
+            tool_type_id=fake_tool_type_id,
+            compose_path="/data/instances/legacy-instance/docker-compose.yml",
+            status="stopped",
+            clone_mode="mount",
+            created_at=datetime.now(),
+            updated_at=datetime.now(),
+        )
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-tool",
+            display_name="Legacy Tool",
+            default_port=8080,
+            definition_type="legacy",
+            manifest_id=None,
+            dockerfile_template=None,
+            compose_template="services:\n  app:\n    image: nginx",
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolInstance and pk == fake_instance_id:
+                return instance
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        # Ensure compose file exists so the check passes
+        with patch("os.path.exists", return_value=True):
+            result = await start_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                instance_id=fake_instance_id,
+                data=None,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert result["status"] == "running"
+        mock_prepare_manifest.assert_not_called()
+        mock_execute_compose.assert_called_once()
+
+    @patch("src.api.tool_instances.wait_for_container_running")
+    @patch("src.api.tool_instances.execute_compose_command")
+    @patch("src.api.tool_instances.get_container_id")
+    @patch("src.api.tool_instances.get_container_name")
+    @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._sanitize_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_compose_type_skips_manifest_flow(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_prepare_manifest,
+        mock_sanitize,
+        mock_connect_network,
+        mock_get_container_name,
+        mock_get_container_id,
+        mock_execute_compose,
+        mock_wait_container,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_instance_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'compose', start_instance uses old flow."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_execute_compose.return_value = (0, "started", "")
+        mock_get_container_id.return_value = "abc123"
+        mock_get_container_name.return_value = "test-container"
+        mock_connect_network.return_value = True
+        mock_wait_container.return_value = {"success": True, "status": "running", "waited_seconds": 0.5}
+
+        instance = ToolInstance(
+            id=fake_instance_id,
+            name="compose-instance",
+            repository_id=fake_repo_id,
+            tool_type_id=fake_tool_type_id,
+            compose_path="/data/instances/compose-instance/docker-compose.yml",
+            status="stopped",
+            clone_mode="mount",
+            created_at=datetime.now(),
+            updated_at=datetime.now(),
+        )
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="compose-tool",
+            display_name="Compose Tool",
+            default_port=8080,
+            definition_type="compose",
+            manifest_id=None,
+            dockerfile_template=None,
+            compose_template="services:\n  app:\n    image: nginx",
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolInstance and pk == fake_instance_id:
+                return instance
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        with patch("os.path.exists", return_value=True):
+            result = await start_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                instance_id=fake_instance_id,
+                data=None,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert result["status"] == "running"
+        mock_prepare_manifest.assert_not_called()
+        mock_execute_compose.assert_called_once()
+
+    @patch("src.api.tool_instances.wait_for_container_running")
+    @patch("src.api.tool_instances.execute_compose_command")
+    @patch("src.api.tool_instances.get_container_id")
+    @patch("src.api.tool_instances.get_container_name")
+    @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._sanitize_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_dockerfile_type_skips_manifest_flow(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_prepare_manifest,
+        mock_sanitize,
+        mock_connect_network,
+        mock_get_container_name,
+        mock_get_container_id,
+        mock_execute_compose,
+        mock_wait_container,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_instance_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'dockerfile', start_instance uses old flow."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_execute_compose.return_value = (0, "started", "")
+        mock_get_container_id.return_value = "abc123"
+        mock_get_container_name.return_value = "test-container"
+        mock_connect_network.return_value = True
+        mock_wait_container.return_value = {"success": True, "status": "running", "waited_seconds": 0.5}
+
+        instance = ToolInstance(
+            id=fake_instance_id,
+            name="df-instance",
+            repository_id=fake_repo_id,
+            tool_type_id=fake_tool_type_id,
+            compose_path="/data/instances/df-instance/docker-compose.yml",
+            status="stopped",
+            clone_mode="mount",
+            created_at=datetime.now(),
+            updated_at=datetime.now(),
+        )
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="df-tool",
+            display_name="Dockerfile Tool",
+            default_port=8080,
+            definition_type="dockerfile",
+            manifest_id=None,
+            dockerfile_template="FROM alpine",
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolInstance and pk == fake_instance_id:
+                return instance
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        with patch("os.path.exists", return_value=True):
+            result = await start_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                instance_id=fake_instance_id,
+                data=None,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert result["status"] == "running"
+        mock_prepare_manifest.assert_not_called()
+        mock_execute_compose.assert_called_once()
+
+
+class TestStartInstanceManifestBranch:
+    """Manifest branch is taken ONLY when definition_type == 'manifest'."""
+
+    @patch("src.api.tool_instances.wait_for_container_running")
+    @patch("src.api.tool_instances.execute_compose_command")
+    @patch("src.api.tool_instances.get_container_id")
+    @patch("src.api.tool_instances.get_container_name")
+    @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._sanitize_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_manifest_type_calls_compiler(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_write_compose,
+        mock_prepare_manifest,
+        mock_sanitize,
+        mock_connect_network,
+        mock_get_container_name,
+        mock_get_container_id,
+        mock_execute_compose,
+        mock_wait_container,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_instance_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'manifest' and manifest_id is set, compiler runs."""
+        from src.models.tool_definition_manifest import ToolDefinitionManifest
+
+        manifest_id = uuid.uuid4()
+
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_execute_compose.return_value = (0, "started", "")
+        mock_get_container_id.return_value = "abc123"
+        mock_get_container_name.return_value = "test-container"
+        mock_connect_network.return_value = True
+        mock_wait_container.return_value = {"success": True, "status": "running", "waited_seconds": 0.5}
+        mock_prepare_manifest.return_value = (
+            "headquarter/test:latest",
+            "services:\n  app:\n    image: test",
+            {"name": "test-manifest"},
+        )
+
+        instance = ToolInstance(
+            id=fake_instance_id,
+            name="manifest-instance",
+            repository_id=fake_repo_id,
+            tool_type_id=fake_tool_type_id,
+            compose_path="/data/instances/manifest-instance/docker-compose.yml",
+            status="stopped",
+            clone_mode="mount",
+            created_at=datetime.now(),
+            updated_at=datetime.now(),
+        )
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="manifest-tool",
+            display_name="Manifest Tool",
+            default_port=8080,
+            definition_type="manifest",
+            manifest_id=manifest_id,
+            dockerfile_template=None,
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+        manifest_def = ToolDefinitionManifest(
+            id=manifest_id,
+            name="test-manifest",
+            display_name="Test Manifest",
+            interface_type="web",
+            manifest={"base_image": "alpine"},
+        )
+
+        async def _get(model, pk):
+            if model is ToolInstance and pk == fake_instance_id:
+                return instance
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            if model is ToolDefinitionManifest and pk == manifest_id:
+                return manifest_def
+            return None
+
+        mock_session.get.side_effect = _get
+
+        with patch("os.path.exists", return_value=True):
+            result = await start_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                instance_id=fake_instance_id,
+                data=None,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert result["status"] == "running"
+        mock_prepare_manifest.assert_called_once()
+        mock_execute_compose.assert_called_once()
@@ -896,6 +896,24 @@
        "node": ">=12"
      }
    },
+    "node_modules/@esbuild/netbsd-arm64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/netbsd-arm64/-/netbsd-arm64-0.28.0.tgz",
+      "integrity": "sha512-CR/RYotgtCKwtftMwJlUU7xCVNg3lMYZ0RzTmAHSfLCXw3NtZtNpswLEj/Kkf6kEL3Gw+BpOekRX0BYCtklhUw==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "netbsd"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
    "node_modules/@esbuild/netbsd-x64": {
      "version": "0.21.5",
      "resolved": "https://registry.npmjs.org/@esbuild/netbsd-x64/-/netbsd-x64-0.21.5.tgz",
@@ -913,6 +931,24 @@
        "node": ">=12"
      }
    },
+    "node_modules/@esbuild/openbsd-arm64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/openbsd-arm64/-/openbsd-arm64-0.28.0.tgz",
+      "integrity": "sha512-cXb5vApOsRsxsEl4mcZ1XY3D4DzcoMxR/nnc4IyqYs0rTI8ZKmW6kyyg+11Z8yvgMfAEldKzP7AdP64HnSC/6g==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "openbsd"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
    "node_modules/@esbuild/openbsd-x64": {
      "version": "0.21.5",
      "resolved": "https://registry.npmjs.org/@esbuild/openbsd-x64/-/openbsd-x64-0.21.5.tgz",
@@ -930,6 +966,24 @@
        "node": ">=12"
      }
    },
+    "node_modules/@esbuild/openharmony-arm64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/openharmony-arm64/-/openharmony-arm64-0.28.0.tgz",
+      "integrity": "sha512-FLGfyizszcef5C3YtoyQDACyg95+dndv79i2EekILBofh5wpCa1KuBqOWKrEHZg3zrL3t5ouE5jgr94vA+Wb2w==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "openharmony"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
    "node_modules/@esbuild/sunos-x64": {
      "version": "0.21.5",
      "resolved": "https://registry.npmjs.org/@esbuild/sunos-x64/-/sunos-x64-0.21.5.tgz",
@@ -1390,9 +1444,6 @@
        "arm64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1410,9 +1461,6 @@
        "arm64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1430,9 +1478,6 @@
        "ppc64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1450,9 +1495,6 @@
        "s390x"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1470,9 +1512,6 @@
        "x64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1490,9 +1529,6 @@
        "x64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1671,9 +1707,6 @@
        "arm"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1688,9 +1721,6 @@
        "arm"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1705,9 +1735,6 @@
        "arm64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1722,9 +1749,6 @@
        "arm64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1739,9 +1763,6 @@
        "loong64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1756,9 +1777,6 @@
        "loong64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1773,9 +1791,6 @@
        "ppc64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1790,9 +1805,6 @@
        "ppc64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1807,9 +1819,6 @@
        "riscv64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1824,9 +1833,6 @@
        "riscv64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1841,9 +1847,6 @@
        "s390x"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1858,9 +1861,6 @@
        "x64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -1875,9 +1875,6 @@
        "x64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MIT",
      "optional": true,
      "os": [
@@ -4360,9 +4357,6 @@
        "arm64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MPL-2.0",
      "optional": true,
      "os": [
@@ -4384,9 +4378,6 @@
        "arm64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MPL-2.0",
      "optional": true,
      "os": [
@@ -4408,9 +4399,6 @@
        "x64"
      ],
      "dev": true,
-      "libc": [
-        "glibc"
-      ],
      "license": "MPL-2.0",
      "optional": true,
      "os": [
@@ -4432,9 +4420,6 @@
        "x64"
      ],
      "dev": true,
-      "libc": [
-        "musl"
-      ],
      "license": "MPL-2.0",
      "optional": true,
      "os": [
@@ -6122,6 +6107,420 @@
        }
      }
    },
+    "node_modules/vitest/node_modules/@esbuild/aix-ppc64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/aix-ppc64/-/aix-ppc64-0.28.0.tgz",
+      "integrity": "sha512-lhRUCeuOyJQURhTxl4WkpFTjIsbDayJHih5kZC1giwE+MhIzAb7mEsQMqMf18rHLsrb5qI1tafG20mLxEWcWlA==",
+      "cpu": [
+        "ppc64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "aix"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/android-arm": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/android-arm/-/android-arm-0.28.0.tgz",
+      "integrity": "sha512-wqh0ByljabXLKHeWXYLqoJ5jKC4XBaw6Hk08OfMrCRd2nP2ZQ5eleDZC41XHyCNgktBGYMbqnrJKq/K/lzPMSQ==",
+      "cpu": [
+        "arm"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "android"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/android-arm64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/android-arm64/-/android-arm64-0.28.0.tgz",
+      "integrity": "sha512-+WzIXQOSaGs33tLEgYPYe/yQHf0WTU0X42Jca3y8NWMbUVhp7rUnw+vAsRC/QiDrdD31IszMrZy+qwPOPjd+rw==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "android"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/android-x64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/android-x64/-/android-x64-0.28.0.tgz",
+      "integrity": "sha512-+VJggoaKhk2VNNqVL7f6S189UzShHC/mR9EE8rDdSkdpN0KflSwWY/gWjDrNxxisg8Fp1ZCD9jLMo4m0OUfeUA==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "android"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/darwin-arm64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/darwin-arm64/-/darwin-arm64-0.28.0.tgz",
+      "integrity": "sha512-0T+A9WZm+bZ84nZBtk1ckYsOvyA3x7e2Acj1KdVfV4/2tdG4fzUp91YHx+GArWLtwqp77pBXVCPn2We7Letr0Q==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "darwin"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/darwin-x64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/darwin-x64/-/darwin-x64-0.28.0.tgz",
+      "integrity": "sha512-fyzLm/DLDl/84OCfp2f/XQ4flmORsjU7VKt8HLjvIXChJoFFOIL6pLJPH4Yhd1n1gGFF9mPwtlN5Wf82DZs+LQ==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "darwin"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/freebsd-arm64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/freebsd-arm64/-/freebsd-arm64-0.28.0.tgz",
+      "integrity": "sha512-l9GeW5UZBT9k9brBYI+0WDffcRxgHQD8ShN2Ur4xWq/NFzUKm3k5lsH4PdaRgb2w7mI9u61nr2gI2mLI27Nh3Q==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "freebsd"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/freebsd-x64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/freebsd-x64/-/freebsd-x64-0.28.0.tgz",
+      "integrity": "sha512-BXoQai/A0wPO6Es3yFJ7APCiKGc1tdAEOgeTNy3SsB491S3aHn4S4r3e976eUnPdU+NbdtmBuLncYir2tMU9Nw==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "freebsd"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-arm": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-arm/-/linux-arm-0.28.0.tgz",
+      "integrity": "sha512-CjaaREJagqJp7iTaNQjjidaNbCKYcd4IDkzbwwxtSvjI7NZm79qiHc8HqciMddQ6CKvJT6aBd8lO9kN/ZudLlw==",
+      "cpu": [
+        "arm"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-arm64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-arm64/-/linux-arm64-0.28.0.tgz",
+      "integrity": "sha512-RVyzfb3FWsGA55n6WY0MEIEPURL1FcbhFE6BffZEMEekfCzCIMtB5yyDcFnVbTnwk+CLAgTujmV/Lgvih56W+A==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-ia32": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-ia32/-/linux-ia32-0.28.0.tgz",
+      "integrity": "sha512-KBnSTt1kxl9x70q+ydterVdl+Cn0H18ngRMRCEQfrbqdUuntQQ0LoMZv47uB97NljZFzY6HcfqEZ2SAyIUTQBQ==",
+      "cpu": [
+        "ia32"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-loong64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-loong64/-/linux-loong64-0.28.0.tgz",
+      "integrity": "sha512-zpSlUce1mnxzgBADvxKXX5sl8aYQHo2ezvMNI8I0lbblJtp8V4odlm3Yzlj7gPyt3T8ReksE6bK+pT3WD+aJRg==",
+      "cpu": [
+        "loong64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-mips64el": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-mips64el/-/linux-mips64el-0.28.0.tgz",
+      "integrity": "sha512-2jIfP6mmjkdmeTlsX/9vmdmhBmKADrWqN7zcdtHIeNSCH1SqIoNI63cYsjQR8J+wGa4Y5izRcSHSm8K3QWmk3w==",
+      "cpu": [
+        "mips64el"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-ppc64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-ppc64/-/linux-ppc64-0.28.0.tgz",
+      "integrity": "sha512-bc0FE9wWeC0WBm49IQMPSPILRocGTQt3j5KPCA8os6VprfuJ7KD+5PzESSrJ6GmPIPJK965ZJHTUlSA6GNYEhg==",
+      "cpu": [
+        "ppc64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-riscv64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-riscv64/-/linux-riscv64-0.28.0.tgz",
+      "integrity": "sha512-SQPZOwoTTT/HXFXQJG/vBX8sOFagGqvZyXcgLA3NhIqcBv1BJU1d46c0rGcrij2B56Z2rNiSLaZOYW5cUk7yLQ==",
+      "cpu": [
+        "riscv64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-s390x": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-s390x/-/linux-s390x-0.28.0.tgz",
+      "integrity": "sha512-SCfR0HN8CEEjnYnySJTd2cw0k9OHB/YFzt5zgJEwa+wL/T/raGWYMBqwDNAC6dqFKmJYZoQBRfHjgwLHGSrn3Q==",
+      "cpu": [
+        "s390x"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/linux-x64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/linux-x64/-/linux-x64-0.28.0.tgz",
+      "integrity": "sha512-us0dSb9iFxIi8srnpl931Nvs65it/Jd2a2K3qs7fz2WfGPHqzfzZTfec7oxZJRNPXPnNYZtanmRc4AL/JwVzHQ==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "linux"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/netbsd-x64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/netbsd-x64/-/netbsd-x64-0.28.0.tgz",
+      "integrity": "sha512-nU1yhmYutL+fQ71Kxnhg8uEOdC0pwEW9entHykTgEbna2pw2dkbFSMeqjjyHZoCmt8SBkOSvV+yNmm94aUrrqw==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "netbsd"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/openbsd-x64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/openbsd-x64/-/openbsd-x64-0.28.0.tgz",
+      "integrity": "sha512-8wZM2qqtv9UP3mzy7HiGYNH/zjTA355mpeuA+859TyR+e+Tc08IHYpLJuMsfpDJwoLo1ikIJI8jC3GFjnRClzA==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "openbsd"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/sunos-x64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/sunos-x64/-/sunos-x64-0.28.0.tgz",
+      "integrity": "sha512-1ZgjUoEdHZZl/YlV76TSCz9Hqj9h9YmMGAgAPYd+q4SicWNX3G5GCyx9uhQWSLcbvPW8Ni7lj4gDa1T40akdlw==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "sunos"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/win32-arm64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/win32-arm64/-/win32-arm64-0.28.0.tgz",
+      "integrity": "sha512-Q9StnDmQ/enxnpxCCLSg0oo4+34B9TdXpuyPeTedN/6+iXBJ4J+zwfQI28u/Jl40nOYAxGoNi7mFP40RUtkmUA==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "win32"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/win32-ia32": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/win32-ia32/-/win32-ia32-0.28.0.tgz",
+      "integrity": "sha512-zF3ag/gfiCe6U2iczcRzSYJKH1DCI+ByzSENHlM2FcDbEeo5Zd2C86Aq0tKUYAJJ1obRP84ymxIAksZUcdztHA==",
+      "cpu": [
+        "ia32"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "win32"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/vitest/node_modules/@esbuild/win32-x64": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/@esbuild/win32-x64/-/win32-x64-0.28.0.tgz",
+      "integrity": "sha512-pEl1bO9mfAmIC+tW5btTmrKaujg3zGtUmWNdCw/xs70FBjwAL3o9OEKNHvNmnyylD6ubxUERiEhdsL0xBQ9efw==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "win32"
+      ],
+      "peer": true,
+      "engines": {
+        "node": ">=18"
+      }
+    },
    "node_modules/vitest/node_modules/@vitest/mocker": {
      "version": "4.1.6",
      "resolved": "https://registry.npmjs.org/@vitest/mocker/-/mocker-4.1.6.tgz",
@@ -6149,6 +6548,50 @@
        }
      }
    },
+    "node_modules/vitest/node_modules/esbuild": {
+      "version": "0.28.0",
+      "resolved": "https://registry.npmjs.org/esbuild/-/esbuild-0.28.0.tgz",
+      "integrity": "sha512-sNR9MHpXSUV/XB4zmsFKN+QgVG82Cc7+/aaxJ8Adi8hyOac+EXptIp45QBPaVyX3N70664wRbTcLTOemCAnyqw==",
+      "dev": true,
+      "hasInstallScript": true,
+      "license": "MIT",
+      "optional": true,
+      "peer": true,
+      "bin": {
+        "esbuild": "bin/esbuild"
+      },
+      "engines": {
+        "node": ">=18"
+      },
+      "optionalDependencies": {
+        "@esbuild/aix-ppc64": "0.28.0",
+        "@esbuild/android-arm": "0.28.0",
+        "@esbuild/android-arm64": "0.28.0",
+        "@esbuild/android-x64": "0.28.0",
+        "@esbuild/darwin-arm64": "0.28.0",
+        "@esbuild/darwin-x64": "0.28.0",
+        "@esbuild/freebsd-arm64": "0.28.0",
+        "@esbuild/freebsd-x64": "0.28.0",
+        "@esbuild/linux-arm": "0.28.0",
+        "@esbuild/linux-arm64": "0.28.0",
+        "@esbuild/linux-ia32": "0.28.0",
+        "@esbuild/linux-loong64": "0.28.0",
+        "@esbuild/linux-mips64el": "0.28.0",
+        "@esbuild/linux-ppc64": "0.28.0",
+        "@esbuild/linux-riscv64": "0.28.0",
+        "@esbuild/linux-s390x": "0.28.0",
+        "@esbuild/linux-x64": "0.28.0",
+        "@esbuild/netbsd-arm64": "0.28.0",
+        "@esbuild/netbsd-x64": "0.28.0",
+        "@esbuild/openbsd-arm64": "0.28.0",
+        "@esbuild/openbsd-x64": "0.28.0",
+        "@esbuild/openharmony-arm64": "0.28.0",
+        "@esbuild/sunos-x64": "0.28.0",
+        "@esbuild/win32-arm64": "0.28.0",
+        "@esbuild/win32-ia32": "0.28.0",
+        "@esbuild/win32-x64": "0.28.0"
+      }
+    },
    "node_modules/vitest/node_modules/picomatch": {
      "version": "4.0.4",
      "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.4.tgz",
@@ -1,4 +1,4 @@
-import axios from "axios";
+import axios, { type AxiosRequestConfig } from "axios";

 const BASE_URL = import.meta.env.VITE_API_BASE_URL ?? "http://localhost:8000";

@@ -14,13 +14,38 @@ export const shouldSkipAuthRedirect = (path: string): boolean => {
  return path.startsWith("/login") || path.startsWith("/auth");
 };

+// Retry config for transient network errors
+const MAX_RETRIES = 2;
+const RETRY_DELAY_MS = 1000;
+
+// Track retry count per request
+const retryCount = new WeakMap<AxiosRequestConfig, number>();
+
 apiClient.interceptors.response.use(
  (response) => response,
-  (error) => {
+  async (error) => {
    const status = error?.response?.status;
    if (status === 401 && !shouldSkipAuthRedirect(window.location.pathname)) {
      window.location.assign(`${BASE_URL}/auth/login`);
+      return Promise.reject(error);
    }
+
+    // Retry on transient network errors (ERR_NETWORK_CHANGED, etc.)
+    const isNetworkError = !error.response && error.message?.includes("Network");
+    const isRetryable = isNetworkError || status >= 502; // 502 Bad Gateway, 503 Service Unavailable, 504 Gateway Timeout
+    
+    if (isRetryable) {
+      const config = error.config;
+      const currentRetry = retryCount.get(config) || 0;
+      
+      if (currentRetry < MAX_RETRIES) {
+        retryCount.set(config, currentRetry + 1);
+        // Wait before retrying
+        await new Promise(resolve => setTimeout(resolve, RETRY_DELAY_MS * (currentRetry + 1)));
+        return apiClient(config);
+      }
+    }
+
    return Promise.reject(error);
  }
 );
@@ -0,0 +1,156 @@
+import { apiClient } from "./client";
+
+export interface ConfigProfile {
+  id: string;
+  user_id: string;
+  name: string;
+  description: string | null;
+  project_id: string | null;
+  tool_type_id: string | null;
+  env_vars: Record<string, string>;
+  runtime_hints: Record<string, unknown>;
+  mounts: ConfigProfileMount[];
+  git_mounts: GitMount[];
+  files: Record<string, string>;
+  is_default: boolean;
+  includes: ConfigProfileInclude[];
+  created_at: string;
+  updated_at: string;
+}
+
+export interface ConfigProfileMount {
+  target: string;
+  mode: "ro" | "rw";
+  files: Record<string, string>;
+}
+
+export interface GitMount {
+  remote_url: string;
+  source_path: string;
+  target_path: string;
+  branch?: string;
+}
+
+export interface ConfigProfileInclude {
+  id: string;
+  included_profile_id: string;
+  order_index: number;
+}
+
+export interface ResolvedProfile {
+  profile_id: string;
+  profile_name: string;
+  env_vars: Record<string, string>;
+  runtime_hints: Record<string, unknown>;
+  mounts: ResolvedMount[];
+  git_mounts: GitMount[];
+  files: Record<string, string>;
+  overrides: {
+    env_vars: Record<string, string>;
+    runtime_hints: Record<string, string>;
+    files: Record<string, string>;
+    mounts: Record<string, string>;
+  };
+  included_profiles: Array<{ id: string; name: string }>;
+}
+
+export interface ResolvedMount {
+  target: string;
+  mode: "ro" | "rw";
+  files: Record<string, string>;
+  overridden_files: Record<string, string>;
+}
+
+export interface CreateConfigProfileRequest {
+  name: string;
+  description?: string;
+  project_id?: string;
+  tool_type_id?: string;
+  env_vars?: Record<string, string>;
+  runtime_hints?: Record<string, unknown>;
+  mounts?: ConfigProfileMount[];
+  git_mounts?: GitMount[];
+  files?: Record<string, string>;
+  is_default?: boolean;
+}
+
+export interface UpdateConfigProfileRequest {
+  name?: string;
+  description?: string;
+  project_id?: string;
+  tool_type_id?: string;
+  env_vars?: Record<string, string>;
+  runtime_hints?: Record<string, unknown>;
+  mounts?: ConfigProfileMount[];
+  git_mounts?: GitMount[];
+  files?: Record<string, string>;
+  is_default?: boolean;
+}
+
+export interface UpdateIncludesRequest {
+  includes: string[];
+}
+
+export const listConfigProfiles = async (
+  projectId?: string,
+  toolTypeId?: string
+): Promise<ConfigProfile[]> => {
+  const response = await apiClient.get<ConfigProfile[]>("/config-profiles", {
+    params: { project_id: projectId, tool_type_id: toolTypeId },
+  });
+  return response.data;
+};
+
+export const getConfigProfile = async (id: string): Promise<ConfigProfile> => {
+  const response = await apiClient.get<ConfigProfile>(`/config-profiles/${id}`);
+  return response.data;
+};
+
+export const createConfigProfile = async (
+  data: CreateConfigProfileRequest
+): Promise<ConfigProfile> => {
+  const response = await apiClient.post<ConfigProfile>("/config-profiles", data);
+  return response.data;
+};
+
+export const updateConfigProfile = async (
+  id: string,
+  data: UpdateConfigProfileRequest
+): Promise<ConfigProfile> => {
+  const response = await apiClient.put<ConfigProfile>(`/config-profiles/${id}`, data);
+  return response.data;
+};
+
+export const deleteConfigProfile = async (id: string): Promise<void> => {
+  await apiClient.delete(`/config-profiles/${id}`);
+};
+
+export const updateProfileIncludes = async (
+  id: string,
+  data: UpdateIncludesRequest
+): Promise<ConfigProfile> => {
+  const response = await apiClient.put<ConfigProfile>(
+    `/config-profiles/${id}/includes`,
+    data
+  );
+  return response.data;
+};
+
+export const previewConfigProfile = async (
+  id: string
+): Promise<ResolvedProfile> => {
+  const response = await apiClient.get<ResolvedProfile>(
+    `/config-profiles/${id}/preview`
+  );
+  return response.data;
+};
+
+export const resolveDefaultProfile = async (
+  projectId: string,
+  toolTypeId: string
+): Promise<{ profile_id: string | null; profile_name: string | null }> => {
+  const response = await apiClient.get("/config-profiles/defaults/resolve", {
+    params: { project_id: projectId, tool_type_id: toolTypeId },
+  });
+  return response.data;
+};
@@ -8,6 +8,7 @@ export interface GitRepository {
  owner_id: string;
  is_mirror: boolean;
  remote_url: string | null;
+  ssh_key_id: string | null;
  last_push: string | null;
  created_at: string | null;
 }
@@ -16,6 +17,7 @@ export interface GitRepositoryCreate {
  name: string;
  remote_url?: string;
  force_original_url?: boolean;
+  ssh_key_id?: string;
 }

 export interface URLParseResult {
@@ -29,12 +31,24 @@ export interface URLParseResult {
 }

 export async function parseGitUrl(url: string): Promise<URLParseResult> {
-  const response = await apiClient.post("/projects/repositories/parse-url", { url });
+  const response = await apiClient.post("/repositories/parse-url", { url });
  return response.data;
 }

-export async function listRepositories(projectId: string): Promise<GitRepository[]> {
-  const response = await apiClient.get(`/projects/${projectId}/repositories`);
+export async function listRepositories(projectId?: string): Promise<GitRepository[]> {
+  if (projectId) {
+    const response = await apiClient.get<GitRepository[]>(
+      `/projects/${projectId}/repositories`
+    );
+    return response.data;
+  }
+  // List all user repositories (including external)
+  const response = await apiClient.get<GitRepository[]>("/repositories");
+  return response.data;
+}
+
+export async function listAllUserRepositories(): Promise<GitRepository[]> {
+  const response = await apiClient.get<GitRepository[]>("/repositories");
  return response.data;
 }

@@ -46,10 +60,50 @@ export async function createRepository(
  return response.data;
 }

+export async function createExternalRepository(
+  data: GitRepositoryCreate
+): Promise<GitRepository> {
+  const response = await apiClient.post<GitRepository>("/repositories", data);
+  return response.data;
+}
+
 export async function deleteRepository(projectId: string, repoId: string): Promise<void> {
  await apiClient.delete(`/projects/${projectId}/repositories/${repoId}`);
 }

+export async function updateRepositorySshKey(
+  projectId: string,
+  repoId: string,
+  sshKeyId: string | null
+): Promise<GitRepository> {
+  const response = await apiClient.patch(
+    `/projects/${projectId}/repositories/${repoId}/ssh-key`,
+    { ssh_key_id: sshKeyId }
+  );
+  return response.data;
+}
+
+export interface Branch {
+  name: string;
+  is_default: boolean;
+  last_commit: string | null;
+}
+
+export interface BranchesResponse {
+  branches: Branch[];
+  default_branch: string;
+}
+
+export async function listRepositoryBranches(
+  projectId: string,
+  repoId: string
+): Promise<BranchesResponse> {
+  const response = await apiClient.get(
+    `/projects/${projectId}/repositories/${repoId}/branches`
+  );
+  return response.data;
+}
+
 export interface CommitHistoryEntry {
  hash: string;
  short_hash: string;
@@ -1,3 +1,4 @@
+import { AxiosError } from "axios";
 import { apiClient } from "./client";

 export interface ToolInstance {
@@ -10,6 +11,7 @@ export interface ToolInstance {
  status: string;
  url: string | null;
  port: number | null;
+  selected_config_profile_id: string | null;
  created_at: string;
 }

@@ -25,6 +27,11 @@ export interface Session {
  project_id: string;
  status: string;
  url: string | null;
+  container_status?: string;
+  probe_status?: string;
+  clone_mode?: string;
+  branch?: string | null;
+  created_at?: string;
 }

 export async function listInstances(
@@ -41,13 +48,21 @@ export async function createInstance(
  projectId: string,
  repoId: string,
  toolTypeId: string,
-  displayName?: string
+  displayName?: string,
+  cloneMode?: string,
+  branch?: string,
+  newBranch?: string,
+  configProfileId?: string
 ): Promise<ToolInstance> {
  const response = await apiClient.post(
    `/projects/${projectId}/repositories/${repoId}/instances`,
    {
      tool_type_id: toolTypeId,
      display_name: displayName,
+      clone_mode: cloneMode || "mount",
+      branch: branch || undefined,
+      new_branch: newBranch || undefined,
+      config_profile_id: configProfileId,
    }
  );
  return response.data;
@@ -56,12 +71,25 @@ export async function createInstance(
 export async function startInstance(
  projectId: string,
  repoId: string,
-  instanceId: string
+  instanceId: string,
+  configProfileId?: string,
+  retries = 2
 ): Promise<{ status: string; url?: string }> {
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/start`
-  );
-  return response.data;
+  try {
+    const response = await apiClient.post(
+      `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/start`,
+      { config_profile_id: configProfileId }
+    );
+    return response.data;
+  } catch (error) {
+    // Retry on network errors (e.g. Docker creating network interfaces)
+    const axiosError = error as AxiosError;
+    if (retries > 0 && !axiosError.response) {
+      await new Promise((r) => setTimeout(r, 1500));
+      return startInstance(projectId, repoId, instanceId, configProfileId, retries - 1);
+    }
+    throw error;
+  }
 }

 export async function stopInstance(
@@ -78,21 +106,36 @@ export async function stopInstance(
 export async function restartInstance(
  projectId: string,
  repoId: string,
-  instanceId: string
+  instanceId: string,
+  configProfileId?: string,
+  retries = 2
 ): Promise<{ status: string; url?: string }> {
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/restart`
-  );
-  return response.data;
+  try {
+    const response = await apiClient.post(
+      `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/restart`,
+      { config_profile_id: configProfileId }
+    );
+    return response.data;
+  } catch (error) {
+    // Retry on network errors (e.g. Docker creating network interfaces)
+    const axiosError = error as AxiosError;
+    if (retries > 0 && !axiosError.response) {
+      await new Promise((r) => setTimeout(r, 1500));
+      return restartInstance(projectId, repoId, instanceId, configProfileId, retries - 1);
+    }
+    throw error;
+  }
 }

 export async function deleteInstance(
  projectId: string,
  repoId: string,
-  instanceId: string
+  instanceId: string,
+  force?: boolean
 ): Promise<void> {
  await apiClient.delete(
-    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}`
+    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}`,
+    { params: { force } }
  );
 }

@@ -101,11 +144,23 @@ export async function getUserSessions(): Promise<Session[]> {
  return response.data.sessions;
 }

+export interface InstanceHealth {
+  healthy: boolean;
+  container_status: string;
+  container_health: string | null;
+  container_exit_code: number | null;
+  tunnel_status: string;
+  tunnel_status_code: number | null;
+  probe_status: string;
+  last_probe_output: string | null;
+  error: string | null;
+}
+
 export async function checkInstanceHealth(
  projectId: string,
  repoId: string,
  instanceId: string
-): Promise<{ healthy: boolean; status_code: number | null; error?: string }> {
+): Promise<InstanceHealth> {
  const response = await apiClient.get(
    `/projects/${projectId}/repositories/${repoId}/instances/${instanceId}/health`
  );
@@ -24,3 +24,30 @@ export async function createSSHKey(data: SSHKeyCreate): Promise<SSHKey> {
 export async function deleteSSHKey(keyId: string): Promise<void> {
  await apiClient.delete(`/ssh-keys/${keyId}`);
 }
+
+export interface SignPayloadRequest {
+  payload: string;
+}
+
+export interface SignatureResponse {
+  signature: string;
+}
+
+export interface VerifySignatureRequest {
+  payload: string;
+  signature: string;
+}
+
+export interface VerifySignatureResponse {
+  valid: boolean;
+}
+
+export async function signPayload(keyId: string, data: SignPayloadRequest): Promise<SignatureResponse> {
+  const response = await apiClient.post<SignatureResponse>(`/ssh-keys/${keyId}/sign`, data);
+  return response.data;
+}
+
+export async function verifySignature(keyId: string, data: VerifySignatureRequest): Promise<VerifySignatureResponse> {
+  const response = await apiClient.post<VerifySignatureResponse>(`/ssh-keys/${keyId}/verify`, data);
+  return response.data;
+}
@@ -0,0 +1,108 @@
+import { apiClient } from "./client";
+
+export interface ToolDefinitionManifest {
+	id: string;
+	name: string;
+	display_name: string;
+	description: string | null;
+	category: string | null;
+	interface_type: string;
+	base_image: string | null;
+	base_definition_id: string | null;
+	base_version: string;
+	manifest: Record<string, unknown>;
+	dockerfile_cache: string | null;
+	compose_cache: string | null;
+	version: string;
+	is_base: boolean;
+	created_at: string;
+	updated_at: string;
+}
+
+export interface CreateToolDefinitionRequest {
+	name: string;
+	display_name: string;
+	description?: string;
+	category?: string;
+	interface_type?: string;
+	base_image?: string;
+	base_definition_id?: string;
+	base_version?: string;
+	manifest: Record<string, unknown>;
+}
+
+export interface UpdateToolDefinitionRequest {
+	display_name?: string;
+	description?: string;
+	category?: string;
+	manifest?: Record<string, unknown>;
+	base_version?: string;
+}
+
+export interface CompileResult {
+	id: string;
+	name: string;
+	dockerfile: string;
+	entrypoint: string;
+	compose: string;
+	image_tag: string;
+}
+
+export const listToolDefinitions = async (
+	includeBases = true,
+): Promise<ToolDefinitionManifest[]> => {
+	const response = await apiClient.get<{
+		definitions: ToolDefinitionManifest[];
+	}>("/tool-definitions", {
+		params: { include_bases: includeBases },
+	});
+	return response.data.definitions;
+};
+
+export const getToolDefinition = async (
+	id: string,
+): Promise<ToolDefinitionManifest> => {
+	const response = await apiClient.get<ToolDefinitionManifest>(
+		`/tool-definitions/${id}`,
+	);
+	return response.data;
+};
+
+export const createToolDefinition = async (
+	data: CreateToolDefinitionRequest,
+): Promise<ToolDefinitionManifest> => {
+	const response = await apiClient.post<ToolDefinitionManifest>(
+		"/tool-definitions",
+		data,
+	);
+	return response.data;
+};
+
+export const updateToolDefinition = async (
+	id: string,
+	data: UpdateToolDefinitionRequest,
+): Promise<ToolDefinitionManifest> => {
+	const response = await apiClient.put<ToolDefinitionManifest>(
+		`/tool-definitions/${id}`,
+		data,
+	);
+	return response.data;
+};
+
+export const deleteToolDefinition = async (
+	id: string,
+): Promise<{ status: string; id: string }> => {
+	const response = await apiClient.delete<{ status: string; id: string }>(
+		`/tool-definitions/${id}`,
+	);
+	return response.data;
+};
+
+export const compileToolDefinition = async (
+	id: string,
+): Promise<CompileResult> => {
+	const response = await apiClient.post<CompileResult>(
+		`/tool-definitions/${id}/compile`,
+	);
+	return response.data;
+};
@@ -1,85 +1,102 @@
 import { apiClient } from "./client";

 export interface ReadinessProbe {
-  command: string;
-  timeout: number;
-  interval: number;
+	command: string;
+	timeout: number;
+	interval: number;
 }

 export interface ToolType {
-  id: string;
-  name: string;
-  display_name: string;
-  description: string | null;
-  category: string;
-  interfaces: string[];
-  default_port: number | null;
-  definition_type: 'compose' | 'dockerfile';
-  compose_template: string | null;
-  dockerfile_template: string | null;
-  build_context: Record<string, string> | null;
-  readiness_probe: ReadinessProbe | null;
-  required_variables: string[];
-  is_builtin: boolean;
-  created_by_id: string | null;
-  created_at: string;
-  updated_at: string;
+	id: string;
+	name: string;
+	display_name: string;
+	description: string | null;
+	category: string;
+	interface_type: string;
+	requires_port: boolean;
+	default_port: number | null;
+	definition_type: "compose" | "dockerfile" | "manifest";
+	manifest_id: string | null;
+	compose_template: string | null;
+	dockerfile_template: string | null;
+	build_context: Record<string, string> | null;
+	readiness_probe: ReadinessProbe | null;
+	startup_command: string | null;
+	required_variables: string[];
+	created_by_id: string | null;
+	created_at: string;
+	updated_at: string;
 }

 export interface CreateToolTypeRequest {
-  name: string;
-  display_name: string;
-  description?: string;
-  category?: string;
-  interfaces?: string[];
-  default_port: number;
-  definition_type?: 'compose' | 'dockerfile';
-  compose_template?: string;
-  dockerfile_template?: string;
-  build_context?: Record<string, string>;
-  readiness_probe?: ReadinessProbe;
-  required_variables: string[];
+	name: string;
+	display_name: string;
+	description?: string;
+	category?: string;
+	interface_type?: string;
+	requires_port?: boolean;
+	default_port: number;
+	definition_type?: "compose" | "dockerfile" | "manifest";
+	manifest_id?: string;
+	compose_template?: string;
+	dockerfile_template?: string;
+	build_context?: Record<string, string>;
+	readiness_probe?: ReadinessProbe;
+	startup_command?: string;
+	required_variables: string[];
 }

 export interface UpdateToolTypeRequest {
-  display_name?: string;
-  description?: string;
-  category?: string;
-  interfaces?: string[];
-  default_port?: number;
-  definition_type?: 'compose' | 'dockerfile';
-  compose_template?: string;
-  dockerfile_template?: string;
-  build_context?: Record<string, string>;
-  readiness_probe?: ReadinessProbe;
-  required_variables?: string[];
+	display_name?: string;
+	description?: string;
+	category?: string;
+	interface_type?: string;
+	requires_port?: boolean;
+	default_port?: number;
+	definition_type?: "compose" | "dockerfile" | "manifest";
+	manifest_id?: string;
+	compose_template?: string;
+	dockerfile_template?: string;
+	build_context?: Record<string, string>;
+	readiness_probe?: ReadinessProbe;
+	startup_command?: string;
+	required_variables?: string[];
 }

 export const listToolTypes = async (): Promise<ToolType[]> => {
-  const response = await apiClient.get<ToolType[]>("/tool-types");
-  return response.data;
+	const response = await apiClient.get<ToolType[]>("/tool-types");
+	return response.data;
 };

 export const getToolType = async (id: string): Promise<ToolType> => {
-  const response = await apiClient.get<ToolType>(`/tool-types/${id}`);
-  return response.data;
+	const response = await apiClient.get<ToolType>(`/tool-types/${id}`);
+	return response.data;
 };

-export const createToolType = async (data: CreateToolTypeRequest): Promise<ToolType> => {
-  const response = await apiClient.post<ToolType>("/tool-types", data);
-  return response.data;
+export const createToolType = async (
+	data: CreateToolTypeRequest,
+): Promise<ToolType> => {
+	const response = await apiClient.post<ToolType>("/tool-types", data);
+	return response.data;
 };

-export const updateToolType = async (id: string, data: UpdateToolTypeRequest): Promise<ToolType> => {
-  const response = await apiClient.put<ToolType>(`/tool-types/${id}`, data);
-  return response.data;
+export const updateToolType = async (
+	id: string,
+	data: UpdateToolTypeRequest,
+): Promise<ToolType> => {
+	const response = await apiClient.put<ToolType>(`/tool-types/${id}`, data);
+	return response.data;
 };

 export const deleteToolType = async (id: string): Promise<void> => {
-  await apiClient.delete(`/tool-types/${id}`);
+	await apiClient.delete(`/tool-types/${id}`);
 };

-export const validateToolType = async (id: string): Promise<{ valid: boolean; errors?: string[] }> => {
-  const response = await apiClient.get<{ valid: boolean; errors?: string[] }>(`/tool-types/${id}/validate`);
-  return response.data;
+export const validateToolType = async (
+	id: string,
+): Promise<{ valid: boolean; errors?: string[] }> => {
+	const response = await apiClient.get<{ valid: boolean; errors?: string[] }>(
+		`/tool-types/${id}/validate`,
+	);
+	return response.data;
 };
@@ -1,18 +1,22 @@
 import { useCallback, useEffect } from "react";
-import { Link, NavLink, Outlet } from "react-router-dom";
+import { Link, NavLink, Outlet, useLocation } from "react-router-dom";

 import { getUserSessions } from "../api/sessions";
 import type { Session } from "../api/sessions";
 import { useTheme } from "../hooks/use-theme";
 import { useAuth } from "../state/auth";
 import { useSessions } from "../state/sessions";
+import { useMobileViewport } from "../hooks/use-mobile-viewport";
 import { Icon } from "./icon";
+import { MobileNav } from "./mobile-nav";
 import type { IconName } from "../utils/icons";

-const NAV_ITEMS: { to: string; label: string; icon: IconName }[] = [
+const NAV_ITEMS: { to: string; label: string; icon: IconName; badge?: "sessions" }[] = [
  { to: "/", label: "Home", icon: "dashboard" },
+  { to: "/sessions", label: "Sessions", icon: "terminal", badge: "sessions" },
  { to: "/projects", label: "Projects", icon: "projects" },
  { to: "/tool-workshop", label: "Tool Workshop", icon: "settings" },
+  { to: "/config-profiles", label: "Config Profiles", icon: "folder" },
  { to: "/settings", label: "Settings", icon: "settings" }
 ];

@@ -38,6 +42,9 @@ export const AppShell = () => {
  useTheme();
  const { user, logout } = useAuth();
  const { sessions, setAllSessions } = useSessions();
+  const location = useLocation();
+  const isMobile = useMobileViewport();
+  const isMobileTerminal = isMobile && location.pathname.includes("/instances/") && location.pathname.includes("/terminal");

  const loadSessions = useCallback(async () => {
    try {
@@ -50,13 +57,21 @@ export const AppShell = () => {

  useEffect(() => {
    void loadSessions();
-    // Poll every 10 seconds
+    // Poll every 30 seconds (reduced from 10s to avoid ERR_NETWORK_CHANGED from Docker network changes)
    const interval = setInterval(() => {
      void loadSessions();
-    }, 10000);
+    }, 30000);
    return () => clearInterval(interval);
  }, [loadSessions]);

+  if (isMobileTerminal) {
+    return (
+      <div className="shell mobile-terminal-shell">
+        <Outlet />
+      </div>
+    );
+  }
+
  return (
    <div className="shell">
      <header className="shell-header">
@@ -81,41 +96,46 @@ export const AppShell = () => {
      </header>

      <div className="shell-body">
-        <aside className="shell-nav" aria-label="Primary navigation">
-          {NAV_ITEMS.map((item) => {
-            const isHome = item.to === "/";
-            const activeCount = sessions.filter((s) => s.status === "running").length;
-            return (
-              <NavLink
-                key={item.to}
-                to={item.to}
-                className={({ isActive }) => (isActive ? "nav-item nav-item-active" : "nav-item")}
-                end={item.to === "/"}
-              >
-                <Icon name={item.icon} size="sm" />
-                {item.label}
-                {isHome && activeCount > 0 && (
-                  <span className="nav-badge">{activeCount}</span>
-                )}
-              </NavLink>
-            );
-          })}
-          
-          {sessions.length > 0 && (
-            <>
-              <div className="nav-divider" />
-              <div className="nav-section-title">Live sessions</div>
-              {sessions.map((session) => (
-                <SessionItem key={session.id} session={session} />
-              ))}
-            </>
-          )}
-        </aside>
+        {!isMobile && (
+          <aside className="shell-nav" aria-label="Primary navigation">
+            {NAV_ITEMS.map((item) => {
+              const activeCount = sessions.filter((s) => s.status === "running").length;
+              return (
+                <NavLink
+                  key={item.to}
+                  to={item.to}
+                  className={({ isActive }) => (isActive ? "nav-item nav-item-active" : "nav-item")}
+                  end={item.to === "/"}
+                >
+                  <Icon name={item.icon} size="sm" />
+                  {item.label}
+                  {item.badge === "sessions" && activeCount > 0 && (
+                    <span className="nav-badge">{activeCount}</span>
+                  )}
+                </NavLink>
+              );
+            })}
+            
+            {sessions.length > 0 && (
+              <>
+                <div className="nav-divider" />
+                <div className="nav-section-title">Live sessions</div>
+                {sessions.map((session) => (
+                  <SessionItem key={session.id} session={session} />
+                ))}
+              </>
+            )}
+          </aside>
+        )}

-        <main className="shell-content">
+        <main className={`shell-content ${isMobile ? "mobile" : ""}`}>
          <Outlet />
        </main>
      </div>
+
+      {isMobile && (
+        <MobileNav sessionCount={sessions.filter((s) => s.status === "running").length} />
+      )}
    </div>
  );
 };
@@ -0,0 +1,521 @@
+import { useState, useEffect } from "react";
+import { Icon } from "./icon";
+import { createInstance, startInstance, type ToolInstance } from "../api/sessions";
+import type { Project } from "../types";
+import { listRepositoryBranches, type GitRepository, type Branch } from "../api/git_repositories";
+import type { ToolType } from "../api/tool_types";
+import { listSSHKeys, type SSHKey } from "../api/ssh_keys";
+import { listConfigProfiles, type ConfigProfile } from "../api/config_profiles";
+
+interface CreateSessionFormProps {
+  projects: Project[];
+  repositories: GitRepository[];
+  toolTypes: ToolType[];
+  fixedProjectId?: string;
+  fixedRepoId?: string;
+  projectName?: string;
+  repoName?: string;
+  showCloneMode?: boolean;
+  showFixedFields?: boolean;
+  onProjectChange?: (projectId: string) => void;
+  onSuccess?: (instance: ToolInstance) => void;
+  onCancel?: () => void;
+  submitLabel?: string;
+  className?: string;
+}
+
+export const CreateSessionForm = ({
+  projects,
+  repositories,
+  toolTypes,
+  fixedProjectId,
+  fixedRepoId,
+  projectName,
+  repoName,
+  showCloneMode = true,
+  showFixedFields = true,
+  onProjectChange,
+  onSuccess,
+  onCancel,
+  submitLabel = "Create Session",
+  className = "",
+}: CreateSessionFormProps) => {
+  const [selectedProject, setSelectedProject] = useState(fixedProjectId || "");
+  const [selectedRepo, setSelectedRepo] = useState(fixedRepoId || "");
+  const [selectedToolType, setSelectedToolType] = useState("");
+  const [displayName, setDisplayName] = useState("");
+  const [cloneMode, setCloneMode] = useState<"mount" | "clone">("mount");
+  const [branch, setBranch] = useState("main");
+  const [sshKeys, setSshKeys] = useState<SSHKey[]>([]);
+  const [configProfiles, setConfigProfiles] = useState<ConfigProfile[]>([]);
+  const [selectedConfigProfile, setSelectedConfigProfile] = useState("");
+  
+  const [branches, setBranches] = useState<Branch[]>([]);
+  const [isLoadingBranches, setIsLoadingBranches] = useState(false);
+  const [isCreatingNewBranch, setIsCreatingNewBranch] = useState(false);
+  const [newBranchName, setNewBranchName] = useState("");
+  const [baseBranch, setBaseBranch] = useState("");
+  
+  const [status, setStatus] = useState<"idle" | "creating" | "error">("idle");
+  const [progress, setProgress] = useState("");
+  const [error, setError] = useState<string | null>(null);
+
+  // Load SSH keys when clone mode is shown
+  useEffect(() => {
+    if (!showCloneMode) return;
+    const loadKeys = async () => {
+      try {
+        const keys = await listSSHKeys();
+        setSshKeys(keys);
+      } catch {
+        // ignore
+      }
+    };
+    void loadKeys();
+  }, [showCloneMode]);
+
+  // Load config profiles when tool type is selected
+  useEffect(() => {
+    const projectId = fixedProjectId || selectedProject;
+    if (!selectedToolType || !projectId) {
+      setConfigProfiles([]);
+      setSelectedConfigProfile("");
+      return;
+    }
+    const loadProfiles = async () => {
+      try {
+        const profiles = await listConfigProfiles(projectId, selectedToolType);
+        setConfigProfiles(profiles);
+        // Auto-select default if available
+        const defaultProfile = profiles.find((p) => p.is_default);
+        if (defaultProfile) {
+          setSelectedConfigProfile(defaultProfile.id);
+        }
+      } catch {
+        // ignore
+      }
+    };
+    void loadProfiles();
+  }, [selectedToolType, selectedProject, fixedProjectId]);
+
+  // Load branches when selected repo changes
+  useEffect(() => {
+    const projectId = fixedProjectId || selectedProject;
+    if (!selectedRepo || !projectId || !showCloneMode) {
+      setBranches([]);
+      return;
+    }
+    const loadBranches = async () => {
+      setIsLoadingBranches(true);
+      try {
+        const response = await listRepositoryBranches(projectId, selectedRepo);
+        setBranches(response.branches);
+        if (response.default_branch) {
+          setBranch(response.default_branch);
+          setBaseBranch(response.default_branch);
+        }
+      } catch {
+        // ignore
+      } finally {
+        setIsLoadingBranches(false);
+      }
+    };
+    void loadBranches();
+  }, [selectedRepo, selectedProject, fixedProjectId, showCloneMode]);
+
+  // Filter repositories by selected project
+  const availableRepos = selectedProject
+    ? repositories.filter((r) => r.project_id === selectedProject)
+    : [];
+
+  const handleSubmit = async (event: React.FormEvent) => {
+    event.preventDefault();
+    setError(null);
+
+    const projectId = fixedProjectId || selectedProject;
+    const repoId = fixedRepoId || selectedRepo;
+
+    if (!projectId || !repoId || !selectedToolType) {
+      setError("Project, repository, and tool type are required");
+      return;
+    }
+
+    if (showCloneMode && cloneMode === "clone") {
+      const repo = repositories.find((r) => r.id === repoId);
+      if (!repo?.ssh_key_id) {
+        setError("Repository must have an SSH key assigned for clone mode");
+        return;
+      }
+    }
+
+    setStatus("creating");
+    setProgress("Creating instance...");
+
+    try {
+      const instance = await createInstance(
+        projectId,
+        repoId,
+        selectedToolType,
+        displayName || undefined,
+        showCloneMode ? cloneMode : undefined,
+        showCloneMode && cloneMode === "clone"
+          ? isCreatingNewBranch
+            ? baseBranch
+            : branch
+          : undefined,
+        showCloneMode && cloneMode === "clone" && isCreatingNewBranch
+          ? newBranchName
+          : undefined,
+        selectedConfigProfile || undefined
+      );
+
+      setProgress("Starting container...");
+      await startInstance(projectId, repoId, instance.id);
+
+      // Reset form
+      if (!fixedProjectId) setSelectedProject("");
+      if (!fixedRepoId) setSelectedRepo("");
+      setSelectedToolType("");
+      setDisplayName("");
+      setCloneMode("mount");
+      setBranch("main");
+      setIsCreatingNewBranch(false);
+      setNewBranchName("");
+      setBaseBranch("");
+      setBranches([]);
+      setStatus("idle");
+      
+      onSuccess?.(instance);
+    } catch {
+      setStatus("error");
+      setError("Failed to create session");
+      setProgress("");
+    }
+  };
+
+  const isSubmitting = status === "creating";
+
+  // Determine which steps are active/unlocked
+  const hasProject = !!(fixedProjectId || selectedProject);
+  const hasRepo = !!(fixedRepoId || selectedRepo);
+  const hasToolType = !!selectedToolType;
+
+  const renderStep = (
+    label: string,
+    number: number,
+    isActive: boolean,
+    isComplete: boolean,
+    children: React.ReactNode
+  ) => {
+    const stepClass = `workflow-step ${isActive ? "active" : ""} ${isComplete ? "complete" : ""}`;
+    return (
+      <div className={stepClass}>
+        <div className="workflow-step-header">
+          <span className="workflow-step-number">{number}</span>
+          <span className="workflow-step-label">{label}</span>
+        </div>
+        <div className="workflow-step-content">
+          {children}
+        </div>
+      </div>
+    );
+  };
+
+  return (
+    <div className={`create-session-form-wrapper ${className}`}>
+      {isSubmitting && (
+        <div className="loading-overlay">
+          <div className="loading-content">
+            <Icon name="loading" size="lg" />
+            <p>{progress || "Creating session..."}</p>
+          </div>
+        </div>
+      )}
+
+      <form onSubmit={handleSubmit} className="stack create-session-form workflow-form">
+        {/* Step 1: Project */}
+        {renderStep("Select Project", 1, true, hasProject,
+          fixedProjectId && showFixedFields ? (
+            <label className="form-field">
+              <input
+                type="text"
+                value={projectName || projects.find((p) => p.id === fixedProjectId)?.name || ""}
+                disabled
+                readOnly
+              />
+            </label>
+          ) : (
+            <label className="form-field">
+              <select
+                value={selectedProject}
+                onChange={(e) => {
+                  const value = e.target.value;
+                  setSelectedProject(value);
+                  setSelectedRepo("");
+                  setSelectedToolType("");
+                  setCloneMode("mount");
+                  setIsCreatingNewBranch(false);
+                  onProjectChange?.(value);
+                }}
+                disabled={isSubmitting}
+              >
+                <option value="">Select project...</option>
+                {projects.map((p) => (
+                  <option key={p.id} value={p.id}>
+                    {p.name}
+                  </option>
+                ))}
+              </select>
+            </label>
+          )
+        )}
+
+        {/* Step 2: Repository */}
+        {hasProject && renderStep("Select Repository", 2, true, hasRepo,
+          fixedRepoId && showFixedFields ? (
+            <label className="form-field">
+              <input
+                type="text"
+                value={repoName || repositories.find((r) => r.id === fixedRepoId)?.name || ""}
+                disabled
+                readOnly
+              />
+            </label>
+          ) : (
+            <label className="form-field">
+              <select
+                value={selectedRepo}
+                onChange={(e) => {
+                  setSelectedRepo(e.target.value);
+                  setSelectedToolType("");
+                  setCloneMode("mount");
+                  setIsCreatingNewBranch(false);
+                }}
+                disabled={!hasProject || isSubmitting}
+              >
+                <option value="">Select repository...</option>
+                {availableRepos.map((r) => (
+                  <option key={r.id} value={r.id}>
+                    {r.name}
+                  </option>
+                ))}
+              </select>
+            </label>
+          )
+        )}
+
+        {/* Step 3: Tool Type */}
+        {hasRepo && renderStep("Select Tool", 3, true, hasToolType,
+          <label className="form-field">
+            <select
+              value={selectedToolType}
+              onChange={(e) => {
+                setSelectedToolType(e.target.value);
+                setCloneMode("mount");
+                setIsCreatingNewBranch(false);
+              }}
+              disabled={!hasRepo || isSubmitting}
+            >
+              <option value="">Select tool...</option>
+              {toolTypes.map((t) => (
+                <option key={t.id} value={t.id}>
+                  {t.display_name}
+                </option>
+              ))}
+            </select>
+          </label>
+        )}
+
+        {/* Step 4: Config Profile */}
+        {hasToolType && renderStep("Config Profile (optional)", 4, true, false,
+          <label className="form-field">
+            <select
+              value={selectedConfigProfile}
+              onChange={(e) => setSelectedConfigProfile(e.target.value)}
+              disabled={!hasToolType || isSubmitting}
+            >
+              <option value="">No profile (use tool defaults)</option>
+              {configProfiles.map((p) => (
+                <option key={p.id} value={p.id}>
+                  {p.name} {p.is_default ? "(default)" : ""}
+                </option>
+              ))}
+            </select>
+          </label>
+        )}
+
+        {/* Step 5: Clone Mode & Branch */}
+        {showCloneMode && hasToolType && renderStep("Repository Access", 5, true, false,
+          <div className="form-row">
+            <label className="form-field">
+              <div className="radio-group">
+                <label className="radio-label">
+                  <input
+                    type="radio"
+                    name="cloneMode"
+                    value="mount"
+                    checked={cloneMode === "mount"}
+                    onChange={(e) => {
+                      setCloneMode(e.target.value as "mount" | "clone");
+                      setIsCreatingNewBranch(false);
+                    }}
+                    disabled={isSubmitting}
+                  />
+                  Mount (live sync)
+                </label>
+                <label className="radio-label">
+                  <input
+                    type="radio"
+                    name="cloneMode"
+                    value="clone"
+                    checked={cloneMode === "clone"}
+                    onChange={(e) => {
+                      setCloneMode(e.target.value as "mount" | "clone");
+                      setIsCreatingNewBranch(false);
+                    }}
+                    disabled={isSubmitting}
+                  />
+                  Clone fresh copy
+                </label>
+              </div>
+            </label>
+
+            {cloneMode === "clone" && (
+              <>
+                <label className="form-field">
+                  Branch
+                  {isLoadingBranches ? (
+                    <span className="muted">Loading branches...</span>
+                  ) : (
+                    <select
+                      value={isCreatingNewBranch ? "__new__" : branch}
+                      onChange={(e) => {
+                        const value = e.target.value;
+                        if (value === "__new__") {
+                          setIsCreatingNewBranch(true);
+                          setNewBranchName("");
+                        } else {
+                          setIsCreatingNewBranch(false);
+                          setBranch(value);
+                          setBaseBranch(value);
+                        }
+                      }}
+                      disabled={isSubmitting}
+                    >
+                      {branches.map((b) => (
+                        <option key={b.name} value={b.name}>
+                          {b.name} {b.is_default ? "(default)" : ""}
+                        </option>
+                      ))}
+                      <option value="__new__">Create new branch...</option>
+                    </select>
+                  )}
+                </label>
+
+                {isCreatingNewBranch && (
+                  <>
+                    <label className="form-field">
+                      New Branch Name
+                      <input
+                        type="text"
+                        value={newBranchName}
+                        onChange={(e) => setNewBranchName(e.target.value)}
+                        placeholder="feature/my-new-branch"
+                        required
+                        disabled={isSubmitting}
+                      />
+                    </label>
+                    <label className="form-field">
+                      Base Branch
+                      <select
+                        value={baseBranch}
+                        onChange={(e) => setBaseBranch(e.target.value)}
+                        disabled={isSubmitting}
+                      >
+                        {branches.map((b) => (
+                          <option key={b.name} value={b.name}>
+                            {b.name} {b.is_default ? "(default)" : ""}
+                          </option>
+                        ))}
+                      </select>
+                    </label>
+                  </>
+                )}
+
+                {selectedRepo && (
+                  <div className="form-field ssh-key-info">
+                    {(() => {
+                      const repo = repositories.find((r) => r.id === selectedRepo);
+                      if (!repo) return null;
+                      if (repo.ssh_key_id) {
+                        const key = sshKeys.find((k) => k.id === repo.ssh_key_id);
+                        return (
+                          <span className="success-text">
+                            SSH key: {key?.name || "Assigned"}
+                          </span>
+                        );
+                      }
+                      return (
+                        <span className="warning-text">
+                          No SSH key assigned to this repository. Clone mode requires an SSH key.
+                        </span>
+                      );
+                    })()}
+                  </div>
+                )}
+              </>
+            )}
+          </div>
+        )}
+
+        {/* Step 6: Display Name */}
+        {hasToolType && renderStep("Display Name (optional)", 6, true, !!displayName,
+          <label className="form-field">
+            <input
+              type="text"
+              value={displayName}
+              onChange={(e) => setDisplayName(e.target.value)}
+              placeholder="My Development Environment"
+              disabled={isSubmitting}
+            />
+          </label>
+        )}
+
+        {/* Error & Submit */}
+        {error && <p className="error-text">{error}</p>}
+
+        {hasToolType && (
+          <div className="form-actions">
+            {onCancel && (
+              <button
+                className="secondary-button"
+                type="button"
+                onClick={onCancel}
+                disabled={isSubmitting}
+              >
+                Cancel
+              </button>
+            )}
+            <button
+              className="primary-button"
+              type="submit"
+              disabled={isSubmitting}
+            >
+              {isSubmitting ? (
+                <>
+                  <Icon name="loading" size="sm" />
+                  Creating...
+                </>
+              ) : (
+                <>
+                  <Icon name="add" size="sm" />
+                  {submitLabel}
+                </>
+              )}
+            </button>
+          </div>
+        )}
+      </form>
+    </div>
+  );
+};
@@ -0,0 +1,34 @@
+import { Icon } from "./icon";
+
+interface LoadingStateProps {
+  message?: string;
+}
+
+export const LoadingState = ({ message = "Loading..." }: LoadingStateProps) => (
+  <p className="muted">{message}</p>
+);
+
+interface ErrorStateProps {
+  message?: string;
+  onRetry?: () => void;
+}
+
+export const ErrorState = ({ message = "Failed to load", onRetry }: ErrorStateProps) => (
+  <div className="card stack">
+    <p>{message}</p>
+    {onRetry && (
+      <button className="secondary-button" onClick={onRetry} type="button">
+        <Icon name="refresh" size="sm" />
+        Retry
+      </button>
+    )}
+  </div>
+);
+
+interface EmptyStateProps {
+  message: string;
+}
+
+export const EmptyState = ({ message }: EmptyStateProps) => (
+  <p className="muted">{message}</p>
+);
@@ -0,0 +1,226 @@
+import { useState } from "react";
+import { Icon } from "./icon";
+import type { GitMount } from "../api/config_profiles";
+
+interface GitMountEditorProps {
+  mounts: GitMount[];
+  onChange: (mounts: GitMount[]) => void;
+}
+
+export const GitMountEditor = ({ mounts, onChange }: GitMountEditorProps) => {
+  const [editingIndex, setEditingIndex] = useState<number | null>(null);
+  const [newMount, setNewMount] = useState<GitMount>({
+    remote_url: "",
+    source_path: ".",
+    target_path: "",
+    branch: "",
+  });
+
+  const handleAdd = (mount: GitMount) => {
+    onChange([...mounts, mount]);
+    setNewMount({ remote_url: "", source_path: ".", target_path: "", branch: "" });
+  };
+
+  const handleUpdate = (index: number, updated: GitMount) => {
+    const updatedMounts = [...mounts];
+    updatedMounts[index] = updated;
+    onChange(updatedMounts);
+    setEditingIndex(null);
+  };
+
+  const handleRemove = (index: number) => {
+    onChange(mounts.filter((_, i) => i !== index));
+  };
+
+  const validatePath = (path: string, isTarget: boolean): string | null => {
+    if (!path) return isTarget ? "Target path is required" : null;
+    if (path.includes("..")) return "Path cannot contain ..";
+    if (!isTarget && path.startsWith("/")) return "Source path must be relative";
+    return null;
+  };
+
+  const validateUrl = (url: string): string | null => {
+    if (!url) return "Git URL is required";
+    if (!url.startsWith("http://") && !url.startsWith("https://") && !url.startsWith("git@") && !url.startsWith("ssh://")) {
+      return "Must be a valid git URL (https://, git@, or ssh://)";
+    }
+    return null;
+  };
+
+  return (
+    <div className="git-mount-editor">
+      <h4 className="section-subtitle">Git Mounts</h4>
+      
+      {mounts.length > 0 && (
+        <div className="git-mount-list">
+          {mounts.map((mount, index) => (
+            <div key={index} className="git-mount-item">
+              {editingIndex === index ? (
+                <GitMountForm
+                  mount={mount}
+                  onSave={(updated) => handleUpdate(index, updated)}
+                  onCancel={() => setEditingIndex(null)}
+                  validatePath={validatePath}
+                  validateUrl={validateUrl}
+                />
+              ) : (
+                <div className="git-mount-display">
+                  <div className="git-mount-info">
+                    <span className="git-mount-repo">{mount.remote_url}</span>
+                    <span className="git-mount-paths">
+                      {mount.source_path || "."} → {mount.target_path}
+                    </span>
+                    {mount.branch && (
+                      <span className="git-mount-branch">@{mount.branch}</span>
+                    )}
+                  </div>
+                  <div className="git-mount-actions">
+                    <button
+                      type="button"
+                      className="icon-button"
+                      onClick={() => setEditingIndex(index)}
+                      title="Edit"
+                    >
+                      <Icon name="edit" size="sm" />
+                    </button>
+                    <button
+                      type="button"
+                      className="icon-button danger"
+                      onClick={() => handleRemove(index)}
+                      title="Remove"
+                    >
+                      <Icon name="delete" size="sm" />
+                    </button>
+                  </div>
+                </div>
+              )}
+            </div>
+          ))}
+        </div>
+      )}
+
+      <div className="git-mount-add">
+        <h5>Add Git Mount</h5>
+        <GitMountForm
+          mount={newMount}
+          onSave={handleAdd}
+          onCancel={() => setNewMount({ remote_url: "", source_path: ".", target_path: "", branch: "" })}
+          validatePath={validatePath}
+          validateUrl={validateUrl}
+          isNew
+        />
+      </div>
+    </div>
+  );
+};
+
+interface GitMountFormProps {
+  mount: GitMount;
+  onSave: (mount: GitMount) => void;
+  onCancel: () => void;
+  validatePath: (path: string, isTarget: boolean) => string | null;
+  validateUrl: (url: string) => string | null;
+  isNew?: boolean;
+}
+
+const GitMountForm = ({ mount, onSave, onCancel, validatePath, validateUrl, isNew }: GitMountFormProps) => {
+  const [form, setForm] = useState<GitMount>({ ...mount });
+  const [errors, setErrors] = useState<Record<string, string>>({});
+
+  const handleChange = (field: keyof GitMount, value: string) => {
+    setForm((prev) => ({ ...prev, [field]: value }));
+    if (errors[field]) {
+      setErrors((prev) => {
+        const next = { ...prev };
+        delete next[field];
+        return next;
+      });
+    }
+  };
+
+  const handleSubmit = () => {
+    const newErrors: Record<string, string> = {};
+    
+    const urlError = validateUrl(form.remote_url);
+    if (urlError) newErrors.remote_url = urlError;
+    
+    const sourceError = validatePath(form.source_path || ".", false);
+    if (sourceError) newErrors.source_path = sourceError;
+    
+    const targetError = validatePath(form.target_path, true);
+    if (targetError) newErrors.target_path = targetError;
+    
+    if (Object.keys(newErrors).length > 0) {
+      setErrors(newErrors);
+      return;
+    }
+    
+    onSave(form);
+    if (isNew) {
+      setForm({ remote_url: "", source_path: ".", target_path: "", branch: "" });
+    }
+  };
+
+  return (
+    <div className="git-mount-form">
+      <div className="form-row">
+        <label>Git URL</label>
+        <input
+          type="text"
+          value={form.remote_url}
+          onChange={(e) => handleChange("remote_url", e.target.value)}
+          placeholder="https://github.com/user/repo.git"
+          className={errors.remote_url ? "error" : ""}
+        />
+        <span className="hint">Repository URL (HTTPS or SSH)</span>
+        {errors.remote_url && <span className="error-text">{errors.remote_url}</span>}
+      </div>
+
+      <div className="form-row">
+        <label>Source Path</label>
+        <input
+          type="text"
+          value={form.source_path || "."}
+          onChange={(e) => handleChange("source_path", e.target.value)}
+          placeholder="e.g., . or configs/*.json"
+          className={errors.source_path ? "error" : ""}
+        />
+        <span className="hint">Relative path in repo (supports glob patterns)</span>
+        {errors.source_path && <span className="error-text">{errors.source_path}</span>}
+      </div>
+
+      <div className="form-row">
+        <label>Target Path</label>
+        <input
+          type="text"
+          value={form.target_path}
+          onChange={(e) => handleChange("target_path", e.target.value)}
+          placeholder="e.g., /app/config"
+          className={errors.target_path ? "error" : ""}
+        />
+        <span className="hint">Use absolute path (e.g. /app/config). Relative paths need working_directory set in tool config.</span>
+        {errors.target_path && <span className="error-text">{errors.target_path}</span>}
+      </div>
+
+      <div className="form-row">
+        <label>Branch (optional)</label>
+        <input
+          type="text"
+          value={form.branch || ""}
+          onChange={(e) => handleChange("branch", e.target.value)}
+          placeholder="e.g., main or v1.0"
+        />
+        <span className="hint">Branch or tag to checkout</span>
+      </div>
+
+      <div className="form-actions">
+        <button type="button" className="primary-button" onClick={handleSubmit}>
+          {isNew ? "Add" : "Save"}
+        </button>
+        <button type="button" className="secondary-button" onClick={onCancel}>
+          Cancel
+        </button>
+      </div>
+    </div>
+  );
+};
@@ -18,6 +18,7 @@ interface GitToolbarProps {
  currentBranch: string;
  branches: string[];
  hasRemote: boolean;
+  isMirror: boolean;
  onBranchChange: (branch: string) => void;
  onRefresh: () => void;
 }
@@ -28,6 +29,7 @@ export const GitToolbar = ({
  currentBranch,
  branches,
  hasRemote,
+  isMirror,
  onBranchChange,
  onRefresh,
 }: GitToolbarProps) => {
@@ -136,7 +138,13 @@ export const GitToolbar = ({
  return (
    <div className="git-toolbar">
      {error && <div className="toolbar-error">{error}</div>}
-      
+      {isMirror && (
+        <div className="warning-message">
+          <Icon name="warning" size="sm" /> This repository is a bare mirror.
+          Editing, committing, pulling, and merging are not available.
+          Delete and recreate it to enable full workspace features.
+        </div>
+      )}
      <div className="toolbar-row">
        <div className="toolbar-group">
          <select
@@ -34,6 +34,7 @@ import {
  Stop,
  Terminal,
  ArrowLeft,
+  DotsSixVertical,
 } from "@phosphor-icons/react";

 export type IconName =
@@ -75,7 +76,8 @@ export type IconName =
  | "play"
  | "stop"
  | "terminal"
-  | "arrow-left";
+  | "arrow-left"
+  | "drag";

 const iconMap: Record<IconName, React.ComponentType<{ size?: number | string; weight?: "thin" | "light" | "regular" | "bold" | "fill" | "duotone" }>> = {
  dashboard: House,
@@ -117,6 +119,7 @@ const iconMap: Record<IconName, React.ComponentType<{ size?: number | string; we
  stop: Stop,
  terminal: Terminal,
  "arrow-left": ArrowLeft,
+  drag: DotsSixVertical,
 };

 export interface IconProps {
@@ -147,7 +150,6 @@ export const Icon: React.FC<IconProps> = ({
  const sizeValue = sizeMap[size];

  if (!IconComponent) {
-    console.warn(`Icon "${name}" not found`);
    return null;
  }

@@ -4,7 +4,6 @@ import { Icon } from "./icon";
 import type { ToolInstance } from "../api/sessions";
 import {
  checkInstanceHealth,
-  createInstance,
  deleteInstance,
  listInstances,
  recreateInstanceTunnel,
@@ -13,30 +12,40 @@ import {
  stopInstance,
 } from "../api/sessions";
 import type { ToolType } from "../api/tool_types";
+import { CreateSessionForm } from "./create-session-form";
+import { listConfigProfiles, type ConfigProfile } from "../api/config_profiles";

 const API_BASE_URL = import.meta.env.VITE_API_BASE_URL ?? "http://localhost:8000";

 interface InstanceListProps {
  projectId: string;
  repoId: string;
+  projectName?: string;
+  repoName?: string;
  toolTypes: ToolType[];
 }

-export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps) => {
+export const InstanceList = ({ projectId, repoId, projectName, repoName, toolTypes }: InstanceListProps) => {
  const navigate = useNavigate();
  const [instances, setInstances] = useState<ToolInstance[]>([]);
  const [loading, setLoading] = useState(false);
  const [showCreate, setShowCreate] = useState(false);
-  const [selectedToolType, setSelectedToolType] = useState("");
-  const [displayName, setDisplayName] = useState("");
  const [error, setError] = useState<string | null>(null);
-  
+
  // Stop confirmation
  const [stopConfirmId, setStopConfirmId] = useState<string | null>(null);
-  
+
  // Health check state
  const [healthStatus, setHealthStatus] = useState<Record<string, { healthy: boolean; lastCheck: number }>>({});

+  // Config profile selection for start/restart
+  const [configProfiles, setConfigProfiles] = useState<ConfigProfile[]>([]);
+  const [profileSelectInstanceId, setProfileSelectInstanceId] = useState<string | null>(null);
+  const [selectedProfileForAction, setSelectedProfileForAction] = useState("");
+
+  // Per-instance busy state for actions
+  const [busyInstanceId, setBusyInstanceId] = useState<string | null>(null);
+
  const loadInstances = useCallback(async () => {
    setLoading(true);
    try {
@@ -83,65 +92,84 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
    return () => clearInterval(interval);
  }, [instances, projectId, repoId]);

-  const handleCreate = async () => {
-    if (!selectedToolType) return;
-    setError(null);
-    try {
-      await createInstance(projectId, repoId, selectedToolType, displayName || undefined);
-      setShowCreate(false);
-      setSelectedToolType("");
-      setDisplayName("");
-      await loadInstances();
-    } catch {
-      setError("Failed to create instance");
-    }
+  const handleCreateSuccess = async () => {
+    setShowCreate(false);
+    await loadInstances();
  };

-  const handleStart = async (instanceId: string) => {
+  const loadConfigProfiles = useCallback(async (toolTypeId: string) => {
    try {
-      await startInstance(projectId, repoId, instanceId);
+      const profiles = await listConfigProfiles(projectId, toolTypeId);
+      setConfigProfiles(profiles);
+    } catch {
+      // ignore
+    }
+  }, [projectId]);
+
+  const handleStart = async (instanceId: string, configProfileId?: string) => {
+    setBusyInstanceId(instanceId);
+    try {
+      await startInstance(projectId, repoId, instanceId, configProfileId);
+      setProfileSelectInstanceId(null);
+      setSelectedProfileForAction("");
      await loadInstances();
    } catch {
      setError("Failed to start instance");
+    } finally {
+      setBusyInstanceId(null);
    }
  };

  const handleStop = async (instanceId: string) => {
+    setBusyInstanceId(instanceId);
    try {
      await stopInstance(projectId, repoId, instanceId);
      setStopConfirmId(null);
      await loadInstances();
    } catch {
      setError("Failed to stop instance");
+    } finally {
+      setBusyInstanceId(null);
    }
  };

-  const handleRestart = async (instanceId: string) => {
+  const handleRestart = async (instanceId: string, configProfileId?: string) => {
+    setBusyInstanceId(instanceId);
    try {
-      await restartInstance(projectId, repoId, instanceId);
+      await restartInstance(projectId, repoId, instanceId, configProfileId);
+      setProfileSelectInstanceId(null);
+      setSelectedProfileForAction("");
      await loadInstances();
    } catch {
      setError("Failed to restart instance");
+    } finally {
+      setBusyInstanceId(null);
    }
  };

  const handleDelete = async (instanceId: string) => {
    if (!confirm("Are you sure you want to delete this instance?")) return;
+    setBusyInstanceId(instanceId);
    try {
      await deleteInstance(projectId, repoId, instanceId);
      // Update state immediately instead of reloading
      setInstances(prev => prev.filter(i => i.id !== instanceId));
    } catch {
      setError("Failed to delete instance");
+    } finally {
+      setBusyInstanceId(null);
    }
  };

  const handleRecreateTunnel = async (instanceId: string) => {
+    setBusyInstanceId(instanceId);
    try {
      await recreateInstanceTunnel(projectId, repoId, instanceId);
      await loadInstances();
    } catch {
      setError("Failed to recreate tunnel");
+    } finally {
+      setBusyInstanceId(null);
    }
  };

@@ -192,7 +220,12 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
      ) : (
        <div className="instance-grid">
          {instances.map((instance) => (
-            <div key={instance.id} className="instance-card">
+            <div key={instance.id} className={`instance-card ${busyInstanceId === instance.id ? "busy" : ""}`}>
+              {busyInstanceId === instance.id && (
+                <div className="instance-busy-overlay">
+                  <Icon name="loading" size="md" />
+                </div>
+              )}
              <div className="instance-info">
                <div className="instance-name">{instance.display_name}</div>
                <div className="instance-meta">
@@ -208,6 +241,13 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
                    </span>
                  )}
                </div>
+                {instance.selected_config_profile_id && (
+                  <div className="instance-profile">
+                    <span className="badge">
+                      Profile: {configProfiles.find((p) => p.id === instance.selected_config_profile_id)?.name || instance.selected_config_profile_id}
+                    </span>
+                  </div>
+                )}
              </div>
              <div className="instance-actions">
                {instance.status === "running" && instance.url && instance.tool_type_interfaces.includes("web") && (
@@ -227,6 +267,7 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
                        onClick={() => void handleRecreateTunnel(instance.id)}
                        type="button"
                        title="Recreate tunnel"
+                        disabled={busyInstanceId === instance.id}
                      >
                        <Icon name="refresh" size="sm" />
                        Fix Tunnel
@@ -239,20 +280,67 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
                    className="secondary-button small"
                    onClick={() => navigate(`/instances/${instance.id}/terminal`)}
                    type="button"
+                    disabled={busyInstanceId === instance.id}
                  >
                    <Icon name="terminal" size="sm" />
                    Terminal
                  </button>
                )}
                {instance.status !== "running" && (
-                  <button
-                    className="secondary-button small"
-                    onClick={() => void handleStart(instance.id)}
-                    type="button"
-                  >
-                    <Icon name="play" size="sm" />
-                    Start
-                  </button>
+                  <>
+                    {profileSelectInstanceId === instance.id ? (
+                      <div className="inline-profile-select">
+                        <select
+                          value={selectedProfileForAction}
+                          onChange={(e) => setSelectedProfileForAction(e.target.value)}
+                        >
+                          <option value="">Default (none)</option>
+                          {configProfiles.map((p) => (
+                            <option key={p.id} value={p.id}>
+                              {p.name}
+                            </option>
+                          ))}
+                        </select>
+                        <button
+                          className="primary-button small"
+                          onClick={() => void handleStart(instance.id, selectedProfileForAction || undefined)}
+                          type="button"
+                          disabled={busyInstanceId === instance.id}
+                        >
+                          <Icon name="play" size="sm" />
+                          Start
+                        </button>
+                        <button
+                          className="ghost-button small"
+                          onClick={() => {
+                            setProfileSelectInstanceId(null);
+                            setSelectedProfileForAction("");
+                          }}
+                          type="button"
+                          disabled={busyInstanceId === instance.id}
+                        >
+                          Cancel
+                        </button>
+                      </div>
+                    ) : (
+                      <button
+                        className="secondary-button small"
+                        onClick={() => {
+                          const toolType = toolTypes.find((t) => t.id === instance.tool_type_id);
+                          if (toolType) {
+                            void loadConfigProfiles(toolType.id);
+                          }
+                          setProfileSelectInstanceId(instance.id);
+                          setSelectedProfileForAction(instance.selected_config_profile_id || "");
+                        }}
+                        type="button"
+                        disabled={busyInstanceId === instance.id}
+                      >
+                        <Icon name="play" size="sm" />
+                        Start
+                      </button>
+                    )}
+                  </>
                )}
                {instance.status === "running" && (
                  <>
@@ -263,6 +351,7 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
                          className="ghost-button small danger-text"
                          onClick={() => void handleStop(instance.id)}
                          type="button"
+                          disabled={busyInstanceId === instance.id}
                        >
                          Yes
                        </button>
@@ -270,6 +359,7 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
                          className="ghost-button small"
                          onClick={() => setStopConfirmId(null)}
                          type="button"
+                          disabled={busyInstanceId === instance.id}
                        >
                          No
                        </button>
@@ -279,23 +369,69 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
                        className="ghost-button small"
                        onClick={() => setStopConfirmId(instance.id)}
                        type="button"
+                        disabled={busyInstanceId === instance.id}
                      >
                        <Icon name="stop" size="sm" />
                      </button>
                    )}
-                    <button
-                      className="ghost-button small"
-                      onClick={() => void handleRestart(instance.id)}
-                      type="button"
-                    >
-                      <Icon name="refresh" size="sm" />
-                    </button>
+                    {profileSelectInstanceId === instance.id ? (
+                      <div className="inline-profile-select">
+                        <select
+                          value={selectedProfileForAction}
+                          onChange={(e) => setSelectedProfileForAction(e.target.value)}
+                        >
+                          <option value="">Default (none)</option>
+                          {configProfiles.map((p) => (
+                            <option key={p.id} value={p.id}>
+                              {p.name}
+                            </option>
+                          ))}
+                        </select>
+                        <button
+                          className="primary-button small"
+                          onClick={() => void handleRestart(instance.id, selectedProfileForAction || undefined)}
+                          type="button"
+                          disabled={busyInstanceId === instance.id}
+                        >
+                          <Icon name="refresh" size="sm" />
+                          Restart
+                        </button>
+                        <button
+                          className="ghost-button small"
+                          onClick={() => {
+                            setProfileSelectInstanceId(null);
+                            setSelectedProfileForAction("");
+                          }}
+                          type="button"
+                          disabled={busyInstanceId === instance.id}
+                        >
+                          Cancel
+                        </button>
+                      </div>
+                    ) : (
+                      <button
+                        className="ghost-button small"
+                        onClick={() => {
+                          const toolType = toolTypes.find((t) => t.id === instance.tool_type_id);
+                          if (toolType) {
+                            void loadConfigProfiles(toolType.id);
+                          }
+                          setProfileSelectInstanceId(instance.id);
+                          setSelectedProfileForAction(instance.selected_config_profile_id || "");
+                        }}
+                        type="button"
+                        disabled={busyInstanceId === instance.id}
+                      >
+                        <Icon name="refresh" size="sm" />
+                      </button>
+                    )}
                  </>
                )}
                <button
                  className="ghost-button small danger-text"
                  onClick={() => void handleDelete(instance.id)}
                  type="button"
+                  disabled={busyInstanceId === instance.id}
                >
                  <Icon name="delete" size="sm" />
                </button>
@@ -309,48 +445,18 @@ export const InstanceList = ({ projectId, repoId, toolTypes }: InstanceListProps
        <div className="dialog-overlay" role="dialog" aria-modal="true">
          <div className="dialog">
            <h2>Launch Tool</h2>
-            <div className="stack">
-              <label className="form-field">
-                Tool Type
-                <select
-                  value={selectedToolType}
-                  onChange={(e) => setSelectedToolType(e.target.value)}
-                >
-                  <option value="">Select a tool...</option>
-                  {toolTypes.map((tool) => (
-                    <option key={tool.id} value={tool.id}>
-                      {tool.display_name}
-                    </option>
-                  ))}
-                </select>
-              </label>
-              <label className="form-field">
-                Display Name (optional)
-                <input
-                  type="text"
-                  value={displayName}
-                  onChange={(e) => setDisplayName(e.target.value)}
-                  placeholder="My Development Environment"
-                />
-              </label>
-              <div className="dialog-actions">
-                <button
-                  className="secondary-button"
-                  onClick={() => setShowCreate(false)}
-                  type="button"
-                >
-                  Cancel
-                </button>
-                <button
-                  className="primary-button"
-                  onClick={() => void handleCreate()}
-                  disabled={!selectedToolType}
-                  type="button"
-                >
-                  Launch
-                </button>
-              </div>
-            </div>
+            <CreateSessionForm
+              projects={[]}
+              repositories={[]}
+              toolTypes={toolTypes}
+              fixedProjectId={projectId}
+              fixedRepoId={repoId}
+              projectName={projectName}
+              repoName={repoName}
+              onSuccess={handleCreateSuccess}
+              onCancel={() => setShowCreate(false)}
+              submitLabel="Launch"
+            />
          </div>
        </div>
      )}
@@ -0,0 +1,849 @@
+import { useState, useEffect, useCallback } from "react";
+import { Icon } from "./icon";
+import { extractErrorMessage } from "../utils/errors";
+import {
+	compileToolDefinition,
+	type ToolDefinitionManifest,
+} from "../api/tool_definitions";
+
+interface PackageEntry {
+	name: string;
+}
+
+interface MountEntry {
+	name: string;
+	target: string;
+	source_type: string;
+	writable: boolean;
+	owner: string;
+	mode: string;
+	file_mode: string;
+	readonly: boolean;
+	git_mount_ref: string;
+}
+
+interface ManifestEditorProps {
+	manifest: Record<string, unknown> | null;
+	baseDefinitions: ToolDefinitionManifest[];
+	onChange: (manifest: Record<string, unknown>) => void;
+	definitionId?: string | null;
+}
+
+export const ManifestEditor = ({
+	manifest,
+	baseDefinitions,
+	onChange,
+	definitionId,
+}: ManifestEditorProps) => {
+	const [baseImage, setBaseImage] = useState("");
+	const [baseDefinitionId, setBaseDefinitionId] = useState("");
+	const [aptPackages, setAptPackages] = useState<PackageEntry[]>([]);
+	const [npmPackages, setNpmPackages] = useState<PackageEntry[]>([]);
+	const [pipPackages, setPipPackages] = useState<PackageEntry[]>([]);
+	const [nodeVersion, setNodeVersion] = useState("");
+	const [userName, setUserName] = useState("user");
+	const [userUid, setUserUid] = useState("1000");
+	const [userGid, setUserGid] = useState("1000");
+	const [envVars, setEnvVars] = useState<{ key: string; value: string }[]>([]);
+	const [buildScripts, setBuildScripts] = useState<string[]>([""]);
+	const [startupScripts, setStartupScripts] = useState<string[]>([""]);
+	const [mounts, setMounts] = useState<MountEntry[]>([]);
+	const [command, setCommand] = useState<string[]>([""]);
+	const [workingDir, setWorkingDir] = useState("/workspace");
+	const [stdinOpen, setStdinOpen] = useState(true);
+	const [tty, setTty] = useState(true);
+
+	const [preview, setPreview] = useState<{
+		dockerfile: string;
+		compose: string;
+		entrypoint: string;
+	} | null>(null);
+	const [previewLoading, setPreviewLoading] = useState(false);
+	const [previewError, setPreviewError] = useState<string | null>(null);
+
+	// Load manifest into form
+	useEffect(() => {
+		if (!manifest) return;
+
+		const pkgs = (manifest.packages as Record<string, unknown>) || {};
+		setBaseImage((manifest.base_image as string) || "");
+		setBaseDefinitionId((manifest.base_definition_id as string) || "");
+		setAptPackages(((pkgs.apt as string[]) || []).map((p) => ({ name: p })));
+		setNpmPackages(
+			((pkgs.npm_global as string[]) || []).map((p) => ({ name: p })),
+		);
+		setPipPackages(((pkgs.pip as string[]) || []).map((p) => ({ name: p })));
+		setNodeVersion((pkgs.node as Record<string, string>)?.version || "");
+
+		const user = (manifest.user as Record<string, unknown>) || {};
+		setUserName((user.name as string) || "user");
+		setUserUid(String(user.uid || "1000"));
+		setUserGid(String(user.gid || "1000"));
+
+		const env = (manifest.env as Record<string, string>) || {};
+		setEnvVars(Object.entries(env).map(([key, value]) => ({ key, value })));
+
+		const scripts = (manifest.scripts as Record<string, string[]>) || {};
+		setBuildScripts((scripts.build || []).length > 0 ? scripts.build : [""]);
+		setStartupScripts(
+			(scripts.startup || []).length > 0 ? scripts.startup : [""],
+		);
+
+		const mts = (manifest.mounts as MountEntry[]) || [];
+		setMounts(mts);
+
+		const runtime = (manifest.runtime as Record<string, unknown>) || {};
+		setCommand((runtime.command as string[]) || [""]);
+		setWorkingDir((runtime.working_dir as string) || "/workspace");
+		setStdinOpen((runtime.stdin_open as boolean) ?? true);
+		setTty((runtime.tty as boolean) ?? true);
+	}, [manifest]);
+
+	// Build manifest from form state
+	const buildManifest = useCallback((): Record<string, unknown> => {
+		const packages: Record<string, unknown> = {};
+		const apt = aptPackages.map((p) => p.name).filter(Boolean);
+		if (apt.length) packages.apt = apt;
+		const npm = npmPackages.map((p) => p.name).filter(Boolean);
+		if (npm.length) packages.npm_global = npm;
+		const pip = pipPackages.map((p) => p.name).filter(Boolean);
+		if (pip.length) packages.pip = pip;
+		if (nodeVersion) packages.node = { version: nodeVersion };
+
+		const env: Record<string, string> = {};
+		envVars.forEach(({ key, value }) => {
+			if (key) env[key] = value;
+		});
+
+		const scripts: Record<string, string[]> = {};
+		const build = buildScripts.filter(Boolean);
+		if (build.length) scripts.build = build;
+		const startup = startupScripts.filter(Boolean);
+		if (startup.length) scripts.startup = startup;
+
+		const mts = mounts.filter((m) => m.name && m.target);
+
+		const result: Record<string, unknown> = {
+			packages,
+			user: {
+				name: userName,
+				uid: parseInt(userUid) || 1000,
+				gid: parseInt(userGid) || 1000,
+				create_home: true,
+				shell: "/bin/bash",
+			},
+			env,
+			scripts,
+			mounts: mts,
+			runtime: {
+				command:
+					command.filter(Boolean).length > 0
+						? command.filter(Boolean)
+						: ["/bin/bash"],
+				stdin_open: stdinOpen,
+				tty: tty,
+				working_dir: workingDir,
+			},
+		};
+
+		if (baseImage) result.base_image = baseImage;
+		if (baseDefinitionId) result.base_definition_id = baseDefinitionId;
+
+		return result;
+	}, [
+		aptPackages,
+		npmPackages,
+		pipPackages,
+		nodeVersion,
+		userName,
+		userUid,
+		userGid,
+		envVars,
+		buildScripts,
+		startupScripts,
+		mounts,
+		command,
+		workingDir,
+		stdinOpen,
+		tty,
+		baseImage,
+		baseDefinitionId,
+	]);
+
+	// Notify parent of changes
+	useEffect(() => {
+		const m = buildManifest();
+		onChange(m);
+	}, [buildManifest, onChange]);
+
+	const handlePreview = async () => {
+		if (!definitionId) {
+			setPreviewError("Save the tool definition first to preview");
+			return;
+		}
+		setPreviewLoading(true);
+		setPreviewError(null);
+		try {
+			const result = await compileToolDefinition(definitionId);
+			setPreview({
+				dockerfile: result.dockerfile,
+				compose: result.compose,
+				entrypoint: result.entrypoint,
+			});
+		} catch (err) {
+			setPreviewError(extractErrorMessage(err));
+		} finally {
+			setPreviewLoading(false);
+		}
+	};
+
+	const addAptPackage = () => setAptPackages([...aptPackages, { name: "" }]);
+	const removeAptPackage = (idx: number) =>
+		setAptPackages(aptPackages.filter((_, i) => i !== idx));
+	const updateAptPackage = (idx: number, name: string) => {
+		const copy = [...aptPackages];
+		copy[idx] = { name };
+		setAptPackages(copy);
+	};
+
+	const addNpmPackage = () => setNpmPackages([...npmPackages, { name: "" }]);
+	const removeNpmPackage = (idx: number) =>
+		setNpmPackages(npmPackages.filter((_, i) => i !== idx));
+	const updateNpmPackage = (idx: number, name: string) => {
+		const copy = [...npmPackages];
+		copy[idx] = { name };
+		setNpmPackages(copy);
+	};
+
+	const addPipPackage = () => setPipPackages([...pipPackages, { name: "" }]);
+	const removePipPackage = (idx: number) =>
+		setPipPackages(pipPackages.filter((_, i) => i !== idx));
+	const updatePipPackage = (idx: number, name: string) => {
+		const copy = [...pipPackages];
+		copy[idx] = { name };
+		setPipPackages(copy);
+	};
+
+	const addEnvVar = () => setEnvVars([...envVars, { key: "", value: "" }]);
+	const removeEnvVar = (idx: number) =>
+		setEnvVars(envVars.filter((_, i) => i !== idx));
+	const updateEnvVar = (idx: number, field: "key" | "value", val: string) => {
+		const copy = [...envVars];
+		copy[idx] = { ...copy[idx], [field]: val };
+		setEnvVars(copy);
+	};
+
+	const addBuildScript = () => setBuildScripts([...buildScripts, ""]);
+	const removeBuildScript = (idx: number) =>
+		setBuildScripts(buildScripts.filter((_, i) => i !== idx));
+	const updateBuildScript = (idx: number, val: string) => {
+		const copy = [...buildScripts];
+		copy[idx] = val;
+		setBuildScripts(copy);
+	};
+
+	const addStartupScript = () => setStartupScripts([...startupScripts, ""]);
+	const removeStartupScript = (idx: number) =>
+		setStartupScripts(startupScripts.filter((_, i) => i !== idx));
+	const updateStartupScript = (idx: number, val: string) => {
+		const copy = [...startupScripts];
+		copy[idx] = val;
+		setStartupScripts(copy);
+	};
+
+	const addMount = () =>
+		setMounts([
+			...mounts,
+			{
+				name: "",
+				target: "",
+				source_type: "repo",
+				writable: true,
+				owner: "",
+				mode: "",
+				file_mode: "",
+				readonly: false,
+				git_mount_ref: "",
+			},
+		]);
+	const removeMount = (idx: number) =>
+		setMounts(mounts.filter((_, i) => i !== idx));
+	const updateMount = (idx: number, field: keyof MountEntry, val: unknown) => {
+		const copy = [...mounts];
+		copy[idx] = { ...copy[idx], [field]: val };
+		setMounts(copy);
+	};
+
+	return (
+		<div className="stack" style={{ gap: "1.5rem" }}>
+			{/* Base Image */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<h4 style={{ margin: 0 }}>Base Image</h4>
+				<div className="row" style={{ gap: "1rem" }}>
+					<div className="form-group" style={{ flex: 1 }}>
+						<label>Base Definition</label>
+						<select
+							value={baseDefinitionId}
+							onChange={(e) => {
+								setBaseDefinitionId(e.target.value);
+								setBaseImage("");
+							}}
+							className="form-input"
+						>
+							<option value="">Custom image...</option>
+							{baseDefinitions.map((b) => (
+								<option key={b.id} value={b.id}>
+									{b.display_name} ({b.version})
+								</option>
+							))}
+						</select>
+					</div>
+					<div className="form-group" style={{ flex: 1 }}>
+						<label>Custom Base Image</label>
+						<input
+							type="text"
+							value={baseImage}
+							onChange={(e) => {
+								setBaseImage(e.target.value);
+								setBaseDefinitionId("");
+							}}
+							placeholder="e.g., ubuntu:24.04"
+							className="form-input"
+							disabled={!!baseDefinitionId}
+						/>
+					</div>
+				</div>
+			</div>
+
+			{/* Packages */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<h4 style={{ margin: 0 }}>Packages</h4>
+
+				<div className="form-group">
+					<label>Node.js Version</label>
+					<input
+						type="text"
+						value={nodeVersion}
+						onChange={(e) => setNodeVersion(e.target.value)}
+						placeholder="e.g., 20"
+						className="form-input"
+						style={{ width: "120px" }}
+					/>
+				</div>
+
+				<div>
+					<label>APT Packages</label>
+					<div className="stack" style={{ gap: "0.5rem", marginTop: "0.5rem" }}>
+						{aptPackages.map((pkg, idx) => (
+							<div key={idx} className="row" style={{ gap: "0.5rem" }}>
+								<input
+									type="text"
+									value={pkg.name}
+									onChange={(e) => updateAptPackage(idx, e.target.value)}
+									placeholder="e.g., neovim"
+									className="form-input"
+								/>
+								<button
+									type="button"
+									onClick={() => removeAptPackage(idx)}
+									className="button-icon"
+									title="Remove"
+								>
+									<Icon name="delete" size="sm" />
+								</button>
+							</div>
+						))}
+						<button
+							type="button"
+							onClick={addAptPackage}
+							className="button-secondary"
+							style={{ width: "fit-content" }}
+						>
+							<Icon name="add" size="sm" /> Add APT Package
+						</button>
+					</div>
+				</div>
+
+				<div>
+					<label>NPM Global Packages</label>
+					<div className="stack" style={{ gap: "0.5rem", marginTop: "0.5rem" }}>
+						{npmPackages.map((pkg, idx) => (
+							<div key={idx} className="row" style={{ gap: "0.5rem" }}>
+								<input
+									type="text"
+									value={pkg.name}
+									onChange={(e) => updateNpmPackage(idx, e.target.value)}
+									placeholder="e.g., @scope/pkg"
+									className="form-input"
+								/>
+								<button
+									type="button"
+									onClick={() => removeNpmPackage(idx)}
+									className="button-icon"
+									title="Remove"
+								>
+									<Icon name="delete" size="sm" />
+								</button>
+							</div>
+						))}
+						<button
+							type="button"
+							onClick={addNpmPackage}
+							className="button-secondary"
+							style={{ width: "fit-content" }}
+						>
+							<Icon name="add" size="sm" /> Add NPM Package
+						</button>
+					</div>
+				</div>
+
+				<div>
+					<label>Pip Packages</label>
+					<div className="stack" style={{ gap: "0.5rem", marginTop: "0.5rem" }}>
+						{pipPackages.map((pkg, idx) => (
+							<div key={idx} className="row" style={{ gap: "0.5rem" }}>
+								<input
+									type="text"
+									value={pkg.name}
+									onChange={(e) => updatePipPackage(idx, e.target.value)}
+									placeholder="e.g., requests"
+									className="form-input"
+								/>
+								<button
+									type="button"
+									onClick={() => removePipPackage(idx)}
+									className="button-icon"
+									title="Remove"
+								>
+									<Icon name="delete" size="sm" />
+								</button>
+							</div>
+						))}
+						<button
+							type="button"
+							onClick={addPipPackage}
+							className="button-secondary"
+							style={{ width: "fit-content" }}
+						>
+							<Icon name="add" size="sm" /> Add Pip Package
+						</button>
+					</div>
+				</div>
+			</div>
+
+			{/* Runtime User */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<h4 style={{ margin: 0 }}>Runtime User</h4>
+				<div className="row" style={{ gap: "1rem" }}>
+					<div className="form-group" style={{ flex: 1 }}>
+						<label>User Name</label>
+						<input
+							type="text"
+							value={userName}
+							onChange={(e) => setUserName(e.target.value)}
+							className="form-input"
+						/>
+					</div>
+					<div className="form-group" style={{ flex: 1 }}>
+						<label>UID</label>
+						<input
+							type="number"
+							value={userUid}
+							onChange={(e) => setUserUid(e.target.value)}
+							className="form-input"
+						/>
+					</div>
+					<div className="form-group" style={{ flex: 1 }}>
+						<label>GID</label>
+						<input
+							type="number"
+							value={userGid}
+							onChange={(e) => setUserGid(e.target.value)}
+							className="form-input"
+						/>
+					</div>
+				</div>
+			</div>
+
+			{/* Environment */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<h4 style={{ margin: 0 }}>Environment Variables</h4>
+				<div className="stack" style={{ gap: "0.5rem" }}>
+					{envVars.map((ev, idx) => (
+						<div key={idx} className="row" style={{ gap: "0.5rem" }}>
+							<input
+								type="text"
+								value={ev.key}
+								onChange={(e) => updateEnvVar(idx, "key", e.target.value)}
+								placeholder="KEY"
+								className="form-input"
+							/>
+							<input
+								type="text"
+								value={ev.value}
+								onChange={(e) => updateEnvVar(idx, "value", e.target.value)}
+								placeholder="value"
+								className="form-input"
+							/>
+							<button
+								type="button"
+								onClick={() => removeEnvVar(idx)}
+								className="button-icon"
+								title="Remove"
+							>
+								<Icon name="delete" size="sm" />
+							</button>
+						</div>
+					))}
+					<button
+						type="button"
+						onClick={addEnvVar}
+						className="button-secondary"
+						style={{ width: "fit-content" }}
+					>
+						<Icon name="add" size="sm" /> Add Env Var
+					</button>
+				</div>
+			</div>
+
+			{/* Build Scripts */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<h4 style={{ margin: 0 }}>Build Scripts (run during docker build)</h4>
+				<div className="stack" style={{ gap: "0.5rem" }}>
+					{buildScripts.map((script, idx) => (
+						<div
+							key={idx}
+							className="row"
+							style={{ gap: "0.5rem", alignItems: "flex-start" }}
+						>
+							<textarea
+								value={script}
+								onChange={(e) => updateBuildScript(idx, e.target.value)}
+								placeholder="git config --global user.email 'dev@example.com'"
+								className="form-input"
+								rows={2}
+								style={{
+									fontFamily: "monospace",
+									fontSize: "0.8125rem",
+									flex: 1,
+								}}
+							/>
+							<button
+								type="button"
+								onClick={() => removeBuildScript(idx)}
+								className="button-icon"
+								title="Remove"
+							>
+								<Icon name="delete" size="sm" />
+							</button>
+						</div>
+					))}
+					<button
+						type="button"
+						onClick={addBuildScript}
+						className="button-secondary"
+						style={{ width: "fit-content" }}
+					>
+						<Icon name="add" size="sm" /> Add Build Script
+					</button>
+				</div>
+			</div>
+
+			{/* Startup Scripts */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<h4 style={{ margin: 0 }}>
+					Startup Scripts (run when container starts)
+				</h4>
+				<div className="stack" style={{ gap: "0.5rem" }}>
+					{startupScripts.map((script, idx) => (
+						<div
+							key={idx}
+							className="row"
+							style={{ gap: "0.5rem", alignItems: "flex-start" }}
+						>
+							<textarea
+								value={script}
+								onChange={(e) => updateStartupScript(idx, e.target.value)}
+								placeholder="chown -R user:user /workspace"
+								className="form-input"
+								rows={2}
+								style={{
+									fontFamily: "monospace",
+									fontSize: "0.8125rem",
+									flex: 1,
+								}}
+							/>
+							<button
+								type="button"
+								onClick={() => removeStartupScript(idx)}
+								className="button-icon"
+								title="Remove"
+							>
+								<Icon name="delete" size="sm" />
+							</button>
+						</div>
+					))}
+					<button
+						type="button"
+						onClick={addStartupScript}
+						className="button-secondary"
+						style={{ width: "fit-content" }}
+					>
+						<Icon name="add" size="sm" /> Add Startup Script
+					</button>
+				</div>
+			</div>
+
+			{/* Mounts */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<h4 style={{ margin: 0 }}>Mount Schema</h4>
+				<div className="stack" style={{ gap: "1rem" }}>
+					{mounts.map((mount, idx) => (
+						<div
+							key={idx}
+							className="stack"
+							style={{
+								gap: "0.5rem",
+								padding: "0.75rem",
+								border: "1px solid var(--border)",
+								borderRadius: "0.375rem",
+							}}
+						>
+							<div className="row" style={{ gap: "0.5rem" }}>
+								<input
+									type="text"
+									value={mount.name}
+									onChange={(e) => updateMount(idx, "name", e.target.value)}
+									placeholder="Name (e.g., workspace)"
+									className="form-input"
+								/>
+								<input
+									type="text"
+									value={mount.target}
+									onChange={(e) => updateMount(idx, "target", e.target.value)}
+									placeholder="Target (e.g., /workspace)"
+									className="form-input"
+								/>
+								<select
+									value={mount.source_type}
+									onChange={(e) =>
+										updateMount(idx, "source_type", e.target.value)
+									}
+									className="form-input"
+								>
+									<option value="repo">Repository</option>
+									<option value="ssh_key">SSH Key</option>
+									<option value="instance">Instance</option>
+									<option value="git_mount">Git Mount</option>
+									<option value="host_path">Host Path</option>
+								</select>
+								<button
+									type="button"
+									onClick={() => removeMount(idx)}
+									className="button-icon"
+									title="Remove"
+								>
+									<Icon name="delete" size="sm" />
+								</button>
+							</div>
+							<div className="row" style={{ gap: "0.5rem" }}>
+								<label
+									style={{
+										display: "flex",
+										alignItems: "center",
+										gap: "0.25rem",
+										fontSize: "0.875rem",
+									}}
+								>
+									<input
+										type="checkbox"
+										checked={mount.writable}
+										onChange={(e) =>
+											updateMount(idx, "writable", e.target.checked)
+										}
+									/>
+									Writable
+								</label>
+								<label
+									style={{
+										display: "flex",
+										alignItems: "center",
+										gap: "0.25rem",
+										fontSize: "0.875rem",
+									}}
+								>
+									<input
+										type="checkbox"
+										checked={mount.readonly}
+										onChange={(e) =>
+											updateMount(idx, "readonly", e.target.checked)
+										}
+									/>
+									Read-only
+								</label>
+								<input
+									type="text"
+									value={mount.owner}
+									onChange={(e) => updateMount(idx, "owner", e.target.value)}
+									placeholder="Owner (e.g., user)"
+									className="form-input"
+									style={{ width: "120px" }}
+								/>
+								<input
+									type="text"
+									value={mount.mode}
+									onChange={(e) => updateMount(idx, "mode", e.target.value)}
+									placeholder="Mode (e.g., 0755)"
+									className="form-input"
+									style={{ width: "100px" }}
+								/>
+								<input
+									type="text"
+									value={mount.file_mode}
+									onChange={(e) =>
+										updateMount(idx, "file_mode", e.target.value)
+									}
+									placeholder="File mode (e.g., 0644)"
+									className="form-input"
+									style={{ width: "120px" }}
+								/>
+								{mount.source_type === "git_mount" && (
+									<input
+										type="text"
+										value={mount.git_mount_ref}
+										onChange={(e) =>
+											updateMount(idx, "git_mount_ref", e.target.value)
+										}
+										placeholder="Git mount ref"
+										className="form-input"
+										style={{ width: "120px" }}
+									/>
+								)}
+							</div>
+						</div>
+					))}
+					<button
+						type="button"
+						onClick={addMount}
+						className="button-secondary"
+						style={{ width: "fit-content" }}
+					>
+						<Icon name="add" size="sm" /> Add Mount
+					</button>
+				</div>
+			</div>
+
+			{/* Runtime */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<h4 style={{ margin: 0 }}>Runtime</h4>
+				<div className="row" style={{ gap: "1rem" }}>
+					<div className="form-group" style={{ flex: 1 }}>
+						<label>Command</label>
+						<input
+							type="text"
+							value={command.join(" ")}
+							onChange={(e) => setCommand(e.target.value.split(" "))}
+							placeholder="/bin/bash"
+							className="form-input"
+						/>
+					</div>
+					<div className="form-group" style={{ flex: 1 }}>
+						<label>Working Directory</label>
+						<input
+							type="text"
+							value={workingDir}
+							onChange={(e) => setWorkingDir(e.target.value)}
+							placeholder="/workspace"
+							className="form-input"
+						/>
+					</div>
+				</div>
+				<div className="row" style={{ gap: "1rem" }}>
+					<label
+						style={{ display: "flex", alignItems: "center", gap: "0.5rem" }}
+					>
+						<input
+							type="checkbox"
+							checked={stdinOpen}
+							onChange={(e) => setStdinOpen(e.target.checked)}
+						/>
+						stdin_open
+					</label>
+					<label
+						style={{ display: "flex", alignItems: "center", gap: "0.5rem" }}
+					>
+						<input
+							type="checkbox"
+							checked={tty}
+							onChange={(e) => setTty(e.target.checked)}
+						/>
+						tty
+					</label>
+				</div>
+			</div>
+
+			{/* Preview */}
+			<div className="card stack" style={{ gap: "1rem", padding: "1rem" }}>
+				<div
+					style={{
+						display: "flex",
+						justifyContent: "space-between",
+						alignItems: "center",
+					}}
+				>
+					<h4 style={{ margin: 0 }}>Live Preview</h4>
+					<button
+						type="button"
+						onClick={handlePreview}
+						disabled={previewLoading}
+						className="button-secondary"
+					>
+						<Icon name="refresh" size="sm" />
+						{previewLoading ? "Compiling..." : "Preview"}
+					</button>
+				</div>
+				{previewError && <p className="text-error">{previewError}</p>}
+				{preview && (
+					<div className="stack" style={{ gap: "1rem" }}>
+						<div>
+							<label style={{ fontWeight: 600, fontSize: "0.875rem" }}>
+								Dockerfile
+							</label>
+							<pre
+								style={{
+									background: "var(--code-bg, #1e1e1e)",
+									color: "var(--code-fg, #d4d4d4)",
+									padding: "1rem",
+									borderRadius: "0.375rem",
+									overflow: "auto",
+									fontSize: "0.8125rem",
+									maxHeight: "300px",
+								}}
+							>
+								{preview.dockerfile}
+							</pre>
+						</div>
+						<div>
+							<label style={{ fontWeight: 600, fontSize: "0.875rem" }}>
+								Compose
+							</label>
+							<pre
+								style={{
+									background: "var(--code-bg, #1e1e1e)",
+									color: "var(--code-fg, #d4d4d4)",
+									padding: "1rem",
+									borderRadius: "0.375rem",
+									overflow: "auto",
+									fontSize: "0.8125rem",
+									maxHeight: "200px",
+								}}
+							>
+								{preview.compose}
+							</pre>
+						</div>
+					</div>
+				)}
+			</div>
+		</div>
+	);
+};
@@ -0,0 +1,88 @@
+import { useEffect, useRef } from "react";
+import { Icon } from "./icon";
+import type { IconName } from "./icon";
+
+export interface MobileActionSheetItem {
+  id: string;
+  label: string;
+  icon?: IconName;
+  variant?: "default" | "danger";
+  onClick: () => void;
+}
+
+interface MobileActionSheetProps {
+  isOpen: boolean;
+  onClose: () => void;
+  title: string;
+  actions: MobileActionSheetItem[];
+}
+
+export function MobileActionSheet({
+  isOpen,
+  onClose,
+  title,
+  actions,
+}: MobileActionSheetProps) {
+  const sheetRef = useRef<HTMLDivElement>(null);
+
+  useEffect(() => {
+    if (isOpen) {
+      document.body.style.overflow = "hidden";
+    } else {
+      document.body.style.overflow = "";
+    }
+    return () => {
+      document.body.style.overflow = "";
+    };
+  }, [isOpen]);
+
+  useEffect(() => {
+    const handleEscape = (e: KeyboardEvent) => {
+      if (e.key === "Escape" && isOpen) {
+        onClose();
+      }
+    };
+    document.addEventListener("keydown", handleEscape);
+    return () => document.removeEventListener("keydown", handleEscape);
+  }, [isOpen, onClose]);
+
+  if (!isOpen) return null;
+
+  return (
+    <div className="mobile-action-sheet-overlay" onClick={onClose}>
+      <div
+        ref={sheetRef}
+        className="mobile-action-sheet"
+        onClick={(e) => e.stopPropagation()}
+      >
+        <div className="mobile-action-sheet-header">
+          <div className="mobile-action-sheet-handle" />
+          <h3>{title}</h3>
+        </div>
+        <div className="mobile-action-sheet-actions">
+          {actions.map((action) => (
+            <button
+              key={action.id}
+              className={`mobile-action-sheet-button ${action.variant || "default"}`}
+              onClick={() => {
+                action.onClick();
+                onClose();
+              }}
+              type="button"
+            >
+              {action.icon && <Icon name={action.icon} size="md" />}
+              <span>{action.label}</span>
+            </button>
+          ))}
+        </div>
+        <button
+          className="mobile-action-sheet-cancel"
+          onClick={onClose}
+          type="button"
+        >
+          Cancel
+        </button>
+      </div>
+    </div>
+  );
+}
@@ -0,0 +1,95 @@
+import { Icon } from "./icon";
+
+interface Field {
+  label: string;
+  value: string | number | boolean | null;
+  type?: "text" | "code" | "json" | "boolean";
+}
+
+interface MobileDetailViewProps {
+  title: string;
+  subtitle?: string;
+  fields: Field[];
+  onEdit: () => void;
+  onDelete: () => void;
+  onBack: () => void;
+}
+
+export const MobileDetailView: React.FC<MobileDetailViewProps> = ({
+  title,
+  subtitle,
+  fields,
+  onEdit,
+  onDelete,
+  onBack,
+}) => {
+  const renderValue = (field: Field) => {
+    if (field.value === null || field.value === undefined) {
+      return <span className="text-muted">Not set</span>;
+    }
+
+    if (field.type === "boolean") {
+      return field.value ? (
+        <span className="badge badge-success">Yes</span>
+      ) : (
+        <span className="badge badge-secondary">No</span>
+      );
+    }
+
+    if (field.type === "code" || field.type === "json") {
+      return (
+        <pre className="mobile-detail-code">
+          {typeof field.value === "string" ? field.value : JSON.stringify(field.value, null, 2)}
+        </pre>
+      );
+    }
+
+    return <span>{String(field.value)}</span>;
+  };
+
+  return (
+    <div className="mobile-detail-view">
+      <header className="mobile-detail-header">
+        <button
+          className="mobile-detail-back"
+          onClick={onBack}
+          type="button"
+          aria-label="Go back"
+        >
+          <Icon name="arrow-left" size="md" />
+        </button>
+        <div className="mobile-detail-header-content">
+          <h1 className="mobile-detail-title">{title}</h1>
+          {subtitle && <p className="mobile-detail-subtitle">{subtitle}</p>}
+        </div>
+        <div className="mobile-detail-actions">
+          <button
+            className="mobile-detail-action"
+            onClick={onEdit}
+            type="button"
+            aria-label="Edit"
+          >
+            <Icon name="edit" size="sm" />
+          </button>
+          <button
+            className="mobile-detail-action mobile-detail-action-danger"
+            onClick={onDelete}
+            type="button"
+            aria-label="Delete"
+          >
+            <Icon name="delete" size="sm" />
+          </button>
+        </div>
+      </header>
+
+      <div className="mobile-detail-fields">
+        {fields.map((field, index) => (
+          <div key={index} className="mobile-detail-field">
+            <label className="mobile-detail-field-label">{field.label}</label>
+            <div className="mobile-detail-field-value">{renderValue(field)}</div>
+          </div>
+        ))}
+      </div>
+    </div>
+  );
+};
@@ -0,0 +1,161 @@
+import { useState } from "react";
+
+interface FormField {
+  name: string;
+  label: string;
+  type: "text" | "textarea" | "number" | "select" | "checkbox" | "code";
+  value: string | number | boolean;
+  options?: { value: string; label: string }[];
+  placeholder?: string;
+  required?: boolean;
+  rows?: number;
+}
+
+interface MobileEditViewProps {
+  title: string;
+  fields?: FormField[];
+  onSave: (data: Record<string, string | number | boolean>) => void;
+  onCancel: () => void;
+  isSaving?: boolean;
+  children?: React.ReactNode;
+}
+
+export const MobileEditView: React.FC<MobileEditViewProps> = ({
+  title,
+  fields,
+  onSave,
+  onCancel,
+  isSaving = false,
+  children,
+}) => {
+  const [formData, setFormData] = useState<Record<string, string | number | boolean>>(
+    () => {
+      const initial: Record<string, string | number | boolean> = {};
+      fields?.forEach((field) => {
+        initial[field.name] = field.value;
+      });
+      return initial;
+    }
+  );
+
+  const handleChange = (name: string, value: string | number | boolean) => {
+    setFormData((prev) => ({ ...prev, [name]: value }));
+  };
+
+  const handleSubmit = (e: React.FormEvent) => {
+    e.preventDefault();
+    onSave(formData);
+  };
+
+  return (
+    <div className="mobile-edit-view">
+      <header className="mobile-edit-header">
+        <button
+          className="mobile-edit-cancel"
+          onClick={onCancel}
+          type="button"
+          disabled={isSaving}
+        >
+          Cancel
+        </button>
+        <h1 className="mobile-edit-title">{title}</h1>
+        <button
+          className="mobile-edit-save"
+          onClick={() => onSave(formData)}
+          type="button"
+          disabled={isSaving}
+        >
+          {isSaving ? "Saving..." : "Save"}
+        </button>
+      </header>
+
+      <form className="mobile-edit-form" onSubmit={handleSubmit}>
+        {children || fields?.map((field) => (
+          <div key={field.name} className="mobile-edit-field">
+            <label className="mobile-edit-field-label" htmlFor={field.name}>
+              {field.label}
+              {field.required && <span className="required">*</span>}
+            </label>
+
+            {field.type === "textarea" && (
+              <textarea
+                id={field.name}
+                name={field.name}
+                value={String(formData[field.name] ?? "")}
+                onChange={(e) => handleChange(field.name, e.target.value)}
+                placeholder={field.placeholder}
+                required={field.required}
+                rows={field.rows || 4}
+                className="mobile-edit-input mobile-edit-textarea"
+              />
+            )}
+
+            {field.type === "select" && (
+              <select
+                id={field.name}
+                name={field.name}
+                value={String(formData[field.name] ?? "")}
+                onChange={(e) => handleChange(field.name, e.target.value)}
+                required={field.required}
+                className="mobile-edit-input"
+              >
+                {field.options?.map((option) => (
+                  <option key={option.value} value={option.value}>
+                    {option.label}
+                  </option>
+                ))}
+              </select>
+            )}
+
+            {field.type === "checkbox" && (
+              <label className="mobile-edit-checkbox">
+                <input
+                  type="checkbox"
+                  id={field.name}
+                  name={field.name}
+                  checked={Boolean(formData[field.name])}
+                  onChange={(e) => handleChange(field.name, e.target.checked)}
+                />
+                <span>{field.label}</span>
+              </label>
+            )}
+
+            {field.type === "code" && (
+              <textarea
+                id={field.name}
+                name={field.name}
+                value={String(formData[field.name] ?? "")}
+                onChange={(e) => handleChange(field.name, e.target.value)}
+                placeholder={field.placeholder}
+                required={field.required}
+                rows={field.rows || 8}
+                className="mobile-edit-input mobile-edit-code"
+                style={{ fontFamily: "monospace" }}
+              />
+            )}
+
+            {(field.type === "text" || field.type === "number") && (
+              <input
+                type={field.type === "number" ? "number" : "text"}
+                id={field.name}
+                name={field.name}
+                value={String(formData[field.name] ?? "")}
+                onChange={(e) =>
+                  handleChange(
+                    field.name,
+                    field.type === "number"
+                      ? Number(e.target.value)
+                      : e.target.value
+                  )
+                }
+                placeholder={field.placeholder}
+                required={field.required}
+                className="mobile-edit-input"
+              />
+            )}
+          </div>
+        ))}
+      </form>
+    </div>
+  );
+};
@@ -0,0 +1,22 @@
+import { Icon } from "./icon";
+
+interface MobileFABProps {
+  onClick: () => void;
+  label?: string;
+}
+
+export const MobileFAB: React.FC<MobileFABProps> = ({
+  onClick,
+  label = "Create new",
+}) => {
+  return (
+    <button
+      className="mobile-fab"
+      onClick={onClick}
+      type="button"
+      aria-label={label}
+    >
+      <Icon name="add" size="md" />
+    </button>
+  );
+};
@@ -0,0 +1,76 @@
+import { Icon } from "./icon";
+import type { IconName } from "../utils/icons";
+
+interface MobileListItem {
+  id: string;
+  title: string;
+  subtitle?: string;
+  icon?: string;
+  status?: string;
+}
+
+interface MobileListViewProps {
+  items: MobileListItem[];
+  onItemClick: (id: string) => void;
+  onItemDelete?: (id: string) => void;
+  onItemDuplicate?: (id: string) => void;
+  emptyMessage?: string;
+  searchPlaceholder?: string;
+  onSearch?: (query: string) => void;
+}
+
+export const MobileListView: React.FC<MobileListViewProps> = ({
+  items,
+  onItemClick,
+  emptyMessage = "No items found",
+  searchPlaceholder = "Search...",
+  onSearch,
+}) => {
+  return (
+    <div className="mobile-list-view">
+      {onSearch && (
+        <div className="mobile-list-search">
+          <input
+            type="search"
+            placeholder={searchPlaceholder}
+            onChange={(e) => onSearch(e.target.value)}
+            className="mobile-list-search-input"
+          />
+        </div>
+      )}
+
+      {items.length === 0 ? (
+        <div className="mobile-list-empty">
+          <Icon name="folder" size="lg" />
+          <p>{emptyMessage}</p>
+        </div>
+      ) : (
+        <div className="mobile-list-items">
+          {items.map((item) => (
+            <button
+              key={item.id}
+              className="mobile-list-item"
+              onClick={() => onItemClick(item.id)}
+              type="button"
+            >
+              {item.icon && (
+                <div className="mobile-list-item-icon">
+                  <Icon name={item.icon as IconName} size="md" />
+                </div>
+              )}
+              <div className="mobile-list-item-content">
+                <div className="mobile-list-item-title">{item.title}</div>
+                {item.subtitle && (
+                  <div className="mobile-list-item-subtitle">{item.subtitle}</div>
+                )}
+              </div>
+              <div className="mobile-list-item-actions" style={{ transform: "rotate(180deg)" }}>
+                <Icon name="arrow-left" size="sm" />
+              </div>
+            </button>
+          ))}
+        </div>
+      )}
+    </div>
+  );
+};
--- a/Show More
+++ b/Show More