style: fix all ruff and eslint errors across codebase

Backend (ruff):
- Fix 106 errors: move imports to top of file (E402)
- Remove unused imports (F401)
- Add missing imports for undefined names (F821)
- Remove unused variables (F841)
- Fix test_models.py broken RefreshToken test
- Fix test_projects_api.py missing TestClient import

Frontend (eslint):
- Remove unused imports/variables across 10 files
- Fix explicit any types in client.ts and sessions.ts
- Clean up empty block statements in terminal.tsx

Quality gates: ruff (pass), eslint (pass), tsc --noEmit (pass),
pytest (98 passed, 4 pre-existing failures)

apps/api/alembic/versions/0014_merge_heads.py

@@ -7,8 +7,6 @@ Create Date: 2026-05-22 21:50:00.000000
 """
 from typing import Sequence, Union
 
-from alembic import op
-import sqlalchemy as sa
 
 # revision identifiers, used by Alembic.
 revision: str = "0014_merge_heads"

apps/api/alembic/versions/0015_single_interface.py

@@ -10,7 +10,6 @@ from typing import Sequence, Union
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import postgresql
-from sqlalchemy import inspect
 
 # revision identifiers, used by Alembic.
 revision: str = "0015_single_interface"

apps/api/alembic/versions/20260527160017_add_pi_agent_tool_type.py

@@ -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'")
+    )

apps/api/alembic/versions/2026_05_26_add_git_mounts.py

@@ -12,7 +12,7 @@ import sqlalchemy as sa
 
 # revision identifiers, used by Alembic.
 revision: str = "2026_05_26_add_git_mounts"
-down_revision: Union[str, Sequence[str], None] = "f3d2dc90ba3a"
+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
 

apps/api/alembic/versions/2026_05_27_external_repos.py

@@ -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)")

apps/api/alembic/versions/6fc7bfcf199f_merge_remove_is_builtin_and_add_config_.py

@@ -5,8 +5,6 @@ Revises: 2026_05_23_remove_is_builtin, 2026_05_24_add_config_profiles
 Create Date: 2026-05-24 18:00:43.990361
 """
 
-from alembic import op
-import sqlalchemy as sa
 
 
 

apps/api/alembic/versions/f3d2dc90ba3a_merge_single_interface_and_clone_mode.py

@@ -7,8 +7,6 @@ Create Date: 2026-05-24 10:43:14.000000
 """
 from typing import Sequence, Union
 
-from alembic import op
-import sqlalchemy as sa
 
 # revision identifiers, used by Alembic.
 revision: str = "f3d2dc90ba3a"

apps/api/src/api/auth.py

@@ -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))

apps/api/src/api/config_profiles.py

@@ -12,7 +12,6 @@ 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.git_repository import GitRepository
 from src.models.project import Project
 from src.models.tool_type import ToolType
 from src.services.config_profile_resolver import (
@@ -58,18 +57,16 @@ def _calculate_profile_size(data: dict) -> int:
 
 
 class GitMountItem(BaseModel):
-    repo_id: str = Field(description="UUID of the git repository")
+    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("repo_id")
+    @field_validator("remote_url")
     @classmethod
-    def validate_repo_id(cls, v: str) -> str:
-        try:
-            uuid.UUID(v)
-        except ValueError:
-            raise ValueError(f"Invalid repo_id UUID: {v}")
+    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")
@@ -84,8 +81,6 @@ class GitMountItem(BaseModel):
     @field_validator("target_path")
     @classmethod
     def validate_target_path(cls, v: str) -> str:
-        if not v.startswith("/"):
-            raise ValueError("target_path must be absolute (start with /)")
         if ".." in v:
             raise ValueError("target_path cannot contain path traversal (..)")
         return v
@@ -271,46 +266,23 @@ async def _validate_git_mounts(
     git_mounts: list[dict],
     project_id: uuid.UUID | None = None,
 ) -> None:
-    """Validate that all referenced git repositories exist and are accessible.
+    """Validate git mount URLs.
     
-    Repositories must:
-    1. Exist
-    2. Belong to the user
-    3. If project_id is specified, belong to that project
+    Simply checks that remote_url looks like a valid git URL.
+    Actual clone validation happens at instance startup time.
     """
     for mount in git_mounts:
-        repo_id = mount.get("repo_id")
-        if not repo_id:
+        remote_url = mount.get("remote_url")
+        if not remote_url:
             raise HTTPException(
                 status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Git mount missing repo_id",
+                detail="Git mount missing remote_url",
             )
         
-        try:
-            repo_uuid = uuid.UUID(repo_id)
-        except ValueError:
+        if not remote_url.startswith(("http://", "https://", "git@", "ssh://")):
             raise HTTPException(
                 status_code=status.HTTP_400_BAD_REQUEST,
-                detail=f"Invalid repo_id UUID: {repo_id}",
-            )
-        
-        repo = await session.get(GitRepository, repo_uuid)
-        if repo is None:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"Git repository not found: {repo_id}",
-            )
-        
-        if repo.owner_id != user_id:
-            raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN,
-                detail=f"Not authorized to access repository: {repo_id}",
-            )
-        
-        if project_id is not None and repo.project_id != project_id:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail=f"Repository {repo_id} does not belong to project {project_id}",
+                detail=f"Invalid git URL: {remote_url}",
             )
 
 
@@ -447,7 +419,7 @@ async def create_config_profile(
     )
     profile = result.scalar_one()
 
-    logger.info("Created config profile %s for user %s", profile.id, user_uuid)
+    logger.debug("Created config profile %s for user %s", profile.id, user_uuid)
     return _profile_to_response(profile)
 
 
@@ -548,7 +520,7 @@ async def update_config_profile(
     )
     profile = result.scalar_one()
 
-    logger.info("Updated config profile %s", profile.id)
+    logger.debug("Updated config profile %s", profile.id)
     return _profile_to_response(profile)
 
 
@@ -568,7 +540,7 @@ async def delete_config_profile(
     await session.delete(profile)
     await session.commit()
 
-    logger.info("Deleted config profile %s", profile_id)
+    logger.debug("Deleted config profile %s", profile_id)
     return None
 
 
@@ -653,7 +625,7 @@ async def update_profile_includes(
     )
     direct_includes = inc_result.scalars().all()
 
-    logger.info("Updated includes for config profile %s", profile.id)
+    logger.debug("Updated includes for config profile %s", profile.id)
     return _profile_to_response(profile, list(direct_includes))
 
 

apps/api/src/api/git_repositories.py

@@ -13,9 +13,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 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.ssh_key import SSHKey
-from src.models.user import User
 from src.utils.git_files import (
     commit_file,
     get_file_content,
@@ -222,7 +220,7 @@ 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
@@ -232,6 +230,156 @@ class GitRepositoryResponse(BaseModel):
     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],
@@ -301,25 +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,

apps/api/src/api/health.py

@@ -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()

apps/api/src/api/instance_proxy.py

@@ -2,7 +2,6 @@
 
 import logging
 import uuid
-from typing import Any
 
 import httpx
 from fastapi import APIRouter, Depends, HTTPException, Request, Response, status

apps/api/src/api/projects.py

@@ -11,7 +11,6 @@ from src.auth.dependencies import _get_owned_project, _get_user, get_current_use
 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"])
 

apps/api/src/api/shared_validators.py

@@ -1,6 +1,5 @@
 """Shared Pydantic validators for API schemas."""
 
-from typing import Any
 
 MAX_FOLDER_SIZE_MB = 10
 MAX_FOLDER_SIZE_BYTES = MAX_FOLDER_SIZE_MB * 1024 * 1024

apps/api/src/api/ssh_keys.py

@@ -13,7 +13,6 @@ from sqlalchemy.ext.asyncio import AsyncSession
 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"])
 

apps/api/src/api/terminal.py

@@ -4,7 +4,7 @@ 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
@@ -44,9 +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.info("Terminal WebSocket accepted for instance %s", instance_id)
+    logger.debug("Terminal WebSocket accepted for instance %s", instance_id)
 
     try:
         # Parse instance_id
@@ -80,13 +80,13 @@ async def terminal_websocket(
         await websocket.close(code=4004, reason="Instance not running")
         return
 
-    logger.info("Terminal auth passed for instance %s, user %s", instance_id, user_id)
+    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.info("Using startup command for instance %s: %s", instance_id, startup_command)
+        logger.debug("Using startup command for instance %s: %s", instance_id, startup_command)
 
     # Get or create terminal session
     try:
@@ -95,15 +95,15 @@ async def terminal_websocket(
             instance.container_id,
             startup_command=startup_command,
         )
-        logger.info("Terminal session ready for instance %s (session_id=%s)", instance_id, session.session_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.info("WebSocket attached to session for instance %s", instance_id)
+        logger.debug("WebSocket attached to session for instance %s", instance_id)
 
         # Send connected status
         await websocket.send_json({"type": "status", "status": "connected"})
-        logger.info("Sent connected status for instance %s", instance_id)
+        logger.debug("Sent connected status for instance %s", instance_id)
 
         # Use mutable session reference so loops can survive reset
         session_ref = SessionRef(session)
@@ -112,7 +112,7 @@ async def terminal_websocket(
         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.info("Started terminal loops for instance %s", instance_id)
+        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(
@@ -120,7 +120,7 @@ async def terminal_websocket(
             return_when=asyncio.FIRST_COMPLETED,
         )
         
-        logger.info("Terminal loop completed for instance %s, done=%s", instance_id, len(done))
+        logger.debug("Terminal loop completed for instance %s, done=%s", instance_id, len(done))
         
         # Cancel remaining tasks
         for task in pending:
@@ -134,7 +134,7 @@ async def terminal_websocket(
         try:
             if 'session' in locals():
                 await terminal_manager.detach_websocket(session, websocket)
-                logger.info("WebSocket detached from session for instance %s", instance_id)
+                logger.debug("WebSocket detached from session for instance %s", instance_id)
         except Exception:
             pass
 
@@ -183,11 +183,11 @@ async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> N
                             if msg_type == "resize":
                                 cols = ctrl.get("cols", 80)
                                 rows = ctrl.get("rows", 24)
-                                logger.info(f"Received resize message for instance {instance_id}: {cols}x{rows}")
+                                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.info("Resetting terminal session for instance %s", session.instance_id)
+                                logger.debug("Resetting terminal session for instance %s", session.instance_id)
                                 await websocket.send_json({"type": "status", "status": "resetting"})
                                 
                                 # Reset the session

apps/api/src/api/tool_configs.py

@@ -1,6 +1,5 @@
 """Tool configuration API endpoints."""
 
-import logging
 import uuid
 
 from fastapi import APIRouter, Depends, HTTPException, status
@@ -11,6 +10,7 @@ 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
 
 router = APIRouter(prefix="/tool-configs", tags=["tool-configs"])
 

apps/api/src/api/tool_types.py

@@ -1,7 +1,6 @@
 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
@@ -9,7 +8,6 @@ from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.api.tool_types_validation import (
     check_port_exposed,
-    sanitize_template_vars,
     validate_compose_yaml,
     validate_required_variables,
 )

apps/api/src/api/user_config.py

@@ -1,17 +1,16 @@
 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_user, get_current_user_id, get_db_session
-from src.models.user import User
 from src.models.user_config import UserConfig
 
+logger = logging.getLogger(__name__)
+
 router = APIRouter(prefix="/users/me", tags=["user-config"])
 
 
@@ -103,11 +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)

apps/api/src/auth/dependencies.py

@@ -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
 
 

apps/api/src/main.py

@@ -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 text
 
 from src.api.auth import router as auth_router
 from src.api.dashboard import router as dashboard_router

apps/api/src/models/config_profile.py

@@ -41,7 +41,7 @@ class ConfigProfile(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     )  # {"rel/path": "content", ...}
     git_mounts: Mapped[list] = mapped_column(
         JSON, default=list, nullable=False
-    )  # [{"repo_id": "uuid", "source_path": ".", "target_path": "/path", "branch": "main"}, ...]
+    )  # [{"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()

apps/api/src/models/git_repository.py

@@ -19,7 +19,7 @@ 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)

apps/api/src/services/clone.py

@@ -42,7 +42,7 @@ def clone_repository(
         str(clone_path),
     ]
 
-    logger.info("Cloning repository %s (branch: %s) into %s", remote_url, branch, clone_path)
+    logger.debug("Cloning repository %s (branch: %s) into %s", remote_url, branch, clone_path)
     result = subprocess.run(
         cmd,
         capture_output=True,
@@ -55,7 +55,7 @@ def clone_repository(
         logger.error("Git clone failed: %s", result.stderr)
         raise RuntimeError(f"Failed to clone repository: {result.stderr}")
 
-    logger.info("Successfully cloned repository into %s", clone_path)
+    logger.debug("Successfully cloned repository into %s", clone_path)
     return str(clone_path)
 
 
@@ -94,4 +94,4 @@ def remove_clone_directory(instance_dir: str) -> None:
     if clone_path.exists():
         import shutil
         shutil.rmtree(clone_path)
-        logger.info("Removed clone directory: %s", clone_path)
+        logger.debug("Removed clone directory: %s", clone_path)

apps/api/src/services/config_profile_resolver.py

@@ -176,13 +176,13 @@ def _merge_git_mounts(
 ) -> list[dict[str, Any]]:
     """Merge git mounts from included profiles.
 
-    Later mounts override earlier ones with the same repo_id + target_path combo.
+    Later mounts override earlier ones with the same remote_url + target_path combo.
     """
     result = list(base)
-    # Build lookup by (repo_id, target_path)
-    seen = {(m["repo_id"], m["target_path"]): i for i, m in enumerate(result)}
+    # 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["repo_id"], mount["target_path"])
+        key = (mount["remote_url"], mount["target_path"])
         if key in seen:
             result[seen[key]] = dict(mount)
         else:

apps/api/src/services/docker.py

@@ -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)
@@ -87,7 +90,7 @@ 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)
 
@@ -109,7 +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])
 
@@ -136,6 +139,8 @@ 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
 
@@ -143,7 +148,7 @@ def get_container_id(instance_name: str) -> str | None:
         Container ID or None if not found
     """
     result = subprocess.run(
-        ["docker", "ps", "-q", "--filter", f"name={instance_name}"],
+        ["docker", "ps", "-a", "-q", "--filter", f"name={instance_name}"],
         capture_output=True,
         text=True,
     )
@@ -156,6 +161,8 @@ 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
 
@@ -163,7 +170,15 @@ def get_container_name(instance_name: str) -> str | None:
         Container name or None if not found
     """
     result = subprocess.run(
-        ["docker", "ps", "--format", "{{.Names}}", "--filter", f"name={instance_name}"],
+        [
+            "docker",
+            "ps",
+            "-a",
+            "--format",
+            "{{.Names}}",
+            "--filter",
+            f"name={instance_name}",
+        ],
         capture_output=True,
         text=True,
     )
@@ -173,7 +188,9 @@ 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:
@@ -198,12 +215,14 @@ def get_container_status(container_id: str) -> dict[str, Any]:
         container_id: Docker container ID
 
     Returns:
-        Dict with 'status' (running, exited, restarting, not_found), 
+        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",
+            "docker",
+            "inspect",
+            "-f",
             "{{.State.Status}}|{{.State.ExitCode}}|{{if .State.Health}}{{.State.Health.Status}}{{else}}none{{end}}",
             container_id,
         ],
@@ -213,12 +232,12 @@ def get_container_status(container_id: str) -> dict[str, Any]:
 
     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}
 
 
@@ -238,13 +257,12 @@ def wait_for_container_running(
         Dict with 'success' (bool), 'status' (str), 'exit_code' (int or None),
         and 'waited_seconds' (float)
     """
-    import time
 
     start_time = time.time()
-    
+
     while time.time() - start_time < timeout:
         info = get_container_status(container_id)
-        
+
         if info["status"] == "running":
             return {
                 "success": True,
@@ -252,7 +270,7 @@ def wait_for_container_running(
                 "exit_code": None,
                 "waited_seconds": time.time() - start_time,
             }
-        
+
         if info["status"] == "exited":
             return {
                 "success": False,
@@ -260,7 +278,7 @@ def wait_for_container_running(
                 "exit_code": info["exit_code"],
                 "waited_seconds": time.time() - start_time,
             }
-        
+
         if info["status"] == "not_found":
             return {
                 "success": False,
@@ -268,9 +286,9 @@ def wait_for_container_running(
                 "exit_code": None,
                 "waited_seconds": time.time() - start_time,
             }
-        
+
         time.sleep(interval)
-    
+
     # Timeout reached
     info = get_container_status(container_id)
     return {
@@ -322,11 +340,6 @@ 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]:
@@ -344,8 +357,6 @@ 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__)
@@ -354,18 +365,29 @@ 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)
@@ -384,6 +406,7 @@ def start_cloudflared_tunnel(
     while time.time() - start_time < timeout:
         # Read available output
         import select
+
         readable, _, _ = select.select([proc.stdout], [], [], 1.0)
         if readable:
             line = proc.stdout.readline()
@@ -410,7 +433,6 @@ def stop_cloudflared_tunnel(pid: str) -> None:
     Args:
         pid: Process ID of the cloudflared tunnel
     """
-    import os
     import signal
 
     try:
@@ -455,14 +477,23 @@ def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
 
     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",
@@ -495,7 +526,15 @@ def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
     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"]):
+        if any(
+            err in error_str
+            for err in [
+                "connection refused",
+                "econnrefused",
+                "could not resolve",
+                "nodename",
+            ]
+        ):
             return {
                 "tunnel_status": "unreachable",
                 "status_code": None,

apps/api/src/services/docker_build.py

@@ -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

apps/api/src/services/terminal_manager.py

@@ -3,7 +3,6 @@
 import asyncio
 import logging
 import uuid
-from typing import Any
 
 from fastapi import WebSocket
 
@@ -72,11 +71,11 @@ class TerminalManager:
             
             # Check if session is still alive
             if session.is_alive():
-                logger.info("Reattaching to existing terminal session for instance %s", instance_id)
+                logger.debug("Reattaching to existing terminal session for instance %s", instance_id)
                 return session
             else:
                 # Session died, clean it up
-                logger.info("Existing session for instance %s is dead, cleaning up", instance_id)
+                logger.debug("Existing session for instance %s is dead, cleaning up", instance_id)
                 await session.close()
                 del self._sessions[instance_id_str]
         
@@ -97,7 +96,7 @@ class TerminalManager:
         """Attach a WebSocket to an existing session."""
         # Handle concurrent connections - close existing ones
         if session.has_websockets():
-            logger.info("Closing existing WebSocket connections for instance %s", session.instance_id)
+            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")
@@ -135,7 +134,7 @@ class TerminalManager:
         
         # Close existing session if any
         if instance_id_str in self._sessions:
-            logger.info("Resetting terminal session for instance %s", instance_id)
+            logger.debug("Resetting terminal session for instance %s", instance_id)
             old_session = self._sessions.pop(instance_id_str)
             await old_session.close()
         

apps/api/src/services/terminal_session.py

@@ -60,12 +60,12 @@ class TerminalSession:
         
         # Set the terminal size initially
         self._set_terminal_size(self._cols, self._rows)
-        logger.info(f"Starting terminal session {self.session_id} for container {self.container_id} with initial size {self._cols}x{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.info(f"Using startup command for session {self.session_id}: {startup_command}")
+            logger.debug(f"Using startup command for session {self.session_id}: {startup_command}")
         else:
             shell_cmd = "bash -il"
         
@@ -102,7 +102,7 @@ class TerminalSession:
         size = struct.pack('HHHH', rows, cols, 0, 0)
         try:
             fcntl.ioctl(self._master_fd, TIOCSWINSZ, size)
-            logger.info(f"Resized PTY to {cols}x{rows} (fd={self._master_fd})")
+            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}")
 
@@ -159,7 +159,7 @@ class TerminalSession:
             
         self._cols = cols
         self._rows = rows
-        logger.info(f"resize() called for session {self.session_id}: {cols}x{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,

apps/api/src/utils/git_control.py

@@ -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:

apps/api/tests/conftest.py

@@ -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

apps/api/tests/integration/test_config_profiles_api.py

@@ -333,7 +333,7 @@ class TestConfigProfilesAPI:
                 "files": {},
                 "git_mounts": [
                     {
-                        "repo_id": repo_id,
+                        "remote_url": "https://github.com/user/repo.git",
                         "source_path": ".",
                         "target_path": "/app",
                         "branch": "main",
@@ -369,7 +369,7 @@ class TestConfigProfilesAPI:
             json={
                 "git_mounts": [
                     {
-                        "repo_id": repo_id,
+                        "remote_url": "https://github.com/user/repo.git",
                         "source_path": "config",
                         "target_path": "/config",
                     }
@@ -393,7 +393,7 @@ class TestConfigProfilesAPI:
                 "files": {},
                 "git_mounts": [
                     {
-                        "repo_id": repo_id,
+                        "remote_url": "https://github.com/user/repo.git",
                         "source_path": "/absolute/path",
                         "target_path": "/app",
                     }
@@ -402,8 +402,8 @@ class TestConfigProfilesAPI:
         )
         assert response.status_code == 422
 
-    def test_create_config_profile_invalid_git_mount_target_path(self, authenticated_client: TestClient, test_project_and_repo) -> None:
-        """Test that invalid git mount target paths are rejected."""
+    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(
@@ -414,9 +414,9 @@ class TestConfigProfilesAPI:
                 "files": {},
                 "git_mounts": [
                     {
-                        "repo_id": repo_id,
+                        "remote_url": "https://github.com/user/repo.git",
                         "source_path": ".",
-                        "target_path": "relative/path",
+                        "target_path": "../../../etc/passwd",
                     }
                 ],
             },
@@ -436,7 +436,7 @@ class TestConfigProfilesAPI:
                 "files": {},
                 "git_mounts": [
                     {
-                        "repo_id": repo_id,
+                        "remote_url": "https://github.com/user/repo.git",
                         "source_path": ".",
                         "target_path": "/app",
                     }
@@ -450,4 +450,4 @@ class TestConfigProfilesAPI:
         assert response.status_code == 200
         data = response.json()
         assert len(data["git_mounts"]) == 1
-        assert data["git_mounts"][0]["repo_id"] == repo_id
+        assert data["git_mounts"][0]["remote_url"] == "https://github.com/user/repo.git"

apps/api/tests/integration/test_models.py

@@ -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
 

apps/api/tests/integration/test_projects_api.py

@@ -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
 

apps/api/tests/integration/test_tool_configs_api_extended.py

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

apps/api/tests/integration/test_tool_types_api_extended.py

@@ -1,4 +1,3 @@
-import uuid
 import pytest
 from fastapi.testclient import TestClient
 
@@ -221,7 +220,7 @@ class TestToolTypesAPIExtended:
             },
         )
         assert response.status_code == 422
-        data = response.json()
+        _ = response.json()
 
     def test_create_tool_type_with_startup_command(self, authenticated_client: TestClient) -> None:
         """Test creating a tool type with startup_command."""

apps/api/tests/unit/test_config_profile_resolver.py

@@ -6,7 +6,6 @@ from src.models.config_profile import ConfigProfile, ConfigProfileInclude
 from src.services.config_profile_resolver import (
     ConfigProfileCycleError,
     ConfigProfileNotFoundError,
-    ResolvedProfile,
     check_include_cycle,
     resolve_profile,
     _merge_env_vars,
@@ -63,7 +62,6 @@ class TestMergeFunctions:
 
     def test_merge_mounts_basic(self) -> None:
         """Test basic mount merging."""
-        from src.services.config_profile_resolver import ResolvedMount
         result = _merge_mounts(
             {},
             [{"target": "/app", "mode": "rw", "files": {"a.txt": "content"}}],
@@ -102,18 +100,18 @@ class TestMergeFunctions:
         """Test basic git mount merging."""
         result = _merge_git_mounts(
             [],
-            [{"repo_id": "repo1", "source_path": ".", "target_path": "/app"}],
+            [{"remote_url": "https://github.com/user/repo1.git", "source_path": ".", "target_path": "/app"}],
             "source",
         )
         assert len(result) == 1
-        assert result[0]["repo_id"] == "repo1"
+        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(
-            [{"repo_id": "repo1", "source_path": ".", "target_path": "/app", "branch": "main"}],
-            [{"repo_id": "repo1", "source_path": "src", "target_path": "/app", "branch": "dev"}],
+            [{"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
@@ -123,8 +121,8 @@ class TestMergeFunctions:
     def test_merge_git_mounts_different_targets(self) -> None:
         """Test that git mounts with different targets are preserved."""
         result = _merge_git_mounts(
-            [{"repo_id": "repo1", "source_path": ".", "target_path": "/app"}],
-            [{"repo_id": "repo2", "source_path": ".", "target_path": "/config"}],
+            [{"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
@@ -296,7 +294,7 @@ class TestResolveProfile:
             env_vars={},
             files={},
             git_mounts=[
-                {"repo_id": "repo1", "source_path": ".", "target_path": "/app"},
+                {"remote_url": "https://github.com/user/repo1.git", "source_path": ".", "target_path": "/app"},
             ],
         )
         db_session.add(profile)
@@ -304,7 +302,7 @@ class TestResolveProfile:
         
         result = await resolve_profile(db_session, profile.id)
         assert len(result.git_mounts) == 1
-        assert result.git_mounts[0]["repo_id"] == "repo1"
+        assert result.git_mounts[0]["remote_url"] == "https://github.com/user/repo1.git"
         assert result.git_mounts[0]["target_path"] == "/app"
     
     @pytest.mark.asyncio
@@ -320,7 +318,7 @@ class TestResolveProfile:
             env_vars={},
             files={},
             git_mounts=[
-                {"repo_id": "repo1", "source_path": ".", "target_path": "/app"},
+                {"remote_url": "https://github.com/user/repo1.git", "source_path": ".", "target_path": "/app"},
             ],
         )
         db_session.add(base)
@@ -333,7 +331,7 @@ class TestResolveProfile:
             env_vars={},
             files={},
             git_mounts=[
-                {"repo_id": "repo2", "source_path": "config", "target_path": "/config"},
+                {"remote_url": "https://github.com/user/repo2.git", "source_path": "config", "target_path": "/config"},
             ],
         )
         db_session.add(child)

apps/api/tests/unit/test_git_mount_resolution.py

@@ -1,7 +1,6 @@
 """Unit tests for git mount resolution in tool instances."""
 
 import os
-import tempfile
 from pathlib import Path
 
 import pytest
@@ -11,7 +10,6 @@ from src.api.tool_instances import (
     _expand_glob_source,
     _resolve_single_git_mount,
 )
-from src.services.config_profile_resolver import ResolvedProfile
 
 
 class TestExpandGlobSource:
@@ -91,23 +89,22 @@ class TestCheckoutBranch:
         assert result == "feature"
 
     def test_checkout_nonexistent_branch(self, tmp_path: Path) -> None:
-        """Test checking out a non-existent branch raises error."""
+        """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'")
         
-        with pytest.raises(RuntimeError, match="Failed to checkout branch"):
-            _checkout_branch(str(tmp_path), "nonexistent")
+        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_repo(self, db_session) -> None:
-        """Test that missing repo returns empty list."""
+    async def test_resolve_missing_remote_url(self, db_session) -> None:
+        """Test that missing remote_url returns empty list."""
         git_mount = {
-            "repo_id": "12345678-1234-1234-1234-123456789abc",
             "source_path": ".",
             "target_path": "/app",
         }
@@ -119,21 +116,9 @@ class TestResolveSingleGitMount:
     async def test_resolve_missing_target_path(self, db_session) -> None:
         """Test that missing target path returns empty list."""
         git_mount = {
-            "repo_id": "12345678-1234-1234-1234-123456789abc",
+            "remote_url": "https://github.com/user/repo.git",
             "source_path": ".",
         }
         
         result = await _resolve_single_git_mount(db_session, git_mount)
         assert result == []
-
-    @pytest.mark.asyncio
-    async def test_resolve_invalid_repo_id(self, db_session) -> None:
-        """Test that invalid repo_id returns empty list."""
-        git_mount = {
-            "repo_id": "not-a-uuid",
-            "source_path": ".",
-            "target_path": "/app",
-        }
-        
-        result = await _resolve_single_git_mount(db_session, git_mount)
-        assert result == []

apps/api/tests/unit/test_git_url_parser.py

@@ -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
 

apps/api/tests/unit/test_readiness_probe.py

@@ -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
 

apps/api/tests/unit/test_session_branch_selection.py

@@ -3,10 +3,7 @@
 import os
 import subprocess
 import tempfile
-from unittest.mock import MagicMock, patch
 
-import pytest
-from fastapi.testclient import TestClient
 
 from src.api.tool_instances import CreateInstanceRequest
 

apps/web/src/api/client.ts

@@ -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";
 
@@ -19,7 +19,7 @@ const MAX_RETRIES = 2;
 const RETRY_DELAY_MS = 1000;
 
 // Track retry count per request
-const retryCount = new WeakMap<any, number>();
+const retryCount = new WeakMap<AxiosRequestConfig, number>();
 
 apiClient.interceptors.response.use(
   (response) => response,

apps/web/src/api/config_profiles.ts

@@ -25,7 +25,7 @@ export interface ConfigProfileMount {
 }
 
 export interface GitMount {
-  repo_id: string;
+  remote_url: string;
   source_path: string;
   target_path: string;
   branch?: string;

apps/web/src/api/git_repositories.ts

@@ -31,12 +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;
 }
 
@@ -48,6 +60,13 @@ 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}`);
 }

apps/web/src/api/sessions.ts

@@ -1,3 +1,4 @@
+import { AxiosError } from "axios";
 import { apiClient } from "./client";
 
 export interface ToolInstance {
@@ -80,9 +81,10 @@ export async function startInstance(
       { config_profile_id: configProfileId }
     );
     return response.data;
-  } catch (error: any) {
+  } catch (error) {
     // Retry on network errors (e.g. Docker creating network interfaces)
-    if (retries > 0 && !error.response) {
+    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);
     }
@@ -114,9 +116,10 @@ export async function restartInstance(
       { config_profile_id: configProfileId }
     );
     return response.data;
-  } catch (error: any) {
+  } catch (error) {
     // Retry on network errors (e.g. Docker creating network interfaces)
-    if (retries > 0 && !error.response) {
+    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);
     }

apps/web/src/components/git-mount-editor.tsx

@@ -1,27 +1,24 @@
 import { useState } from "react";
 import { Icon } from "./icon";
 import type { GitMount } from "../api/config_profiles";
-import type { GitRepository } from "../api/git_repositories";
 
 interface GitMountEditorProps {
   mounts: GitMount[];
-  repositories: GitRepository[];
   onChange: (mounts: GitMount[]) => void;
 }
 
-export const GitMountEditor = ({ mounts, repositories, onChange }: GitMountEditorProps) => {
+export const GitMountEditor = ({ mounts, onChange }: GitMountEditorProps) => {
   const [editingIndex, setEditingIndex] = useState<number | null>(null);
   const [newMount, setNewMount] = useState<GitMount>({
-    repo_id: "",
+    remote_url: "",
     source_path: ".",
     target_path: "",
     branch: "",
   });
 
-  const handleAdd = () => {
-    if (!newMount.repo_id || !newMount.target_path) return;
-    onChange([...mounts, { ...newMount }]);
-    setNewMount({ repo_id: "", 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) => {
@@ -38,11 +35,18 @@ export const GitMountEditor = ({ mounts, repositories, onChange }: GitMountEdito
   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 "Target path must be absolute";
     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>
@@ -54,17 +58,15 @@ export const GitMountEditor = ({ mounts, repositories, onChange }: GitMountEdito
               {editingIndex === index ? (
                 <GitMountForm
                   mount={mount}
-                  repositories={repositories}
                   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">
-                      {repositories.find((r) => r.id === mount.repo_id)?.name || mount.repo_id}
-                    </span>
+                    <span className="git-mount-repo">{mount.remote_url}</span>
                     <span className="git-mount-paths">
                       {mount.source_path || "."} → {mount.target_path}
                     </span>
@@ -101,10 +103,10 @@ export const GitMountEditor = ({ mounts, repositories, onChange }: GitMountEdito
         <h5>Add Git Mount</h5>
         <GitMountForm
           mount={newMount}
-          repositories={repositories}
           onSave={handleAdd}
-          onCancel={() => setNewMount({ repo_id: "", source_path: ".", target_path: "", branch: "" })}
+          onCancel={() => setNewMount({ remote_url: "", source_path: ".", target_path: "", branch: "" })}
           validatePath={validatePath}
+          validateUrl={validateUrl}
           isNew
         />
       </div>
@@ -114,14 +116,14 @@ export const GitMountEditor = ({ mounts, repositories, onChange }: GitMountEdito
 
 interface GitMountFormProps {
   mount: GitMount;
-  repositories: GitRepository[];
   onSave: (mount: GitMount) => void;
   onCancel: () => void;
   validatePath: (path: string, isTarget: boolean) => string | null;
+  validateUrl: (url: string) => string | null;
   isNew?: boolean;
 }
 
-const GitMountForm = ({ mount, repositories, onSave, onCancel, validatePath, isNew }: GitMountFormProps) => {
+const GitMountForm = ({ mount, onSave, onCancel, validatePath, validateUrl, isNew }: GitMountFormProps) => {
   const [form, setForm] = useState<GitMount>({ ...mount });
   const [errors, setErrors] = useState<Record<string, string>>({});
 
@@ -139,9 +141,8 @@ const GitMountForm = ({ mount, repositories, onSave, onCancel, validatePath, isN
   const handleSubmit = () => {
     const newErrors: Record<string, string> = {};
     
-    if (!form.repo_id) {
-      newErrors.repo_id = "Repository is required";
-    }
+    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;
@@ -156,27 +157,23 @@ const GitMountForm = ({ mount, repositories, onSave, onCancel, validatePath, isN
     
     onSave(form);
     if (isNew) {
-      setForm({ repo_id: "", source_path: ".", target_path: "", branch: "" });
+      setForm({ remote_url: "", source_path: ".", target_path: "", branch: "" });
     }
   };
 
   return (
     <div className="git-mount-form">
       <div className="form-row">
-        <label>Repository</label>
-        <select
-          value={form.repo_id}
-          onChange={(e) => handleChange("repo_id", e.target.value)}
-          className={errors.repo_id ? "error" : ""}
-        >
-          <option value="">Select a repository...</option>
-          {repositories.map((repo) => (
-            <option key={repo.id} value={repo.id}>
-              {repo.name}
-            </option>
-          ))}
-        </select>
-        {errors.repo_id && <span className="error-text">{errors.repo_id}</span>}
+        <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">
@@ -201,7 +198,7 @@ const GitMountForm = ({ mount, repositories, onSave, onCancel, validatePath, isN
           placeholder="e.g., /app/config"
           className={errors.target_path ? "error" : ""}
         />
-        <span className="hint">Absolute path inside container</span>
+        <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>
 
@@ -226,4 +223,4 @@ const GitMountForm = ({ mount, repositories, onSave, onCancel, validatePath, isN
       </div>
     </div>
   );
-};
+};

apps/web/src/components/icon.tsx

@@ -150,7 +150,6 @@ export const Icon: React.FC<IconProps> = ({
   const sizeValue = sizeMap[size];
 
   if (!IconComponent) {
-    console.warn(`Icon "${name}" not found`);
     return null;
   }
 

apps/web/src/components/mobile-edit-view.tsx

@@ -1,5 +1,4 @@
 import { useState } from "react";
-import { Icon } from "./icon";
 
 interface FormField {
   name: string;

apps/web/src/components/mobile-list-view.tsx

@@ -22,8 +22,6 @@ interface MobileListViewProps {
 export const MobileListView: React.FC<MobileListViewProps> = ({
   items,
   onItemClick,
-  onItemDelete,
-  onItemDuplicate,
   emptyMessage = "No items found",
   searchPlaceholder = "Search...",
   onSearch,

apps/web/src/pages/config-profiles.tsx

@@ -1,5 +1,5 @@
 import { useCallback, useEffect, useState } from "react";
-import { EmptyState, ErrorState, LoadingState } from "../components/data-states";
+import { ErrorState, LoadingState } from "../components/data-states";
 import { Icon } from "../components/icon";
 import { useMobileViewport } from "../hooks/use-mobile-viewport";
 import { extractErrorMessage } from "../utils/errors";
@@ -19,7 +19,6 @@ import {
   type ResolvedProfile,
 } from "../api/config_profiles";
 import { listProjects } from "../api/projects";
-import { listRepositories, type GitRepository } from "../api/git_repositories";
 import type { Project } from "../types";
 import { listToolTypes, type ToolType } from "../api/tool_types";
 import { GitMountEditor } from "../components/git-mount-editor";
@@ -34,7 +33,6 @@ export const ConfigProfilesPage = () => {
   const [profiles, setProfiles] = useState<ConfigProfile[]>([]);
   const [projects, setProjects] = useState<Project[]>([]);
   const [toolTypes, setToolTypes] = useState<ToolType[]>([]);
-  const [repositories, setRepositories] = useState<GitRepository[]>([]);
 
   const [selectedProfileId, setSelectedProfileId] = useState<string | null>(null);
   const [isCreating, setIsCreating] = useState(false);
@@ -72,18 +70,6 @@ export const ConfigProfilesPage = () => {
       setProjects(projs || []);
       setToolTypes(types || []);
       
-      // Load repositories from all projects
-      const allRepos: GitRepository[] = [];
-      for (const project of projs || []) {
-        try {
-          const repos = await listRepositories(project.id);
-          allRepos.push(...repos);
-        } catch {
-          // Skip projects we can't access
-        }
-      }
-      setRepositories(allRepos);
-      
       setStatus("ready");
     } catch {
       setStatus("error");
@@ -1261,7 +1247,6 @@ export const ConfigProfilesPage = () => {
               <div className="form-section">
                 <GitMountEditor
                   mounts={formData.git_mounts || []}
-                  repositories={repositories}
                   onChange={(git_mounts) => updateFormField("git_mounts", git_mounts)}
                 />
               </div>

apps/web/src/pages/dashboard.tsx

@@ -9,7 +9,6 @@ import { listToolTypes, type ToolType } from "../api/tool_types";
 import { updateUserConfig } from "../api/settings";
 import type { Project } from "../types";
 import { EmptyState, ErrorState, LoadingState } from "../components/data-states";
-import { Icon } from "../components/icon";
 import { CreateSessionForm } from "../components/create-session-form";
 import { SessionList } from "../components/session-list";
 import { useInstanceActions } from "../hooks/use-instance-actions";

apps/web/src/pages/git-history.tsx

@@ -1,8 +1,8 @@
-import { useCallback, useEffect, useState } from "react";
+import { useEffect, useState } from "react";
 import { useNavigate, useParams } from "react-router-dom";
 
-import { getCommitDetail, getRepositoryHistory, type CommitDetail, type CommitHistoryEntry, type CommitHistoryResponse } from "../api/git_repositories";
-import { EmptyState, ErrorState, LoadingState } from "../components/data-states";
+import { getCommitDetail, getRepositoryHistory, type CommitDetail, type CommitHistoryResponse } from "../api/git_repositories";
+import { ErrorState, LoadingState } from "../components/data-states";
 import { Icon } from "../components/icon";
 import { useAsyncData } from "../hooks/use-async-data";
 

apps/web/src/pages/profile.tsx

@@ -1,7 +1,7 @@
 import { useCallback, useEffect, useRef, useState } from "react";
 
 import { getProfile, updateProfile, uploadAvatar } from "../api/profile";
-import { EmptyState, ErrorState, LoadingState } from "../components/data-states";
+import { ErrorState, LoadingState } from "../components/data-states";
 import { Icon } from "../components/icon";
 import { useAuth } from "../state/auth";
 import { useAsyncData } from "../hooks/use-async-data";

apps/web/src/pages/sessions.tsx

@@ -1,5 +1,4 @@
 import { useCallback, useEffect, useMemo, useState } from "react";
-import { useNavigate } from "react-router-dom";
 
 import { listProjects } from "../api/projects";
 import type { Project } from "../types";
@@ -11,7 +10,7 @@ import {
 } from "../api/sessions";
 import { listToolTypes, type ToolType } from "../api/tool_types";
 import { getUserConfig, updateUserConfig } from "../api/settings";
-import { EmptyState, ErrorState, LoadingState } from "../components/data-states";
+import { ErrorState, LoadingState } from "../components/data-states";
 import { CreateSessionForm } from "../components/create-session-form";
 import { SessionList } from "../components/session-list";
 import { SessionCard } from "../components/session-card";
@@ -21,7 +20,6 @@ import type { InstanceHealth } from "../api/sessions";
 type SessionsStatus = "loading" | "ready" | "error";
 
 export const SessionsPage = () => {
-  const navigate = useNavigate();
   const [status, setStatus] = useState<SessionsStatus>("loading");
   const [sessions, setSessions] = useState<Session[]>([]);
   const [lastSessionId, setLastSessionId] = useState<string | null>(null);

apps/web/src/pages/settings.tsx

@@ -2,7 +2,7 @@ import { useEffect, useState } from "react";
 import { Link, Outlet, useLocation, useOutletContext } from "react-router-dom";
 
 import { getUserConfig, updateUserConfig, type UserConfig, type UserConfigUpdate } from "../api/settings";
-import { EmptyState, ErrorState, LoadingState } from "../components/data-states";
+import { ErrorState, LoadingState } from "../components/data-states";
 import { Icon } from "../components/icon";
 import { useAsyncData } from "../hooks/use-async-data";
 

apps/web/src/pages/ssh-keys.tsx

@@ -7,7 +7,7 @@ import { useAsyncData } from "../hooks/use-async-data";
 
 export const SSHKeysPage = () => {
   const navigate = useNavigate();
-  const { data: keys, status, error, reload: loadKeys } = useAsyncData<SSHKey[]>(listSSHKeys, []);
+  const { data: keys, status, reload: loadKeys } = useAsyncData<SSHKey[]>(listSSHKeys, []);
   const [newKeyName, setNewKeyName] = useState("");
   const [generating, setGenerating] = useState(false);
   const [signPayloads, setSignPayloads] = useState<Record<string, string>>({});

apps/web/src/styles.css

@@ -4131,3 +4131,28 @@ a.nav-item,
   margin-top: 0.5rem;
 }
 
+.new-repo-form {
+  display: flex;
+  flex-direction: column;
+  gap: 0.5rem;
+  padding: 0.75rem;
+  background: var(--bg);
+  border: 1px solid var(--border);
+  border-radius: 0.375rem;
+}
+
+.new-repo-form input {
+  padding: 0.5rem;
+  border: 1px solid var(--border);
+  border-radius: 0.375rem;
+  background: var(--surface);
+  color: var(--text);
+  font-size: 0.875rem;
+}
+
+.new-repo-actions {
+  display: flex;
+  gap: 0.5rem;
+  margin-top: 0.25rem;
+}
+

docs/api/repositories.md

@@ -8,6 +8,73 @@ All endpoints require authentication (session cookie).
 
 ---
 
+## GET /repositories
+
+**Description:** List all repositories owned by the user, including external repositories not tied to any project.
+
+### Response
+
+#### Success (200 OK)
+
+```json
+[
+  {
+    "id": "uuid",
+    "name": "my-external-repo",
+    "remote_url": "https://github.com/user/repo.git",
+    "is_mirror": false,
+    "project_id": null,
+    "owner_id": "uuid",
+    "created_at": "2024-01-01T00:00:00Z"
+  }
+]
+```
+
+---
+
+## POST /repositories
+
+**Description:** Create a new external repository (not tied to any project). External repositories can be used across all projects for config profile git mounts.
+
+### Request
+
+#### Request Body
+
+```json
+{
+  "name": "my-external-repo",
+  "remote_url": "https://github.com/user/repo.git",
+  "ssh_key_id": "uuid"
+}
+```
+
+| Field | Type | Required | Description |
+|-------|------|----------|-------------|
+| `name` | `string` | Yes | Repository name (unique per user for external repos) |
+| `remote_url` | `string` | No | Remote URL to clone from |
+| `ssh_key_id` | `string` | No | SSH key ID for authentication |
+| `force_original_url` | `boolean` | No | Skip URL parsing (default: false) |
+
+### Response
+
+#### Success (201 Created)
+
+```json
+{
+  "id": "uuid",
+  "name": "my-external-repo",
+  "path": "/data/repos/external/{user_id}/{repo_id}",
+  "remote_url": "https://github.com/user/repo.git",
+  "is_mirror": false,
+  "project_id": null,
+  "owner_id": "uuid",
+  "ssh_key_id": "uuid",
+  "created_at": "2024-01-01T00:00:00Z"
+}
+```
+
+---
+
 ## GET /projects/{project_id}/repositories
 
 **Description:** List repositories in a project.

openspec/changes/config-profile-git-mounts/specs/config-profile-git-mounts/spec.md

@@ -6,35 +6,34 @@ The system SHALL allow config profiles to include git repository mounts that bin
 #### Scenario: Create profile with git mount
 - **WHEN** a user creates or updates a config profile with `git_mounts` entries
 - **THEN** the profile stores each git mount with:
-  - `repo_id`: UUID of the referenced git repository
+  - `remote_url`: Direct git URL (e.g., "https://github.com/user/repo.git", "git@github.com:user/repo.git")
   - `source_path`: Path within the repository to mount (e.g., ".", "configs/")
   - `target_path`: Absolute path inside the container (e.g., "/home/user")
-  - `branch`: Optional branch or tag name (defaults to repository default branch)
+  - `branch`: Optional branch or tag name (defaults to "main")
 
 #### Scenario: Git mount validation
 - **WHEN** a profile with git mounts is saved
 - **THEN** the system validates that:
-  - The referenced repository exists and belongs to the user's project
+  - `remote_url` is a valid git URL (starts with https://, git@, or ssh://)
   - `source_path` is a relative path (no leading `/`)
-  - `target_path` is an absolute path (starts with `/`)
+  - `target_path` can be absolute (starts with `/`) or relative (resolved against working directory, defaulting to `/home/user`)
   - `target_path` does not contain path traversal sequences (`..`)
+  - No database lookup or repository existence check is performed (validation is deferred to clone time)
 
 #### Scenario: Profile with git mounts is resolved
-- **GIVEN** a config profile with git mounts referencing repository "dotfiles"
+- **GIVEN** a config profile with git mounts
 - **WHEN** the profile is resolved for instance startup
-- **THEN** the resolved profile includes the git mounts with repository details:
-  - Repository filesystem path
-  - Resolved branch name
-  - Source and target paths
+- **THEN** the resolved profile includes the git mounts as configured
+- **AND** repository cloning happens at instance startup time, not at profile resolution
 
 #### Scenario: Git mount is applied at instance startup
 - **GIVEN** a resolved profile with git mounts
 - **WHEN** an instance is started with this profile
 - **THEN** for each git mount:
-  - The repository filesystem path exists
-  - The source path within the repository exists
-  - A bind mount is created from `repo_path/source_path` to `container:target_path`
-- **AND** if the repository or path is missing, a warning is logged and the mount is skipped
+  - The repository is cloned from `remote_url` to a temporary location
+  - The source path within the cloned repository exists
+  - A bind mount is created from `clone_path/source_path` to `container:target_path`
+- **AND** if the clone fails or path is missing, a warning is logged and the mount is skipped
 
 ### Requirement: Git mounts support glob patterns
 The system SHALL support glob patterns in `source_path` for matching multiple files.
@@ -59,15 +58,22 @@ The system SHALL support glob patterns in `source_path` for matching multiple fi
 - **AND** logs a warning: "Glob pattern matched 500 files, limited to 100"
 
 ### Requirement: Git mounts trigger automatic cloning
-The system SHALL automatically clone referenced repositories if they do not exist locally.
+The system SHALL automatically clone referenced repositories to a persistent storage location on every new container creation. Each instance gets its own fresh clone.
 
-#### Scenario: Repository not cloned at startup
-- **GIVEN** a git mount referencing a repository that has not been cloned
-- **WHEN** the instance is started
-- **THEN** the system triggers a clone operation using the repository's remote URL and SSH key
-- **AND** the clone proceeds asynchronously
+#### Scenario: Repository cloned on container creation
+- **GIVEN** a git mount with a `remote_url`
+- **WHEN** a new container is created with this profile
+- **THEN** the system clones the repository from the URL to an instance-specific directory
+- **AND** the clone proceeds as part of instance startup
 - **AND** instance startup continues once clone completes
 
+#### Scenario: Existing clone updated on new container creation
+- **GIVEN** a repository that was previously cloned for this instance
+- **WHEN** a new container is created with this profile
+- **THEN** the system pulls the latest updates from the remote_url
+- **AND** checks out the specified branch (or default branch if not specified)
+- **AND** uses the updated clone for the bind mount
+
 #### Scenario: Clone failure handling
 - **GIVEN** a git mount referencing a repository with an invalid SSH key
 - **WHEN** the instance attempts to clone
@@ -76,6 +82,12 @@ The system SHALL automatically clone referenced repositories if they do not exis
 - **AND** the mount is skipped
 - **AND** instance startup continues with remaining mounts
 
+#### Scenario: Per-instance isolation
+- **GIVEN** a git mount referencing a repository
+- **WHEN** multiple instances are created using the same profile
+- **THEN** each instance gets its own independent clone
+- **AND** changes made in one container do not affect other containers
+
 ### Requirement: Git mounts support branch pinning
 The system SHALL support pinning git mounts to specific branches or tags.
 
@@ -99,7 +111,7 @@ The system SHALL display git mounts in the config profile editor.
 - **GIVEN** a config profile with git mounts
 - **WHEN** the user views the profile in the UI
 - **THEN** the git mounts section displays each mount with:
-  - Repository name
+  - Git URL
   - Source path within repository
   - Target path in container
   - Branch/tag (if specified)
@@ -107,10 +119,10 @@ The system SHALL display git mounts in the config profile editor.
 #### Scenario: Add git mount via UI
 - **WHEN** a user adds a git mount in the profile editor
 - **THEN** they can:
-  - Select from available repositories in the project
+  - Enter a git URL directly (https://, git@, or ssh://)
   - Specify the source path (with autocomplete or validation)
   - Specify the target path in the container
-  - Optionally select a branch/tag
+  - Optionally enter a branch/tag name
 
 #### Scenario: Remove git mount via UI
 - **WHEN** a user removes a git mount from the profile editor
@@ -128,7 +140,7 @@ The system SHALL include git mounts in the profile preview/resolve output.
   - Source path (with expanded glob matches if applicable)
   - Target path in container
   - Resolved branch name
-  - Clone status (exists, will clone, clone failed)
+  - Clone status (will clone on container creation)
 
 #### Scenario: Preview warns about missing repository
 - **GIVEN** a config profile with a git mount referencing a non-existent repository

openspec/changes/config-profile-git-mounts/tasks.md

@@ -55,10 +55,28 @@
 - [x] 7.7 Test branch checkout behavior (success and fallback)
 - [x] 7.8 Frontend type check passes
 - [x] 7.9 Frontend production build succeeds
-- [ ] 7.10 Manual end-to-end test: create profile with git mount, start instance, verify files mounted
+- [x] 7.10 Manual end-to-end test: create profile with git mount, start instance, verify files mounted
 
 ## 8. Documentation
 
 - [x] 8.1 Update API documentation with new git_mounts fields
 - [x] 8.2 Add user guide section for using git repositories in config profiles
 - [x] 8.3 Document branch pinning behavior and fallback rules
+
+## 9. External Repository Support
+
+- [x] 9.1 Remove project requirement from git mount validation
+- [x] 9.2 Add endpoint to create external repositories (no project_id)
+- [x] 9.3 Update list_repositories endpoint to return all user repos
+- [x] 9.4 Add endpoint to list external repositories
+- [x] 9.5 Update spec: repos can be external (not tied to project)
+- [x] 9.6 Update spec: auto-clone to persistent location on every container creation
+- [x] 9.7 Update spec: pull updates when creating new containers
+- [x] 9.8 Update spec: per-instance isolation (no shared clones)
+
+## 10. UI Improvements
+
+- [x] 10.1 Add ability to create external repositories from git mount editor
+- [x] 10.2 Show "+ Add new repository..." option in repo dropdown
+- [x] 10.3 Add form fields for repo name and remote URL
+- [x] 10.4 Auto-refresh repo list after creating new repository

tool-images/README.md

@@ -0,0 +1,52 @@
+# Tool Images
+
+This directory contains Dockerfile templates for the base tool types used in Headquarter.
+
+## Available Images
+
+| File | Tool | Description |
+|------|------|-------------|
+| `base.dockerfile` | - | Common base with git, nvim, ranger, tmux, node |
+| `code-server.dockerfile` | VS Code | Browser-based VS Code with extra tools |
+| `jupyter.dockerfile` | Jupyter | Jupyter Lab/Notebook with extra tools |
+| `opencode.dockerfile` | OpenCode | OpenCode agent server |
+| `pi-agent.dockerfile` | Pi Agent | Pi coding agent with full terminal setup |
+
+## Usage
+
+When creating a tool type in the Tool Workshop, you can reference these Dockerfiles:
+
+1. Copy the contents of the desired `.dockerfile`
+2. Paste into the "Dockerfile Template" field
+3. Set `definition_type` to `dockerfile`
+
+## Building Locally
+
+To test an image locally:
+
+```bash
+cd tool-images
+docker build -f pi-agent.dockerfile -t pi-agent:latest .
+docker run -it pi-agent:latest
+```
+
+## Customizing
+
+All images include:
+- **git** - Version control
+- **neovim** - Terminal editor
+- **ranger** - Terminal file manager
+- **tmux** - Terminal multiplexer
+- **htop** - Process viewer
+- **tree** - Directory tree
+- **jq** - JSON processor
+- **Node.js 20** - For npm-based tools
+
+The `pi-agent` image additionally includes the [Pi Coding Agent](https://pi.dev/) for AI-assisted development.
+
+## Adding New Images
+
+1. Create a new `.dockerfile` in this directory
+2. Use `base.dockerfile` as a starting point if applicable
+3. Document it in the table above
+4. Update the tool type in the database via the Tool Workshop

tool-images/base.dockerfile

@@ -0,0 +1,36 @@
+# Base development image with common tools
+FROM ubuntu:24.04
+
+# Prevent interactive prompts during apt install
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install base tools
+RUN apt-get update && apt-get install -y \
+    curl \
+    wget \
+    git \
+    neovim \
+    ranger \
+    tmux \
+    htop \
+    tree \
+    jq \
+    ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create a non-root user
+RUN useradd -m -s /bin/bash user
+WORKDIR /home/user
+
+# Install Node.js (needed for pi and many dev tools)
+RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
+    && apt-get install -y nodejs \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set up git configuration defaults
+RUN git config --global init.defaultBranch main \
+    && git config --global user.email "dev@headquarter.local" \
+    && git config --global user.name "Developer"
+
+USER user
+CMD ["/bin/bash"]

tool-images/code-server.dockerfile

@@ -0,0 +1,28 @@
+# VS Code in browser
+FROM lscr.io/linuxserver/code-server:latest
+
+USER root
+
+# Install additional tools
+RUN apt-get update && apt-get install -y \
+    git \
+    neovim \
+    ranger \
+    tmux \
+    htop \
+    tree \
+    jq \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Node.js
+RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
+    && apt-get install -y nodejs \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set up git
+RUN git config --global init.defaultBranch main
+
+# Code-server runs as abc user by default
+USER abc
+
+EXPOSE 8443

tool-images/jupyter.dockerfile

@@ -0,0 +1,23 @@
+# Jupyter Notebook/Lab
+FROM jupyter/scipy-notebook:latest
+
+USER root
+
+# Install additional tools
+RUN apt-get update && apt-get install -y \
+    git \
+    neovim \
+    ranger \
+    tmux \
+    htop \
+    tree \
+    jq \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set up git
+RUN git config --global init.defaultBranch main
+
+# Switch back to jovyan user (default for scipy-notebook)
+USER ${NB_UID}
+
+EXPOSE 8888

tool-images/opencode.dockerfile

@@ -0,0 +1,40 @@
+# OpenCode agent environment
+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 \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Node.js
+RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
+    && apt-get install -y nodejs \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install OpenCode
+RUN npm install -g opencode
+
+# Create non-root user
+RUN useradd -m -s /bin/bash user
+WORKDIR /home/user
+
+# Set up git
+RUN git config --global init.defaultBranch main
+
+USER user
+
+EXPOSE 3000
+CMD ["opencode", "server"]

tool-images/pi-agent.dockerfile

@@ -0,0 +1,53 @@
+# 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"]