fix: notification center always on top

The notification dropdown was at z-index: 100, well below fullscreen
terminals (1000), modal overlays (1000), and dialog overlays (1000).
Because .notification-center creates a stacking context with no explicit
z-index, the dropdown was trapped behind any of those overlays and
became unclickable.

- Set .notification-center z-index to 9999 so it competes above all
  other overlays in the root stacking context.
- Set .notification-dropdown z-index to 9999 for consistency.

Quality gates: tsc --noEmit (pass), build (pass)

apps/api/.dockerignore

@@ -0,0 +1,42 @@
+# Python cache
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Test artifacts
+.pytest_cache/
+.coverage
+htmlcov/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# Git
+.git/
+.gitignore
+
+# Local env files
+.env
+.env.local
+
+# Alembic cache
+alembic/versions/__pycache__/
+
+# Pi lens cache
+.pi-lens/
+
+# Documentation
+docs/
+*.md
+
+# Scripts not needed in container
+scripts/

apps/api/alembic/versions/0013_add_config_profiles.py

@@ -0,0 +1,204 @@
+"""add config profiles, includes, mounts, and tool instance profile selection
+
+Revision ID: 0013_add_config_profiles
+Revises: 0012_default_port_req
+Create Date: 2026-05-24 12:00:00.000000
+
+"""
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0013_add_config_profiles"
+down_revision: str | None = "0012_default_port_req"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def _table_exists(table_name: str) -> bool:
+    return sa.inspect(op.get_bind()).has_table(table_name)
+
+
+def _column_exists(table_name: str, column_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return column_name in {
+        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
+    }
+
+
+def _index_exists(table_name: str, index_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return index_name in {
+        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
+    }
+
+
+def _foreign_key_exists(
+    table_name: str,
+    constrained_columns: list[str],
+    referred_table: str,
+) -> bool:
+    if not _table_exists(table_name):
+        return False
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if (
+            foreign_key.get("constrained_columns") == constrained_columns
+            and foreign_key.get("referred_table") == referred_table
+        ):
+            return True
+    return False
+
+
+def upgrade() -> None:
+    # Earlier branches may already have created config_profiles. Keep this
+    # migration defensive so databases can converge onto the current graph.
+    if not _table_exists("config_profiles"):
+        op.create_table(
+            "config_profiles",
+            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("user_id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("name", sa.String(length=255), nullable=False),
+            sa.Column("description", sa.Text(), nullable=True),
+            sa.Column(
+                "created_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.Column(
+                "updated_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.ForeignKeyConstraint(["user_id"], ["users.id"], ondelete="CASCADE"),
+            sa.PrimaryKeyConstraint("id"),
+            sa.UniqueConstraint(
+                "user_id", "name", name="uq_config_profiles_user_name"
+            ),
+        )
+    if not _index_exists("config_profiles", "idx_config_profiles_user"):
+        op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
+
+    if not _table_exists("config_includes"):
+        op.create_table(
+            "config_includes",
+            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column(
+                "included_profile_id", postgresql.UUID(as_uuid=True), nullable=False
+            ),
+            sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+            sa.Column(
+                "created_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.Column(
+                "updated_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.ForeignKeyConstraint(
+                ["profile_id"], ["config_profiles.id"], ondelete="CASCADE"
+            ),
+            sa.ForeignKeyConstraint(
+                ["included_profile_id"],
+                ["config_profiles.id"],
+                ondelete="CASCADE",
+            ),
+            sa.PrimaryKeyConstraint("id"),
+            sa.UniqueConstraint(
+                "profile_id", "included_profile_id", name="uq_config_includes_pair"
+            ),
+        )
+    if not _index_exists("config_includes", "idx_config_includes_profile"):
+        op.create_index("idx_config_includes_profile", "config_includes", ["profile_id"])
+    if not _index_exists("config_includes", "idx_config_includes_included"):
+        op.create_index(
+            "idx_config_includes_included", "config_includes", ["included_profile_id"]
+        )
+
+    if not _table_exists("config_mounts"):
+        op.create_table(
+            "config_mounts",
+            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("mount_path", sa.String(length=1024), nullable=False),
+            sa.Column("content", sa.Text(), nullable=True),
+            sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+            sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+            sa.Column(
+                "created_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.Column(
+                "updated_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.ForeignKeyConstraint(
+                ["profile_id"], ["config_profiles.id"], ondelete="CASCADE"
+            ),
+            sa.ForeignKeyConstraint(
+                ["source_profile_id"], ["config_profiles.id"], ondelete="SET NULL"
+            ),
+            sa.PrimaryKeyConstraint("id"),
+        )
+    if not _index_exists("config_mounts", "idx_config_mounts_profile"):
+        op.create_index("idx_config_mounts_profile", "config_mounts", ["profile_id"])
+
+    if not _column_exists("tool_instances", "selected_profile_id"):
+        op.add_column(
+            "tool_instances",
+            sa.Column("selected_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _foreign_key_exists(
+        "tool_instances", ["selected_profile_id"], "config_profiles"
+    ):
+        op.create_foreign_key(
+            "fk_tool_instances_selected_profile",
+            "tool_instances",
+            "config_profiles",
+            ["selected_profile_id"],
+            ["id"],
+            ondelete="SET NULL",
+        )
+    if not _index_exists("tool_instances", "idx_tool_instances_selected_profile"):
+        op.create_index(
+            "idx_tool_instances_selected_profile",
+            "tool_instances",
+            ["selected_profile_id"],
+        )
+
+
+def downgrade() -> None:
+    # Remove selected_profile_id from tool_instances
+    op.drop_index("idx_tool_instances_selected_profile", table_name="tool_instances")
+    op.drop_constraint(
+        "fk_tool_instances_selected_profile", "tool_instances", type_="foreignkey"
+    )
+    op.drop_column("tool_instances", "selected_profile_id")
+
+    # Drop config_mounts
+    op.drop_index("idx_config_mounts_profile", table_name="config_mounts")
+    op.drop_table("config_mounts")
+
+    # Drop config_includes
+    op.drop_index("idx_config_includes_included", table_name="config_includes")
+    op.drop_index("idx_config_includes_profile", table_name="config_includes")
+    op.drop_table("config_includes")
+
+    # Drop config_profiles
+    op.drop_index("idx_config_profiles_user", table_name="config_profiles")
+    op.drop_table("config_profiles")

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

@@ -0,0 +1,180 @@
+"""add profile resolver fields to config profiles and mounts
+
+Revision ID: 0014_add_profile_resolver_fields
+Revises: 0013_add_config_profiles
+Create Date: 2026-05-24 14:00:00.000000
+
+"""
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0014_add_profile_resolver_fields"
+down_revision: str | None = "0013_add_config_profiles"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def _table_exists(table_name: str) -> bool:
+    return sa.inspect(op.get_bind()).has_table(table_name)
+
+
+def _column_exists(table_name: str, column_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return column_name in {
+        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
+    }
+
+
+def _index_exists(table_name: str, index_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return index_name in {
+        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
+    }
+
+
+def _foreign_key_exists(
+    table_name: str,
+    constrained_columns: list[str],
+    referred_table: str,
+) -> bool:
+    if not _table_exists(table_name):
+        return False
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if (
+            foreign_key.get("constrained_columns") == constrained_columns
+            and foreign_key.get("referred_table") == referred_table
+        ):
+            return True
+    return False
+
+
+def _foreign_key_names_for_column(table_name: str, column_name: str) -> list[str]:
+    if not _table_exists(table_name):
+        return []
+    names: list[str] = []
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if column_name in foreign_key.get("constrained_columns", []):
+            name = foreign_key.get("name")
+            if name:
+                names.append(name)
+    return names
+
+
+def upgrade() -> None:
+    if not _column_exists("config_profiles", "project_id"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _column_exists("config_profiles", "tool_type_id"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _column_exists("config_profiles", "environment_variables"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("environment_variables", sa.JSON(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "start_command"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("start_command", sa.Text(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "working_directory"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("working_directory", sa.Text(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "port"):
+        op.add_column("config_profiles", sa.Column("port", sa.Integer(), nullable=True))
+    if not _column_exists("config_profiles", "is_default"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
+        )
+
+    if not _foreign_key_exists("config_profiles", ["project_id"], "projects"):
+        op.create_foreign_key(
+            "fk_config_profiles_project",
+            "config_profiles",
+            "projects",
+            ["project_id"],
+            ["id"],
+            ondelete="CASCADE",
+        )
+    if not _foreign_key_exists("config_profiles", ["tool_type_id"], "tool_types"):
+        op.create_foreign_key(
+            "fk_config_profiles_tool_type",
+            "config_profiles",
+            "tool_types",
+            ["tool_type_id"],
+            ["id"],
+            ondelete="CASCADE",
+        )
+
+    if not _index_exists("config_profiles", "idx_config_profiles_project"):
+        op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
+    if not _index_exists("config_profiles", "idx_config_profiles_tool_type"):
+        op.create_index(
+            "idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"]
+        )
+
+    if _column_exists("config_mounts", "mount_path") and not _column_exists(
+        "config_mounts", "target_path"
+    ):
+        op.alter_column("config_mounts", "mount_path", new_column_name="target_path")
+    if not _column_exists("config_mounts", "mode"):
+        op.add_column(
+            "config_mounts",
+            sa.Column("mode", sa.String(length=10), nullable=False, server_default="rw"),
+        )
+    if not _column_exists("config_mounts", "files"):
+        op.add_column(
+            "config_mounts",
+            sa.Column("files", sa.JSON(), nullable=True),
+        )
+    for constraint_name in _foreign_key_names_for_column(
+        "config_mounts", "source_profile_id"
+    ):
+        op.drop_constraint(constraint_name, "config_mounts", type_="foreignkey")
+    if _column_exists("config_mounts", "content"):
+        op.drop_column("config_mounts", "content")
+    if _column_exists("config_mounts", "source_profile_id"):
+        op.drop_column("config_mounts", "source_profile_id")
+
+
+def downgrade() -> None:
+    # Restore config_mounts
+    op.add_column(
+        "config_mounts",
+        sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.add_column(
+        "config_mounts",
+        sa.Column("content", sa.Text(), nullable=True),
+    )
+    op.drop_column("config_mounts", "files")
+    op.drop_column("config_mounts", "mode")
+    op.alter_column("config_mounts", "target_path", new_column_name="mount_path")
+
+    # Restore config_profiles
+    op.drop_index("idx_config_profiles_tool_type", table_name="config_profiles")
+    op.drop_index("idx_config_profiles_project", table_name="config_profiles")
+    op.drop_constraint(
+        "fk_config_profiles_tool_type", "config_profiles", type_="foreignkey"
+    )
+    op.drop_constraint("fk_config_profiles_project", "config_profiles", type_="foreignkey")
+    op.drop_column("config_profiles", "is_default")
+    op.drop_column("config_profiles", "port")
+    op.drop_column("config_profiles", "working_directory")
+    op.drop_column("config_profiles", "start_command")
+    op.drop_column("config_profiles", "environment_variables")
+    op.drop_column("config_profiles", "tool_type_id")
+    op.drop_column("config_profiles", "project_id")

apps/api/alembic/versions/86cec91fdb00_merge_profile_resolver_and_workspaces_.py

@@ -0,0 +1,20 @@
+"""merge profile resolver and workspaces heads
+
+Revision ID: 86cec91fdb00
+Revises: 0014_add_profile_resolver_fields, 2026_06_01_add_workspaces
+Create Date: 2026-06-03 12:48:36.145702
+"""
+
+# revision identifiers, used by Alembic.
+revision = "86cec91fdb00"
+down_revision = ("0014_add_profile_resolver_fields", "2026_06_01_add_workspaces")
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    pass
+
+
+def downgrade() -> None:
+    pass

apps/api/src/api/__init__.py

@@ -1,6 +1 @@
-from src.api.auth import router as auth_router
+"""API routers package."""
-from src.api.events import router as events_router
-from src.api.notifications import router as notifications_router
-from src.api.users import router as users_router
-
-__all__ = ["auth_router", "events_router", "notifications_router", "users_router"]

apps/api/src/api/config/__init__.py

@@ -0,0 +1,6 @@
+"""Config API routers module."""
+
+from src.api.config.config_profiles import router as config_profiles_router
+from src.api.config.user_config import router as user_config_router
+
+__all__ = ["config_profiles_router", "user_config_router"]

apps/api/src/api/config/config_profiles.py

@@ -7,17 +7,25 @@ import uuid
 from typing import Any
 
 from fastapi import APIRouter, Depends, HTTPException, Query, status
-from pydantic import BaseModel, Field, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 
-from src.api.shared_validators import validate_env_vars as _validate_env_vars
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models import ConfigProfile, ConfigProfileInclude
 from src.models.project import Project
-from src.models.tool_type import ToolType
+from src.models import ToolType
-from src.services.config_profile_resolver import (
+from src.models import UserConfig
+from src.schemas.config import (
+    ConfigProfileCreate,
+    ConfigProfileIncludeUpdate,
+    ConfigProfileResponse,
+    ConfigProfileUpdate,
+    DefaultProfilesUpdate,
+    ValidateGitUrlRequest,
+    ValidateGitUrlResponse,
+)
+from src.services.config.config_profile_resolver import (
     ConfigProfileCycleError,
     check_include_cycle,
     resolve_profile,
@@ -33,16 +41,6 @@ MAX_PROFILE_SIZE_MB = 10
 MAX_PROFILE_SIZE_BYTES = MAX_PROFILE_SIZE_MB * 1024 * 1024
 
 
-def _validate_uuid(v: str | None) -> str | None:
-    if v is None:
-        return v
-    try:
-        uuid.UUID(v)
-    except ValueError:
-        raise ValueError(f"Invalid UUID: {v}")
-    return v
-
-
 def _calculate_profile_size(data: dict) -> int:
     """Calculate approximate serialized size of profile data."""
     total = 0
@@ -60,247 +58,6 @@ def _calculate_profile_size(data: dict) -> int:
     return total
 
 
-class GitMountMapping(BaseModel):
-    source_path: str = Field(
-        description="Path within repository (supports glob patterns)"
-    )
-    target_path: str = Field(description="Absolute path inside container")
-
-    @field_validator("source_path")
-    @classmethod
-    def validate_source_path(cls, v: str) -> str:
-        if v.startswith("/"):
-            raise ValueError("source_path must be relative (no leading /)")
-        if ".." in v:
-            raise ValueError("source_path cannot contain path traversal (..)")
-        return v
-
-    @field_validator("target_path")
-    @classmethod
-    def validate_target_path(cls, v: str) -> str:
-        if ".." in v:
-            raise ValueError("target_path cannot contain path traversal (..)")
-        return v
-
-
-class GitMountItem(BaseModel):
-    remote_url: str = Field(description="Git remote URL (HTTPS or SSH)")
-    source_path: str | None = Field(
-        default=None, description="Path within repository (legacy single mapping)"
-    )
-    target_path: str | None = Field(
-        default=None,
-        description="Absolute path inside container (legacy single mapping)",
-    )
-    branch: str | None = Field(default=None, description="Optional branch or tag name")
-    mappings: list[GitMountMapping] | None = Field(
-        default=None, description="Multiple source/target mappings from the same repo"
-    )
-
-    @field_validator("remote_url")
-    @classmethod
-    def validate_remote_url(cls, v: str) -> str:
-        if not v.startswith(("http://", "https://", "git@", "ssh://")):
-            raise ValueError(
-                "remote_url must be a valid git URL (https://, git@, or ssh://)"
-            )
-        return v
-
-    @field_validator("source_path")
-    @classmethod
-    def validate_source_path(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if v.startswith("/"):
-            raise ValueError("source_path must be relative (no leading /)")
-        if ".." in v:
-            raise ValueError("source_path cannot contain path traversal (..)")
-        return v
-
-    @field_validator("target_path")
-    @classmethod
-    def validate_target_path(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if ".." in v:
-            raise ValueError("target_path cannot contain path traversal (..)")
-        return v
-
-    @model_validator(mode="after")
-    def check_mappings_or_legacy(self):
-        has_legacy = self.source_path is not None and self.target_path is not None
-        has_mappings = self.mappings is not None and len(self.mappings) > 0
-        if not has_legacy and not has_mappings:
-            raise ValueError(
-                "Git mount must have either 'mappings' (non-empty array) or both 'source_path' and 'target_path'"
-            )
-        return self
-
-
-class MountItem(BaseModel):
-    target: str = Field(description="Absolute mount target path")
-    mode: str = Field(default="rw", description="Mount mode: ro or rw")
-    files: dict = Field(
-        default_factory=dict, description="Files as {relative_path: content}"
-    )
-
-    @field_validator("target")
-    @classmethod
-    def validate_target(cls, v: str) -> str:
-        if not v.startswith("/"):
-            raise ValueError("Mount target must be absolute (start with /)")
-        return v
-
-    @field_validator("mode")
-    @classmethod
-    def validate_mode(cls, v: str) -> str:
-        if v not in ("ro", "rw"):
-            raise ValueError("Mount mode must be 'ro' or 'rw'")
-        return v
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict) -> dict:
-        for path in v.keys():
-            if ".." in path or not path:
-                raise ValueError(f"Invalid file path: {path}")
-            if path.startswith("/"):
-                raise ValueError(
-                    f"Mount file paths must be relative (got: {path}). "
-                    f"The mount target defines the absolute container path."
-                )
-        return v
-
-
-class ConfigProfileCreate(BaseModel):
-    name: str = Field(description="Profile name (unique per user)")
-    description: str | None = Field(default=None, description="Optional description")
-    project_id: str | None = Field(default=None, description="Optional project ID")
-    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
-    env_vars: dict = Field(default_factory=dict, description="Environment variables")
-    runtime_hints: dict = Field(default_factory=dict, description="Runtime hints")
-    mounts: list[MountItem] = Field(
-        default_factory=list, description="Mount definitions"
-    )
-    files: dict = Field(
-        default_factory=dict, description="Files as {relative_path: content}"
-    )
-    git_mounts: list[GitMountItem] = Field(
-        default_factory=list, description="Git repository mounts"
-    )
-    is_default: bool = Field(
-        default=False, description="Whether this is the default profile for its scope"
-    )
-
-    @field_validator("project_id", "tool_type_id")
-    @classmethod
-    def validate_uuids(cls, v: str | None) -> str | None:
-        return _validate_uuid(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict) -> dict:
-        for path in v.keys():
-            if ".." in path or not path:
-                raise ValueError(f"Invalid file path: {path}")
-            if path.startswith("/"):
-                raise ValueError(
-                    f"File paths must be relative (got: {path}). "
-                    f"Use Mounts for absolute container paths."
-                )
-        return v
-
-    @field_validator("env_vars")
-    @classmethod
-    def validate_env_vars(cls, v: dict) -> dict:
-        result = _validate_env_vars(v)
-        if result is None:
-            raise ValueError("env_vars must be a JSON object")
-        return result
-
-    @field_validator("runtime_hints")
-    @classmethod
-    def validate_runtime_hints(cls, v: dict) -> dict:
-        if not isinstance(v, dict):
-            raise ValueError("runtime_hints must be a JSON object")
-        return v
-
-    @field_validator("mounts")
-    @classmethod
-    def validate_mounts(cls, v: list) -> list:
-        if not isinstance(v, list):
-            raise ValueError("mounts must be a JSON array")
-        return v
-
-
-class ConfigProfileUpdate(BaseModel):
-    name: str | None = Field(default=None, description="Profile name")
-    description: str | None = Field(default=None, description="Optional description")
-    project_id: str | None = Field(default=None, description="Optional project ID")
-    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
-    env_vars: dict | None = Field(default=None, description="Environment variables")
-    runtime_hints: dict | None = Field(default=None, description="Runtime hints")
-    mounts: list[MountItem] | None = Field(
-        default=None, description="Mount definitions"
-    )
-    files: dict | None = Field(
-        default=None, description="Files as {relative_path: content}"
-    )
-    git_mounts: list[GitMountItem] | None = Field(
-        default=None, description="Git repository mounts"
-    )
-    is_default: bool | None = Field(
-        default=None, description="Whether this is the default profile"
-    )
-
-    @field_validator("project_id", "tool_type_id")
-    @classmethod
-    def validate_uuids(cls, v: str | None) -> str | None:
-        return _validate_uuid(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict | None) -> dict | None:
-        if v is None:
-            return v
-        for path in v.keys():
-            if ".." in path or path.startswith("/") or not path:
-                raise ValueError(f"Invalid file path: {path}")
-        return v
-
-
-class ConfigProfileIncludeUpdate(BaseModel):
-    includes: list[str] = Field(description="Ordered list of included profile IDs")
-
-    @field_validator("includes")
-    @classmethod
-    def validate_includes(cls, v: list) -> list:
-        for item in v:
-            try:
-                uuid.UUID(item)
-            except ValueError:
-                raise ValueError(f"Invalid UUID in includes: {item}")
-        return v
-
-
-class ConfigProfileResponse(BaseModel):
-    id: str
-    user_id: str
-    name: str
-    description: str | None
-    project_id: str | None
-    tool_type_id: str | None
-    env_vars: dict
-    runtime_hints: dict
-    mounts: list
-    files: dict
-    git_mounts: list
-    is_default: bool
-    includes: list[dict]
-    created_at: str
-    updated_at: str
-
-
 async def _get_profile_with_includes(
     session: AsyncSession, profile_id: uuid.UUID
 ) -> ConfigProfile | None:
@@ -840,20 +597,97 @@ async def resolve_default_profile(
     return {"profile_id": str(first.id), "profile_name": first.name}
 
 
-class ValidateGitUrlRequest(BaseModel):
+# ---------------------------------------------------------------------------
-    url: str = Field(description="Git remote URL to validate")
+# Default profile management
-    ssh_key_id: str | None = Field(
+# ---------------------------------------------------------------------------
-        default=None, description="Optional SSH key ID for private repos"
+
+
+async def _get_or_create_user_config(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+) -> UserConfig:
+    """Get existing user config or create a new one."""
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
     )
+    user_config = result.scalar_one_or_none()
+    if user_config is None:
+        user_config = UserConfig(user_id=user_id, config={})
+        session.add(user_config)
+    return user_config
 
 
-class ValidateGitUrlResponse(BaseModel):
+async def _validate_default_profiles(
-    valid: bool
+    session: AsyncSession,
-    suggested_url: str | None = None
+    user_id: uuid.UUID,
-    branches: list[str] | None = None
+    default_profiles: dict[str, str],
-    default_branch: str | None = None
+) -> None:
-    error: str | None = None
+    """Validate that all profile IDs in default_profiles belong to the user."""
-    error_code: str | None = None
+    for tool_type_id, profile_id_str in default_profiles.items():
+        try:
+            profile_uuid = uuid.UUID(profile_id_str)
+        except ValueError:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail=f"Invalid profile ID for tool type {tool_type_id}: {profile_id_str}",
+            )
+        profile = await session.get(ConfigProfile, profile_uuid)
+        if profile is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Profile not found: {profile_id_str}",
+            )
+        if profile.user_id != user_id:
+            raise HTTPException(
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail=f"Profile does not belong to user: {profile_id_str}",
+            )
+
+
+@router.get("/defaults")
+async def get_default_profiles_endpoint(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get all default profile mappings for the current user."""
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
+    )
+    user_config = result.scalar_one_or_none()
+    return {"default_profiles": user_config.default_profiles if user_config else {}}
+
+
+@router.put("/defaults")
+async def set_default_profiles_endpoint(
+    data: DefaultProfilesUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Set default profile mappings for the current user."""
+    await _validate_default_profiles(session, user_id, data.default_profiles)
+    user_config = await _get_or_create_user_config(session, user_id)
+    user_config.config = {
+        **user_config.config,
+        "default_profiles": data.default_profiles,
+    }
+    await session.commit()
+    await session.refresh(user_config)
+    return {"default_profiles": user_config.default_profiles}
+
+
+@router.get("/defaults/{tool_type_id}")
+async def get_default_profile_for_tool_type_endpoint(
+    tool_type_id: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get the default profile ID for a specific tool type."""
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
+    )
+    user_config = result.scalar_one_or_none()
+    profile_id = user_config.default_profiles.get(tool_type_id) if user_config else None
+    return {"tool_type_id": tool_type_id, "profile_id": profile_id}
 
 
 @router.post("/validate-git-url", response_model=ValidateGitUrlResponse)
@@ -891,8 +725,8 @@ async def validate_git_url(
     env = None
     key_path = None
     if data.ssh_key_id:
-        from src.models.ssh_key import SSHKey
+        from src.models import SSHKey
-        from src.services.ssh_keys import _get_fernet
+        from src.services.shared.ssh_keys import _get_fernet
 
         try:
             ssh_key_uuid = uuid.UUID(data.ssh_key_id)

apps/api/src/api/config/user_config.py

@@ -2,12 +2,12 @@ import logging
 import uuid
 
 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_config import UserConfig
+from src.models import UserConfig
+from src.schemas.user import UserConfigResponse, UserConfigUpdate
 
 logger = logging.getLogger(__name__)
 
@@ -38,28 +38,6 @@ async def _get_or_create_config(
     return config
 
 
-class UserConfigResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    default_editor: str | None = None
-    theme: str = "system"
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-    notification_mute_categories: list[str] | None = None
-    notification_toast_level: str | None = None
-
-
-class UserConfigUpdate(BaseModel):
-    default_editor: str | None = None
-    theme: str | None = None
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-    notification_mute_categories: list[str] | None = None
-    notification_toast_level: str | None = None
-
-
 @router.get(
     "/config",
     response_model=UserConfigResponse,

apps/api/src/api/project/__init__.py

@@ -0,0 +1,6 @@
+"""Project API routers module."""
+
+from src.api.project.git_repositories import router as git_repositories_router
+from src.api.project.projects import router as projects_router
+
+__all__ = ["git_repositories_router", "projects_router"]

apps/api/src/api/project/git_repositories.py

@@ -3,10 +3,9 @@ import os
 import shutil
 import subprocess
 import uuid
-from datetime import datetime
 
 from fastapi import APIRouter, Depends, HTTPException, Response, status
-from pydantic import BaseModel, ConfigDict
+from pydantic import BaseModel
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
@@ -17,8 +16,15 @@ from src.auth.dependencies import (
     get_db_session,
 )
 from src.config import Settings
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
+from src.schemas.project import (
+    GitRepositoryCreate,
+    GitRepositoryResponse,
+    URLParseRequest,
+    URLParseResponse,
+    UpdateSSHKeyRequest,
+)
 from src.utils.git_files import (
     commit_file,
     get_file_content,
@@ -38,7 +44,7 @@ from src.utils.git_control import (
 )
 from src.utils.git_history import get_commit_detail, get_commit_history
 from src.utils.git_url_parser import parse_git_url
-from src.services.ssh_keys import _get_fernet
+from src.services.shared.ssh_keys import _get_fernet
 
 router = APIRouter(prefix="/projects", tags=["git-repositories"])
 
@@ -218,43 +224,6 @@ def _init_working_repository(repo_path: str) -> None:
         )
 
 
-class GitRepositoryCreate(BaseModel):
-    name: str
-    remote_url: str | None = None
-    force_original_url: bool = False
-    ssh_key_id: str | None = None
-
-
-class URLParseRequest(BaseModel):
-    url: str
-
-
-class URLParseResponse(BaseModel):
-    original_url: str
-    base_url: str | None
-    is_valid_clone_url: bool
-    needs_parsing: bool
-    host: str | None
-    message: str
-    error_code: str | None
-
-
-class GitRepositoryResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    path: str
-    project_id: uuid.UUID | None
-    owner_id: uuid.UUID
-    is_mirror: bool
-    remote_url: str | None
-    last_push: datetime | None
-    ssh_key_id: uuid.UUID | None
-    created_at: datetime
-    updated_at: datetime
-
-
 @router.get(
     "/repositories",
     response_model=list[GitRepositoryResponse],
@@ -599,10 +568,6 @@ async def create_repository(
     return repo
 
 
-class UpdateSSHKeyRequest(BaseModel):
-    ssh_key_id: str | None = None
-
-
 @router.patch(
     "/{project_id}/repositories/{repo_id}/ssh-key",
     response_model=GitRepositoryResponse,

apps/api/src/api/project/projects.py

@@ -3,7 +3,6 @@ import shutil
 import uuid
 
 from fastapi import APIRouter, Depends, HTTPException, Response, status
-from pydantic import BaseModel, ConfigDict
 from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession
 
@@ -13,38 +12,20 @@ from src.auth.dependencies import (
     get_current_user_id,
     get_db_session,
 )
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
-from src.models.tool_instance import ToolInstance
+from src.models import ToolInstance
+from src.schemas.project import (
+    ProjectCreate,
+    ProjectResponse,
+    ProjectUpdate,
+    SetDefaultSSHKeyRequest,
+)
 
 router = APIRouter(prefix="/projects", tags=["projects"])
 
 
-class ProjectCreate(BaseModel):
-    name: str
-    description: str | None = None
-
-
-class ProjectUpdate(BaseModel):
-    name: str | None = None
-    description: str | None = None
-
-
-class ProjectResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    description: str | None
-    owner_id: uuid.UUID
-    default_ssh_key_id: uuid.UUID | None
-
-
-class SetDefaultSSHKeyRequest(BaseModel):
-    ssh_key_id: uuid.UUID
-
-
 @router.post(
     "",
     response_model=ProjectResponse,
@@ -101,7 +82,7 @@ async def list_projects(
     )
     projects = result.scalars().all()
 
-    from src.models.workspace import Workspace
+    from src.models import Workspace
 
     enriched = []
     for project in projects:

apps/api/src/api/system/__init__.py

@@ -0,0 +1,17 @@
+"""System API routers module."""
+
+from src.api.system.dashboard import router as dashboard_router
+from src.api.system.events import router as events_router
+from src.api.system.health import router as health_router
+from src.api.system.instance_proxy import router as instance_proxy_router
+from src.api.system.notifications import router as notifications_router
+from src.api.system.terminal import router as terminal_router
+
+__all__ = [
+    "dashboard_router",
+    "events_router",
+    "health_router",
+    "instance_proxy_router",
+    "notifications_router",
+    "terminal_router",
+]

apps/api/src/api/system/dashboard.py

@@ -5,9 +5,9 @@ from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
 
 router = APIRouter(prefix="/dashboard", tags=["dashboard"])
 

apps/api/src/api/system/events.py

@@ -10,7 +10,7 @@ from fastapi import APIRouter, Depends, HTTPException, Request, status
 from fastapi.responses import StreamingResponse
 
 from src.auth.dependencies import get_current_user_id
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
+from src.services.instance.event_bus import InstanceEventBus, InstanceEventPayload
 
 router = APIRouter(prefix="/events", tags=["events"])
 

apps/api/src/api/system/health.py

@@ -5,10 +5,16 @@ from datetime import datetime, timezone
 from typing import Any
 
 from fastapi import APIRouter
-from pydantic import BaseModel, Field
 from sqlalchemy import text
 
 from src.database import SessionLocal
+from src.schemas.system import (
+    DatabaseHealth,
+    DatabaseHealthResponse,
+    DiskHealth,
+    HealthChecks,
+    HealthResponse,
+)
 
 router = APIRouter()
 
@@ -16,45 +22,6 @@ router = APIRouter()
 _start_time = time.time()
 
 
-class DatabaseHealth(BaseModel):
-    """Database health check result."""
-
-    status: str = Field(description="Database health status", examples=["healthy"])
-    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
-
-
-class DiskHealth(BaseModel):
-    """Disk space health check result."""
-
-    status: str = Field(description="Disk health status", examples=["healthy"])
-    free_gb: float = Field(description="Free disk space in GB", examples=[45.2])
-    total_gb: float = Field(description="Total disk space in GB", examples=[100.0])
-
-
-class HealthChecks(BaseModel):
-    """Individual health checks."""
-
-    database: DatabaseHealth | None = None
-    disk: DiskHealth | None = None
-
-
-class HealthResponse(BaseModel):
-    """Overall health check response."""
-
-    status: str = Field(description="Overall health status", examples=["healthy"])
-    timestamp: str = Field(description="ISO 8601 timestamp", examples=["2026-05-19T12:00:00Z"])
-    version: str = Field(description="API version", examples=["0.1.0"])
-    checks: HealthChecks = Field(description="Individual health checks")
-    uptime_seconds: float = Field(description="Server uptime in seconds", examples=[3600.0])
-
-
-class DatabaseHealthResponse(BaseModel):
-    """Database-specific health check response."""
-
-    status: str = Field(description="Database health status", examples=["healthy"])
-    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
-
-
 @router.get(
     "/health",
     response_model=HealthResponse,

apps/api/src/api/system/instance_proxy.py

@@ -8,8 +8,8 @@ from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_instance import ToolInstance
+from src.models import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import ToolType
 
 logger = logging.getLogger(__name__)
 

apps/api/src/api/system/notifications.py

@@ -9,8 +9,8 @@ from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user, get_db_session
 from src.models.user import User
-from src.models.user_config import UserConfig
+from src.models import UserConfig
-from src.services.notification_service import notification_service
+from src.services.shared.notification_service import notification_service
 
 router = APIRouter(prefix="/notifications", tags=["notifications"])
 

apps/api/src/api/system/terminal.py

@@ -12,10 +12,10 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from starlette.websockets import WebSocketDisconnect
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.terminal_session import TerminalSessionModel
+from src.models import TerminalSessionModel
-from src.models.tool_instance import ToolInstance
+from src.models import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import ToolType
-from src.services.terminal_manager import MaxSessionsExceededError, terminal_manager
+from src.services.terminal.terminal_manager import MaxSessionsExceededError, terminal_manager
 
 router = APIRouter()
 logger = logging.getLogger(__name__)

apps/api/src/api/tool/__init__.py

@@ -0,0 +1,13 @@
+"""Tool API routers module."""
+
+from src.api.tool.sessions import sessions_router
+from src.api.tool.tool_definitions import router as tool_definitions_router
+from src.api.tool.tool_instances import router as tool_instances_router
+from src.api.tool.tool_types import router as tool_types_router
+
+__all__ = [
+    "sessions_router",
+    "tool_definitions_router",
+    "tool_instances_router",
+    "tool_types_router",
+]

apps/api/src/api/tool/sessions.py

@@ -0,0 +1,80 @@
+"""Sessions API endpoints (running instances for current user)."""
+
+import uuid
+
+from fastapi import APIRouter, Depends
+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 import GitRepository
+from src.models import Project
+from src.models import ToolInstance
+from src.models import ToolType
+
+sessions_router = APIRouter(prefix="/users", tags=["sessions"])
+
+
+@sessions_router.get(
+    "/me/sessions",
+    summary="Get user sessions",
+    description="Get all active sessions (running instances) for the current user.",
+)
+async def get_user_sessions(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get all active sessions for the current user.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Dictionary containing list of active sessions with instance details.
+    """
+    _user = await _get_user(session, user_id)
+
+    result = await session.execute(
+        select(ToolInstance)
+        .where(ToolInstance.owner_id == user_id)
+        .where(
+            ToolInstance.status.in_(
+                ["running", "building", "pending", "stopped", "error"]
+            )
+        )
+        .order_by(ToolInstance.created_at.desc())
+    )
+    instances = result.scalars().all()
+
+    sessions = []
+    for instance in instances:
+        tool_type = await session.get(ToolType, instance.tool_type_id)
+        repo = await session.get(GitRepository, instance.repository_id)
+        project = await session.get(Project, instance.project_id)
+
+        sessions.append(
+            {
+                "id": str(instance.id),
+                "display_name": instance.display_name,
+                "tool_type_name": tool_type.name if tool_type else "unknown",
+                "tool_icon": tool_type.name if tool_type else "code",
+                "tool_type_interfaces": [tool_type.interface_type] if tool_type else [],
+                "repository_name": repo.name if repo else "unknown",
+                "repository_id": str(instance.repository_id),
+                "project_name": project.name if project else "unknown",
+                "project_id": str(instance.project_id),
+                "status": instance.status,
+                "url": instance.url,
+                "clone_mode": instance.clone_mode,
+                "branch": instance.branch,
+                "selected_config_profile_id": str(instance.selected_config_profile_id)
+                if instance.selected_config_profile_id
+                else None,
+                "created_at": instance.created_at.isoformat()
+                if instance.created_at
+                else None,
+            }
+        )
+
+    return {"sessions": sessions}

apps/api/src/api/tool/tool_definitions.py

@@ -9,9 +9,9 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_definition_manifest import ToolDefinitionManifest
+from src.models import ToolDefinitionManifest
-from src.models.tool_type import ToolType
+from src.models import ToolType
-from src.services.manifest_compiler import (
+from src.services.build.manifest_compiler import (
     compile_compose,
     compile_dockerfile,
     compile_entrypoint,
@@ -173,7 +173,7 @@ async def list_tool_definitions(
     """
     query = select(ToolDefinitionManifest)
     if not include_bases:
-        query = query.where(ToolDefinitionManifest.is_base == False)
+        query = query.where(ToolDefinitionManifest.is_base.is_(False))
 
     result = await session.execute(
         query.order_by(ToolDefinitionManifest.created_at.desc())

apps/api/src/api/tool/tool_instances.py

@@ -11,14 +11,12 @@ from datetime import datetime
 import httpx
 from fastapi import (
     APIRouter,
-    APIRouter as FastAPIRouter,
     Depends,
     HTTPException,
     Request,
     Response,
     status,
 )
-from pydantic import BaseModel, Field
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
@@ -28,16 +26,15 @@ from src.auth.dependencies import (
     get_current_user_id,
     get_db_session,
 )
-from src.services.event_bus import InstanceEventBus
+from src.services.instance.event_bus import InstanceEventBus
-from src.services.lifecycle_hooks import publish_lifecycle_event
+from src.services.instance.lifecycle_hooks import publish_lifecycle_event
-from src.models.config_profile import ConfigProfile
+from src.models import ConfigProfile
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
-from src.models.project import Project
+from src.models import SSHKey
-from src.models.ssh_key import SSHKey
+from src.models import ToolInstance
-from src.models.tool_instance import ToolInstance
+from src.models import ToolType
-from src.models.tool_type import ToolType
+from src.services.git.clone import check_dirty_state, clone_repository
-from src.services.clone import check_dirty_state, clone_repository
+from src.services.config.config_profile_resolver import (
-from src.services.config_profile_resolver import (
     ConfigProfileCycleError,
     ResolvedProfile,
     apply_resolved_profile,
@@ -62,14 +59,14 @@ from src.services.docker import (
     write_config_files,
     write_env_file,
 )
-from src.services.tunnel import (
+from src.services.shared.tunnel import (
     check_tunnel_health,
     recreate_tunnel,
     start_tunnel,
     stop_tunnel,
 )
-from src.services.docker_build import build_image
+from src.services.build.docker_build import build_image
-from src.services.manifest_compiler import (
+from src.services.build.manifest_compiler import (
     compile_compose,
     compile_dockerfile,
     compile_entrypoint,
@@ -79,9 +76,13 @@ from src.services.manifest_compiler import (
     merge_with_config,
     resolve_base,
 )
-from src.services.permission_fixer import apply_mount_permissions, apply_ssh_permissions
+from src.services.shared.permission_fixer import (
-from src.services.readiness_probe import execute_probe
+    apply_mount_permissions,
-from src.services.ssh_keys import cleanup_ssh_key_files, prepare_ssh_key_files
+    apply_ssh_permissions,
+)
+from src.services.shared.readiness_probe import execute_probe
+from src.services.shared.ssh_keys import cleanup_ssh_key_files, prepare_ssh_key_files
+from src.schemas.tool import CreateInstanceRequest, StartInstanceRequest
 
 logger = logging.getLogger(__name__)
 _event_bus = InstanceEventBus()
@@ -418,48 +419,6 @@ def _expand_glob_source(source_path: str, repo_path: str) -> list[str]:
 router = APIRouter(prefix="/projects", tags=["tool-instances"])
 
 
-class CreateInstanceRequest(BaseModel):
-    """Request body for creating a tool instance."""
-
-    model_config = {"extra": "ignore"}
-
-    tool_type_id: str = Field(description="UUID of the tool type to instantiate")
-    display_name: str | None = Field(
-        default=None, description="Optional display name for the instance"
-    )
-    workspace_id: str | None = Field(
-        default=None, description="UUID of workspace to mount (replaces clone_mode)"
-    )
-    clone_mode: str = Field(
-        default="mount", description="Repository access mode: 'mount' or 'clone'"
-    )
-    branch: str | None = Field(
-        default="main", description="Branch to clone (when clone_mode='clone')"
-    )
-    new_branch: str | None = Field(
-        default=None, description="Create a new local branch after cloning"
-    )
-    config_profile_id: str | None = Field(
-        default=None, description="Optional config profile ID for launch"
-    )
-    ssh_key_ids: list[str] = Field(
-        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
-    )
-
-
-class StartInstanceRequest(BaseModel):
-    """Request body for starting a tool instance."""
-
-    model_config = {"extra": "ignore"}
-
-    config_profile_id: str | None = Field(
-        default=None, description="Config profile ID to apply, or null for none"
-    )
-    ssh_key_ids: list[str] = Field(
-        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
-    )
-
-
 async def _validate_config_profile(
     session: AsyncSession,
     profile_id: str | None,
@@ -856,7 +815,7 @@ async def create_instance(
     workspace = None
     workspace_id = None
     if data.workspace_id:
-        from src.models.workspace import Workspace as WorkspaceModel
+        from src.models import Workspace as WorkspaceModel
 
         try:
             workspace_id = uuid.UUID(data.workspace_id)
@@ -893,9 +852,37 @@ async def create_instance(
 
         # Generate unique name
         instance_name = f"{tool_type.name}-{repo.name}-{uuid.uuid4().hex[:8]}"
-        instance_display = (
+
-            data.display_name or f"{tool_type.display_name} - {repo.name}"
+        # Auto-generate display name with scoped numbering.
-        )
+        # When a workspace is provided, use workspace name + tool type.
+        # Otherwise fall back to repo name + tool type.
+        if data.display_name:
+            instance_display = data.display_name
+        else:
+            scope_name = workspace.name if workspace else repo.name
+            auto_name = f"{scope_name} / {tool_type.display_name}"
+
+            if workspace:
+                count_query = (
+                    select(ToolInstance)
+                    .where(ToolInstance.workspace_id == workspace_id)
+                    .where(ToolInstance.tool_type_id == tool_type_id)
+                    .where(ToolInstance.owner_id == user_id)
+                )
+            else:
+                count_query = (
+                    select(ToolInstance)
+                    .where(ToolInstance.repository_id == repo_id)
+                    .where(ToolInstance.tool_type_id == tool_type_id)
+                    .where(ToolInstance.owner_id == user_id)
+                )
+
+            result = await session.execute(count_query)
+            existing_count = len(result.scalars().all())
+            if existing_count > 0:
+                instance_display = f"{auto_name} #{existing_count + 1}"
+            else:
+                instance_display = auto_name
 
         # Create instance directory
         instance_dir = ensure_instance_directory(instance_name)
@@ -1040,7 +1027,7 @@ services:
 
         elif tool_type.definition_type == "manifest":
             # Manifest-based: generate compose only; image built lazily on start
-            from src.models.tool_definition_manifest import ToolDefinitionManifest
+            from src.models import ToolDefinitionManifest
 
             manifest_def = await session.get(
                 ToolDefinitionManifest, tool_type.manifest_id
@@ -1325,7 +1312,7 @@ async def _prepare_manifest_instance(
     Returns:
         Tuple of (image_tag, compose_content, resolved_manifest, home_dir)
     """
-    from src.models.tool_definition_manifest import ToolDefinitionManifest
+    from src.models import ToolDefinitionManifest
 
     tool_type = await session.get(ToolType, instance.tool_type_id)
     manifest_def = await session.get(ToolDefinitionManifest, tool_type.manifest_id)
@@ -1521,7 +1508,7 @@ async def start_instance(
     container_uid = 0
     container_gid = 0
     if tool_type and tool_type.definition_type == "manifest" and tool_type.manifest_id:
-        from src.models.tool_definition_manifest import ToolDefinitionManifest
+        from src.models import ToolDefinitionManifest
 
         manifest_def = await session.get(ToolDefinitionManifest, tool_type.manifest_id)
         if manifest_def:
@@ -1611,7 +1598,7 @@ async def start_instance(
 
     # Mount selected SSH keys into container home dir
     if instance.ssh_key_ids:
-        from src.services.ssh_keys import write_ssh_config, _sanitize_filename
+        from src.services.shared.ssh_keys import write_ssh_config, _sanitize_filename
 
         # Collect all valid keys first
         ssh_keys_to_mount = []
@@ -1708,7 +1695,7 @@ async def start_instance(
         # Determine repo path (workspace takes precedence)
         repo_path = ""
         if instance.workspace_id:
-            from src.models.workspace import Workspace as WorkspaceModel
+            from src.models import Workspace as WorkspaceModel
 
             workspace = await session.get(WorkspaceModel, instance.workspace_id)
             if workspace:
@@ -2751,7 +2738,7 @@ async def get_instance_events(
         List of event dictionaries.
     """
     from sqlalchemy import select
-    from src.models.instance_event import InstanceEvent
+    from src.models import InstanceEvent
 
     _user = await _get_user(session, user_id)
     _project = await _get_owned_project(project_id, user_id, session)
@@ -2911,71 +2898,3 @@ async def proxy_to_instance(
         status_code=response.status_code,
         headers=response_headers,
     )
-
-
-sessions_router = FastAPIRouter(prefix="/users", tags=["sessions"])
-
-
-@sessions_router.get(
-    "/me/sessions",
-    summary="Get user sessions",
-    description="Get all active sessions (running instances) for the current user.",
-)
-async def get_user_sessions(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get all active sessions for the current user.
-
-    Args:
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        Dictionary containing list of active sessions with instance details.
-    """
-    _user = await _get_user(session, user_id)
-
-    result = await session.execute(
-        select(ToolInstance)
-        .where(ToolInstance.owner_id == user_id)
-        .where(
-            ToolInstance.status.in_(
-                ["running", "building", "pending", "stopped", "error"]
-            )
-        )
-        .order_by(ToolInstance.created_at.desc())
-    )
-    instances = result.scalars().all()
-
-    sessions = []
-    for instance in instances:
-        tool_type = await session.get(ToolType, instance.tool_type_id)
-        repo = await session.get(GitRepository, instance.repository_id)
-        project = await session.get(Project, instance.project_id)
-
-        sessions.append(
-            {
-                "id": str(instance.id),
-                "display_name": instance.display_name,
-                "tool_type_name": tool_type.name if tool_type else "unknown",
-                "tool_icon": tool_type.name if tool_type else "code",
-                "tool_type_interfaces": [tool_type.interface_type] if tool_type else [],
-                "repository_name": repo.name if repo else "unknown",
-                "repository_id": str(instance.repository_id),
-                "project_name": project.name if project else "unknown",
-                "project_id": str(instance.project_id),
-                "status": instance.status,
-                "url": instance.url,
-                "clone_mode": instance.clone_mode,
-                "branch": instance.branch,
-                "selected_config_profile_id": str(instance.selected_config_profile_id)
-                if instance.selected_config_profile_id
-                else None,
-                "created_at": instance.created_at.isoformat()
-                if instance.created_at
-                else None,
-            }
-        )
-
-    return {"sessions": sessions}

apps/api/src/api/tool/tool_types.py

@@ -1,19 +1,23 @@
 import uuid
-from datetime import datetime
 
 from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, ConfigDict, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.api.tool_types_validation import (
+from src.api.tool.tool_types_validation import (
     check_port_exposed,
     validate_compose_yaml,
     validate_required_variables,
 )
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
-from src.models.tool_type import ToolType
+from src.models import ToolType
 from src.models.user import User
+from src.schemas.tool import (
+    ToolTypeCreate,
+    ToolTypeResponse,
+    ToolTypeUpdate,
+    ToolTypeValidateRequest,
+)
 
 router = APIRouter(prefix="/tool-types", tags=["tool-types"])
 
@@ -29,237 +33,6 @@ async def _require_admin(user: User) -> None:
     pass
 
 
-class ToolTypeCreate(BaseModel):
-    name: str
-    display_name: str
-    description: str | None = None
-    default_port: int = 0
-    definition_type: str = "compose"
-    manifest_id: uuid.UUID | None = None
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-    build_context: dict | None = None
-    readiness_probe: dict | None = None
-    startup_command: str | None = None
-    required_variables: list[str] = []
-    category: str = "other"
-    interface_type: str = "web"
-    requires_port: bool = True
-
-    @field_validator("definition_type")
-    @classmethod
-    def validate_definition_type(cls, v: str) -> str:
-        if v not in ("compose", "dockerfile", "manifest"):
-            raise ValueError(
-                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
-            )
-        return v
-
-    @field_validator("compose_template")
-    @classmethod
-    def validate_compose_template(cls, v: str | None, info) -> str | None:
-        data = info.data
-        if data.get("definition_type") != "compose":
-            return v
-
-        if v is None or not v.strip():
-            raise ValueError(
-                "compose_template is required when definition_type is 'compose'"
-            )
-
-        validate_compose_yaml(v)
-        return v
-
-    @field_validator("dockerfile_template")
-    @classmethod
-    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
-        data = info.data
-        if data.get("definition_type") != "dockerfile":
-            return v
-
-        if v is None or not v.strip():
-            raise ValueError(
-                "dockerfile_template is required when definition_type is 'dockerfile'"
-            )
-
-        if not v.strip().startswith("FROM"):
-            raise ValueError("Dockerfile must start with a FROM instruction")
-
-        return v
-
-    @field_validator("interface_type")
-    @classmethod
-    def validate_interface_type(cls, v: str) -> str:
-        if v not in ("web", "terminal"):
-            raise ValueError("interface_type must be 'web' or 'terminal'")
-        return v
-
-    @field_validator("default_port")
-    @classmethod
-    def validate_default_port(cls, v: int, info) -> int:
-        data = info.data
-        requires_port = data.get("requires_port", True)
-        if not requires_port:
-            return v
-        if v <= 0 or v > 65535:
-            raise ValueError("Port must be between 1 and 65535")
-        return v
-
-    @field_validator("required_variables")
-    @classmethod
-    def validate_required_variables(cls, v: list[str], info) -> list[str]:
-        if not v:
-            return v
-
-        data = info.data
-        if data.get("definition_type") != "compose":
-            return v
-
-        template = data.get("compose_template")
-        if not template:
-            return v
-
-        for var in v:
-            placeholder = f"{{{{{var}}}}}"
-            if placeholder not in template:
-                raise ValueError(
-                    f"Required variable '{var}' not found in compose template"
-                )
-
-        return v
-
-    @model_validator(mode="after")
-    def validate_templates(self) -> "ToolTypeCreate":
-        if self.definition_type == "manifest":
-            if self.manifest_id is None:
-                raise ValueError(
-                    "manifest_id is required when definition_type is 'manifest'"
-                )
-            return self
-
-        if self.definition_type == "dockerfile" and (
-            self.dockerfile_template is None or not self.dockerfile_template.strip()
-        ):
-            raise ValueError(
-                "dockerfile_template is required when definition_type is 'dockerfile'"
-            )
-        if self.definition_type == "compose" and (
-            self.compose_template is None or not self.compose_template.strip()
-        ):
-            raise ValueError(
-                "compose_template is required when definition_type is 'compose'"
-            )
-
-        # Validate that default_port is exposed in compose template (only if requires_port)
-        if (
-            self.requires_port
-            and self.definition_type == "compose"
-            and self.compose_template
-        ):
-            try:
-                parsed = validate_compose_yaml(self.compose_template)
-            except ValueError:
-                return self
-
-            if not check_port_exposed(parsed, self.default_port):
-                raise ValueError(
-                    f"Port {self.default_port} is not exposed in the compose template. Add it to the 'ports' section."
-                )
-
-        return self
-
-
-class ToolTypeUpdate(BaseModel):
-    display_name: str | None = None
-    description: str | None = None
-    default_port: int | None = None
-    definition_type: str | None = None
-    manifest_id: uuid.UUID | None = None
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-    build_context: dict | None = None
-    readiness_probe: dict | None = None
-    startup_command: str | None = None
-    required_variables: list[str] | None = None
-    category: str | None = None
-    interface_type: str | None = None
-    requires_port: bool | None = None
-
-    @field_validator("definition_type")
-    @classmethod
-    def validate_definition_type(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if v not in ("compose", "dockerfile", "manifest"):
-            raise ValueError(
-                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
-            )
-        return v
-
-    @field_validator("interface_type")
-    @classmethod
-    def validate_interface_type(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if v not in ("web", "terminal"):
-            raise ValueError("interface_type must be 'web' or 'terminal'")
-        return v
-
-    @field_validator("compose_template")
-    @classmethod
-    def validate_compose_template(cls, v: str | None, info) -> str | None:
-        if v is None:
-            return v
-
-        data = info.data
-        definition_type = data.get("definition_type")
-        if definition_type and definition_type != "compose":
-            return v
-
-        validate_compose_yaml(v)
-        return v
-
-    @field_validator("dockerfile_template")
-    @classmethod
-    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
-        if v is None:
-            return v
-
-        data = info.data
-        definition_type = data.get("definition_type")
-        if definition_type and definition_type != "dockerfile":
-            return v
-
-        if not v.strip().startswith("FROM"):
-            raise ValueError("Dockerfile must start with a FROM instruction")
-
-        return v
-
-
-class ToolTypeResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    display_name: str
-    description: str | None
-    category: str
-    interface_type: str
-    requires_port: bool
-    default_port: int
-    definition_type: str
-    manifest_id: uuid.UUID | None
-    compose_template: str | None
-    dockerfile_template: str | None
-    build_context: dict | None
-    readiness_probe: dict | None
-    startup_command: str | None
-    required_variables: list[str]
-    created_by_id: uuid.UUID | None
-    created_at: datetime
-    updated_at: datetime
-
-
 @router.post(
     "",
     response_model=ToolTypeResponse,
@@ -461,12 +234,6 @@ async def update_tool_type(
     return tool_type
 
 
-class ToolTypeValidateRequest(BaseModel):
-    definition_type: str
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-
-
 @router.post(
     "/validate",
     summary="Validate tool type template",

apps/api/src/api/user/__init__.py

@@ -0,0 +1,7 @@
+"""User API routers module."""
+
+from src.api.user.auth import router as auth_router
+from src.api.user.ssh_keys import router as ssh_keys_router
+from src.api.user.users import router as users_router
+
+__all__ = ["auth_router", "ssh_keys_router", "users_router"]

apps/api/src/api/user/ssh_keys.py

@@ -1,18 +1,24 @@
 import base64
 import uuid
-from datetime import datetime
 
 from cryptography.fernet import Fernet
 from cryptography.hazmat.primitives import serialization
 from cryptography.hazmat.primitives.asymmetric.ed25519 import Ed25519PrivateKey
 from fastapi import APIRouter, Depends, HTTPException, status
-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.config import Settings
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
+from src.schemas.project import (
+    SSHKeyCreate,
+    SSHKeyResponse,
+    SignPayloadRequest,
+    SignatureResponse,
+    VerifySignatureRequest,
+    VerifySignatureResponse,
+)
 
 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
 
@@ -21,7 +27,7 @@ def _get_fernet() -> Fernet:
     """Generate a valid Fernet key from the session secret."""
     import base64
     import hashlib
-    
+
     settings = Settings()
     # Derive a 32-byte key from the session secret using SHA256
     key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
@@ -53,36 +59,6 @@ def generate_ssh_key_pair() -> tuple[str, str]:
     return private_bytes.decode("utf-8"), public_bytes.decode("utf-8")
 
 
-class SSHKeyCreate(BaseModel):
-    name: str
-
-
-class SSHKeyResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    public_key: str
-    created_at: datetime
-
-
-class SignPayloadRequest(BaseModel):
-    payload: str
-
-
-class SignatureResponse(BaseModel):
-    signature: str
-
-
-class VerifySignatureRequest(BaseModel):
-    payload: str
-    signature: str
-
-
-class VerifySignatureResponse(BaseModel):
-    valid: bool
-
-
 @router.post(
     "",
     response_model=SSHKeyResponse,
@@ -171,7 +147,9 @@ async def delete_ssh_key(
     user = await _get_user(session, user_id)
     ssh_key = await session.get(SSHKey, key_id)
     if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+        )
 
     await session.delete(ssh_key)
     await session.commit()
@@ -203,7 +181,9 @@ async def sign_payload(
     user = await _get_user(session, user_id)
     ssh_key = await session.get(SSHKey, key_id)
     if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+        )
 
     fernet = _get_fernet()
     private_key_pem = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
@@ -242,7 +222,9 @@ async def verify_signature(
     user = await _get_user(session, user_id)
     ssh_key = await session.get(SSHKey, key_id)
     if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+        )
 
     public_key = serialization.load_ssh_public_key(ssh_key.public_key.encode())
 

apps/api/src/api/user/users.py

@@ -2,11 +2,11 @@ import uuid
 from pathlib import Path
 
 from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
-from pydantic import BaseModel, ConfigDict
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.user import User
+from src.schemas.user import UserProfileResponse, UserProfileUpdate
 
 router = APIRouter(prefix="/users", tags=["users"])
 
@@ -16,20 +16,6 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
 
 
-class UserProfileResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    email: str
-    name: str
-    avatar_url: str | None
-
-
-class UserProfileUpdate(BaseModel):
-    name: str | None = None
-    email: str | None = None
-
-
 @router.get(
     "/me",
     response_model=UserProfileResponse,
@@ -77,12 +63,16 @@ async def update_profile(
 
     if data.name is not None:
         if len(data.name.strip()) == 0:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="name cannot be empty")
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST, detail="name cannot be empty"
+            )
         user.name = data.name.strip()
 
     if data.email is not None:
         if "@" not in data.email:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid email")
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST, detail="invalid email"
+            )
         user.email = data.email.strip()
 
     await session.commit()

apps/api/src/api/workspace/__init__.py

@@ -0,0 +1,17 @@
+"""Workspace API routers module."""
+
+from src.api.workspace.workspace_files import router as workspace_files_router
+from src.api.workspace.workspace_git import router as workspace_git_router
+from src.api.workspace.workspace_instances import router as workspace_instances_router
+from src.api.workspace.workspaces import (
+    all_workspaces_router,
+    router as workspaces_router,
+)
+
+__all__ = [
+    "all_workspaces_router",
+    "workspace_files_router",
+    "workspace_git_router",
+    "workspace_instances_router",
+    "workspaces_router",
+]

apps/api/src/api/workspace/workspace_files.py

@@ -6,8 +6,8 @@ from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.workspace import Workspace
+from src.models import Workspace
-from src.services.file_service import FileService
+from src.services.shared.file_service import FileService
 
 router = APIRouter(prefix="/workspaces/{workspace_id}/files")
 
@@ -103,7 +103,7 @@ async def write_file(
         raise HTTPException(status_code=400, detail=str(exc)) from exc
 
     if commit_message:
-        from src.services.git_operations import GitOperations
+        from src.services.git.git_operations import GitOperations
 
         git = GitOperations(workspace)
         try:

apps/api/src/api/workspace/workspace_git.py

@@ -6,8 +6,8 @@ from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.workspace import Workspace
+from src.models import Workspace
-from src.services.git_operations import GitOperations
+from src.services.git.git_operations import GitOperations
 
 router = APIRouter(prefix="/workspaces/{workspace_id}/git")
 

apps/api/src/api/workspace/workspace_instances.py

@@ -7,8 +7,8 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_instance import ToolInstance
+from src.models import ToolInstance
-from src.models.workspace import Workspace
+from src.models import Workspace
 
 router = APIRouter(prefix="/workspaces/{workspace_id}/instances")
 

apps/api/src/api/workspace/workspaces.py

@@ -9,10 +9,10 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
-from src.models.tool_instance import ToolInstance
+from src.models import ToolInstance
-from src.models.workspace import Workspace
+from src.models import Workspace
-from src.services.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
+from src.services.shared.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
 
 logger = logging.getLogger(__name__)
 

apps/api/src/logging_config.py

@@ -10,7 +10,7 @@ from collections.abc import Callable
 from fastapi import Request, Response
 from starlette.middleware.base import BaseHTTPMiddleware
 
-from src.services.correlation import get_correlation_id
+from src.services.shared.correlation import get_correlation_id
 
 logger = logging.getLogger(__name__)
 

apps/api/src/main.py

@@ -7,39 +7,42 @@ from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import JSONResponse
 from fastapi.staticfiles import StaticFiles
 
-from src.api.auth import router as auth_router
+from src.api.config import config_profiles_router, user_config_router
-from src.api.dashboard import router as dashboard_router
+from src.api.project import git_repositories_router, projects_router
-from src.api.events import router as events_router
+from src.api.system import (
-from src.api.git_repositories import router as git_repositories_router
+    dashboard_router,
-from src.api.health import router as health_router
+    events_router,
-from src.api.projects import router as projects_router
+    health_router,
-from src.api.ssh_keys import router as ssh_keys_router
+    instance_proxy_router,
-from src.api.terminal import router as terminal_router
+    notifications_router,
-from src.api.instance_proxy import router as instance_proxy_router
+    terminal_router,
-from src.api.config_profiles import router as config_profiles_router
+)
-from src.api.tool_definitions import router as tool_definitions_router
+from src.api.tool import (
-from src.api.tool_instances import router as tool_instances_router
+    sessions_router,
-from src.api.tool_instances import sessions_router
+    tool_definitions_router,
-from src.api.tool_types import router as tool_types_router
+    tool_instances_router,
-from src.api.notifications import router as notifications_router
+    tool_types_router,
-from src.api.user_config import router as user_config_router
+)
-from src.api.users import router as users_router
+from src.api.user import auth_router, ssh_keys_router, users_router
-from src.api.workspace_files import router as workspace_files_router
+from src.api.workspace import (
-from src.api.workspace_git import router as workspace_git_router
+    all_workspaces_router,
-from src.api.workspace_instances import router as workspace_instances_router
+    workspace_files_router,
-from src.api.workspaces import all_workspaces_router, router as workspaces_router
+    workspace_git_router,
+    workspace_instances_router,
+    workspaces_router,
+)
 from src.config import Settings
-from src.models.notification import Notification  # noqa: F401 – Alembic model discovery
+from src.models import Notification  # noqa: F401 – Alembic model discovery
-from src.models.terminal_session import TerminalSessionModel  # noqa: F401 – Alembic model discovery
+from src.models import TerminalSessionModel  # noqa: F401 – Alembic model discovery
 from src.database import init_database
 from src.logging_config import (
     ExceptionLoggingMiddleware,
     RequestLoggingMiddleware,
     configure_logging,
 )
-from src.services.correlation import CorrelationIdMiddleware
+from src.seeds.builtin_tool_types import seed_builtin_tool_types
-from src.services.event_bus import InstanceEventBus
+from src.services.instance import InstanceEventBus, HealthMonitor
-from src.services.health_monitor import HealthMonitor
+from src.services.shared import CorrelationIdMiddleware
 
 # Configure logging early
 log_level = os.getenv("LOG_LEVEL", "INFO").upper()
@@ -135,6 +138,10 @@ async def on_startup():
     _health_monitor.start()
     logger.info("Health monitor started")
 
+    # Seed built-in tool types
+    await seed_builtin_tool_types()
+    logger.info("Built-in tool types seeded")
+
     logger.info("Startup complete.")
 
 

apps/api/src/models/__init__.py

@@ -1,18 +1,18 @@
 from src.models.base import Base
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models.config.config_profile import ConfigProfile, ConfigProfileInclude
-from src.models.git_repository import GitRepository
+from src.models.project.git_repository import GitRepository
-from src.models.health_check import HealthCheck
+from src.models.project.project import Project
-from src.models.instance_event import InstanceEvent
+from src.models.project.workspace import Workspace
-from src.models.notification import Notification
+from src.models.system.health_check import HealthCheck
-from src.models.project import Project
+from src.models.system.instance_event import InstanceEvent
-from src.models.ssh_key import SSHKey
+from src.models.system.notification import Notification
-from src.models.terminal_session import TerminalSessionModel
+from src.models.system.terminal_session import TerminalSessionModel
-from src.models.tool_definition_manifest import ToolDefinitionManifest
+from src.models.tool.tool_definition_manifest import ToolDefinitionManifest
-from src.models.tool_instance import ToolInstance
+from src.models.tool.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
+from src.models.tool.tool_type import ToolType
-from src.models.user import User
+from src.models.user.ssh_key import SSHKey
-from src.models.user_config import UserConfig
+from src.models.user.user import User
-from src.models.workspace import Workspace
+from src.models.user.user_config import UserConfig
 
 __all__ = [
     "Base",

apps/api/src/models/config/__init__.py

@@ -0,0 +1,5 @@
+"""Config models module."""
+
+from src.models.config.config_profile import ConfigProfile, ConfigProfileInclude
+
+__all__ = ["ConfigProfile", "ConfigProfileInclude"]

apps/api/src/models/config/config_profile.py

@@ -1,7 +1,15 @@
 import uuid
 from typing import TYPE_CHECKING
 
-from sqlalchemy import ForeignKey, JSON, Integer, String, Text, Boolean
+from sqlalchemy import (
+    Boolean,
+    ForeignKey,
+    JSON,
+    Integer,
+    String,
+    Text,
+    UniqueConstraint,
+)
 from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
@@ -9,12 +17,15 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
-    from src.models.tool_type import ToolType
+    from src.models import ToolType
     from src.models.user import User
 
 
 class ConfigProfile(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     __tablename__ = "config_profiles"
+    __table_args__ = (
+        UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
+    )
 
     user_id: Mapped[uuid.UUID] = mapped_column(
         UUID(), ForeignKey("users.id", ondelete="CASCADE"), nullable=False

apps/api/src/models/project/__init__.py

@@ -0,0 +1,7 @@
+"""Project models module."""
+
+from src.models.project.git_repository import GitRepository
+from src.models.project.project import Project
+from src.models.project.workspace import Workspace
+
+__all__ = ["GitRepository", "Project", "Workspace"]

apps/api/src/models/project/git_repository.py

@@ -10,7 +10,7 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
-    from src.models.ssh_key import SSHKey
+    from src.models import SSHKey
     from src.models.user import User
 
 

apps/api/src/models/project/project.py

@@ -8,8 +8,8 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
-    from src.models.git_repository import GitRepository
+    from src.models import GitRepository
-    from src.models.ssh_key import SSHKey
+    from src.models import SSHKey
     from src.models.user import User
 
 

apps/api/src/models/project/workspace.py

@@ -12,7 +12,7 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from src.models.base import Base, TimestampMixin
 
 if TYPE_CHECKING:
-    from src.models.git_repository import GitRepository
+    from src.models import GitRepository
     from src.models.user import User
 
 

apps/api/src/models/system/__init__.py

@@ -0,0 +1,8 @@
+"""System models module."""
+
+from src.models.system.health_check import HealthCheck
+from src.models.system.instance_event import InstanceEvent
+from src.models.system.notification import Notification
+from src.models.system.terminal_session import TerminalSessionModel
+
+__all__ = ["HealthCheck", "InstanceEvent", "Notification", "TerminalSessionModel"]

apps/api/src/models/tool/__init__.py

@@ -0,0 +1,7 @@
+"""Tool models module."""
+
+from src.models.tool.tool_definition_manifest import ToolDefinitionManifest
+from src.models.tool.tool_instance import ToolInstance
+from src.models.tool.tool_type import ToolType
+
+__all__ = ["ToolDefinitionManifest", "ToolInstance", "ToolType"]

apps/api/src/models/tool/tool_instance.py

@@ -9,12 +9,12 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
-    from src.models.config_profile import ConfigProfile
+    from src.models import ConfigProfile
-    from src.models.git_repository import GitRepository
+    from src.models import GitRepository
     from src.models.project import Project
-    from src.models.tool_type import ToolType
+    from src.models import ToolType
     from src.models.user import User
-    from src.models.workspace import Workspace
+    from src.models import Workspace
 
 
 class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):

apps/api/src/models/tool/tool_type.py

@@ -6,8 +6,7 @@ from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
+from src.models.tool.tool_definition_manifest import ToolDefinitionManifest
-from src.models.tool_definition_manifest import ToolDefinitionManifest
 
 if TYPE_CHECKING:
     from src.models.user import User

apps/api/src/models/user/__init__.py

@@ -0,0 +1,7 @@
+"""User models module."""
+
+from src.models.user.ssh_key import SSHKey
+from src.models.user.user import User
+from src.models.user.user_config import UserConfig
+
+__all__ = ["SSHKey", "User", "UserConfig"]

apps/api/src/models/user/user.py

@@ -7,8 +7,8 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
-    from src.models.ssh_key import SSHKey
+    from src.models import SSHKey
-    from src.models.user_config import UserConfig
+    from src.models import UserConfig
 
 
 class User(UUIDPrimaryKeyMixin, TimestampMixin, Base):

apps/api/src/models/user/user_config.py

@@ -0,0 +1,51 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, JSON
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.user import User
+
+
+class UserConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "user_configs"
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id"), nullable=False, unique=True
+    )
+    config: Mapped[dict[str, object]] = mapped_column(
+        JSON, default=dict, nullable=False
+    )
+
+    user: Mapped["User"] = relationship(back_populates="user_config")
+
+    @property
+    def default_profile_id(self) -> uuid.UUID | None:
+        """Return the legacy global default profile ID from config JSON."""
+        profile_id = self.config.get("default_profile_id")
+        if isinstance(profile_id, str):
+            return uuid.UUID(profile_id)
+        return None
+
+    @default_profile_id.setter
+    def default_profile_id(self, value: uuid.UUID | None) -> None:
+        if value is not None:
+            self.config["default_profile_id"] = str(value)
+        elif "default_profile_id" in self.config:
+            del self.config["default_profile_id"]
+
+    @property
+    def default_profiles(self) -> dict[str, str]:
+        """Return per-tool-type default profile IDs from config JSON."""
+        value = self.config.get("default_profiles", {})
+        if isinstance(value, dict):
+            return {str(k): str(v) for k, v in value.items()}
+        return {}
+
+    @default_profiles.setter
+    def default_profiles(self, value: dict[str, str]) -> None:
+        self.config["default_profiles"] = value

apps/api/src/models/user_config.py

@@ -1,20 +0,0 @@
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import ForeignKey
-from sqlalchemy import JSON, Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.user import User
-
-
-class UserConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    __tablename__ = "user_configs"
-
-    user_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("users.id"), nullable=False, unique=True)
-    config: Mapped[dict[str, object]] = mapped_column(JSON, default=dict, nullable=False)
-
-    user: Mapped["User"] = relationship(back_populates="user_config")

apps/api/src/schemas/config/__init__.py

@@ -0,0 +1,27 @@
+"""Config schemas module."""
+
+from src.schemas.config.config_profile import (
+    ConfigProfileCreate,
+    ConfigProfileIncludeUpdate,
+    ConfigProfileResponse,
+    ConfigProfileUpdate,
+    DefaultProfilesUpdate,
+    GitMountItem,
+    GitMountMapping,
+    MountItem,
+    ValidateGitUrlRequest,
+    ValidateGitUrlResponse,
+)
+
+__all__ = [
+    "ConfigProfileCreate",
+    "ConfigProfileIncludeUpdate",
+    "ConfigProfileResponse",
+    "ConfigProfileUpdate",
+    "DefaultProfilesUpdate",
+    "GitMountItem",
+    "GitMountMapping",
+    "MountItem",
+    "ValidateGitUrlRequest",
+    "ValidateGitUrlResponse",
+]

apps/api/src/schemas/config/config_profile.py

@@ -0,0 +1,280 @@
+"""Config profile request/response schemas."""
+
+import uuid
+
+from pydantic import BaseModel, Field, field_validator, model_validator
+
+from src.api.shared_validators import validate_env_vars as _validate_env_vars
+
+
+def _validate_uuid(v: str | None) -> str | None:
+    if v is None:
+        return v
+    try:
+        uuid.UUID(v)
+    except ValueError as exc:
+        raise ValueError(f"Invalid UUID: {v}") from exc
+    return v
+
+
+class GitMountMapping(BaseModel):
+    source_path: str = Field(
+        description="Path within repository (supports glob patterns)"
+    )
+    target_path: str = Field(description="Absolute path inside container")
+
+    @field_validator("source_path")
+    @classmethod
+    def validate_source_path(cls, v: str) -> str:
+        if v.startswith("/"):
+            raise ValueError("source_path must be relative (no leading /)")
+        if ".." in v:
+            raise ValueError("source_path cannot contain path traversal (..)")
+        return v
+
+    @field_validator("target_path")
+    @classmethod
+    def validate_target_path(cls, v: str) -> str:
+        if ".." in v:
+            raise ValueError("target_path cannot contain path traversal (..)")
+        return v
+
+
+class GitMountItem(BaseModel):
+    remote_url: str = Field(description="Git remote URL (HTTPS or SSH)")
+    source_path: str | None = Field(
+        default=None, description="Path within repository (legacy single mapping)"
+    )
+    target_path: str | None = Field(
+        default=None,
+        description="Absolute path inside container (legacy single mapping)",
+    )
+    branch: str | None = Field(default=None, description="Optional branch or tag name")
+    mappings: list[GitMountMapping] | None = Field(
+        default=None, description="Multiple source/target mappings from the same repo"
+    )
+
+    @field_validator("remote_url")
+    @classmethod
+    def validate_remote_url(cls, v: str) -> str:
+        if not v.startswith(("http://", "https://", "git@", "ssh://")):
+            raise ValueError(
+                "remote_url must be a valid git URL (https://, git@, or ssh://)"
+            )
+        return v
+
+    @field_validator("source_path")
+    @classmethod
+    def validate_source_path(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v.startswith("/"):
+            raise ValueError("source_path must be relative (no leading /)")
+        if ".." in v:
+            raise ValueError("source_path cannot contain path traversal (..)")
+        return v
+
+    @field_validator("target_path")
+    @classmethod
+    def validate_target_path(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if ".." in v:
+            raise ValueError("target_path cannot contain path traversal (..)")
+        return v
+
+    @model_validator(mode="after")
+    def check_mappings_or_legacy(self):
+        has_legacy = self.source_path is not None and self.target_path is not None
+        has_mappings = self.mappings is not None and len(self.mappings) > 0
+        if not has_legacy and not has_mappings:
+            raise ValueError(
+                "Git mount must have either 'mappings' (non-empty array) or both 'source_path' and 'target_path'"
+            )
+        return self
+
+
+class MountItem(BaseModel):
+    target: str = Field(description="Absolute mount target path")
+    mode: str = Field(default="rw", description="Mount mode: ro or rw")
+    files: dict = Field(
+        default_factory=dict, description="Files as {relative_path: content}"
+    )
+
+    @field_validator("target")
+    @classmethod
+    def validate_target(cls, v: str) -> str:
+        if not v.startswith("/"):
+            raise ValueError("Mount target must be absolute (start with /)")
+        return v
+
+    @field_validator("mode")
+    @classmethod
+    def validate_mode(cls, v: str) -> str:
+        if v not in ("ro", "rw"):
+            raise ValueError("Mount mode must be 'ro' or 'rw'")
+        return v
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict) -> dict:
+        for path in v:
+            if ".." in path or not path:
+                raise ValueError(f"Invalid file path: {path}")
+            if path.startswith("/"):
+                raise ValueError(
+                    f"Mount file paths must be relative (got: {path}). "
+                    f"The mount target defines the absolute container path."
+                )
+        return v
+
+
+class ConfigProfileCreate(BaseModel):
+    name: str = Field(description="Profile name (unique per user)")
+    description: str | None = Field(default=None, description="Optional description")
+    project_id: str | None = Field(default=None, description="Optional project ID")
+    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
+    env_vars: dict = Field(default_factory=dict, description="Environment variables")
+    runtime_hints: dict = Field(default_factory=dict, description="Runtime hints")
+    mounts: list[MountItem] = Field(
+        default_factory=list, description="Mount definitions"
+    )
+    files: dict = Field(
+        default_factory=dict, description="Files as {relative_path: content}"
+    )
+    git_mounts: list[GitMountItem] = Field(
+        default_factory=list, description="Git repository mounts"
+    )
+    is_default: bool = Field(
+        default=False, description="Whether this is the default profile for its scope"
+    )
+
+    @field_validator("project_id", "tool_type_id")
+    @classmethod
+    def validate_uuids(cls, v: str | None) -> str | None:
+        return _validate_uuid(v)
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict) -> dict:
+        for path in v:
+            if ".." in path or not path:
+                raise ValueError(f"Invalid file path: {path}")
+            if path.startswith("/"):
+                raise ValueError(
+                    f"File paths must be relative (got: {path}). "
+                    f"Use Mounts for absolute container paths."
+                )
+        return v
+
+    @field_validator("env_vars")
+    @classmethod
+    def validate_env_vars(cls, v: dict) -> dict:
+        result = _validate_env_vars(v)
+        if result is None:
+            raise ValueError("env_vars must be a JSON object")
+        return result
+
+    @field_validator("runtime_hints")
+    @classmethod
+    def validate_runtime_hints(cls, v: dict) -> dict:
+        if not isinstance(v, dict):
+            raise ValueError("runtime_hints must be a JSON object")
+        return v
+
+    @field_validator("mounts")
+    @classmethod
+    def validate_mounts(cls, v: list) -> list:
+        if not isinstance(v, list):
+            raise ValueError("mounts must be a JSON array")
+        return v
+
+
+class ConfigProfileUpdate(BaseModel):
+    name: str | None = Field(default=None, description="Profile name")
+    description: str | None = Field(default=None, description="Optional description")
+    project_id: str | None = Field(default=None, description="Optional project ID")
+    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
+    env_vars: dict | None = Field(default=None, description="Environment variables")
+    runtime_hints: dict | None = Field(default=None, description="Runtime hints")
+    mounts: list[MountItem] | None = Field(
+        default=None, description="Mount definitions"
+    )
+    files: dict | None = Field(
+        default=None, description="Files as {relative_path: content}"
+    )
+    git_mounts: list[GitMountItem] | None = Field(
+        default=None, description="Git repository mounts"
+    )
+    is_default: bool | None = Field(
+        default=None, description="Whether this is the default profile"
+    )
+
+    @field_validator("project_id", "tool_type_id")
+    @classmethod
+    def validate_uuids(cls, v: str | None) -> str | None:
+        return _validate_uuid(v)
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict | None) -> dict | None:
+        if v is None:
+            return v
+        for path in v:
+            if ".." in path or path.startswith("/") or not path:
+                raise ValueError(f"Invalid file path: {path}")
+        return v
+
+
+class ConfigProfileIncludeUpdate(BaseModel):
+    includes: list[str] = Field(description="Ordered list of included profile IDs")
+
+    @field_validator("includes")
+    @classmethod
+    def validate_includes(cls, v: list) -> list:
+        for item in v:
+            try:
+                uuid.UUID(item)
+            except ValueError as exc:
+                raise ValueError(f"Invalid UUID in includes: {item}") from exc
+        return v
+
+
+class ConfigProfileResponse(BaseModel):
+    id: str
+    user_id: str
+    name: str
+    description: str | None
+    project_id: str | None
+    tool_type_id: str | None
+    env_vars: dict
+    runtime_hints: dict
+    mounts: list
+    files: dict
+    git_mounts: list
+    is_default: bool
+    includes: list[dict]
+    created_at: str
+    updated_at: str
+
+
+class DefaultProfilesUpdate(BaseModel):
+    default_profiles: dict[str, str] = Field(
+        description="Mapping of tool_type_id -> profile_id for default profiles"
+    )
+
+
+class ValidateGitUrlRequest(BaseModel):
+    url: str = Field(description="Git remote URL to validate")
+    ssh_key_id: str | None = Field(
+        default=None, description="Optional SSH key ID for private repos"
+    )
+
+
+class ValidateGitUrlResponse(BaseModel):
+    valid: bool
+    suggested_url: str | None = None
+    branches: list[str] | None = None
+    default_branch: str | None = None
+    error: str | None = None
+    error_code: str | None = None

apps/api/src/schemas/project/__init__.py

@@ -0,0 +1,41 @@
+"""Project schemas module."""
+
+from src.schemas.project.git_repository import (
+    GitRepositoryCreate,
+    GitRepositoryResponse,
+    UpdateSSHKeyRequest,
+    URLParseRequest,
+    URLParseResponse,
+)
+from src.schemas.project.project import (
+    ProjectCreate,
+    ProjectResponse,
+    ProjectUpdate,
+    SetDefaultSSHKeyRequest,
+)
+from src.schemas.project.ssh_key import (
+    SSHKeyCreate,
+    SSHKeyResponse,
+    SignPayloadRequest,
+    SignatureResponse,
+    VerifySignatureRequest,
+    VerifySignatureResponse,
+)
+
+__all__ = [
+    "GitRepositoryCreate",
+    "GitRepositoryResponse",
+    "ProjectCreate",
+    "ProjectResponse",
+    "ProjectUpdate",
+    "SSHKeyCreate",
+    "SSHKeyResponse",
+    "SetDefaultSSHKeyRequest",
+    "SignPayloadRequest",
+    "SignatureResponse",
+    "URLParseRequest",
+    "URLParseResponse",
+    "UpdateSSHKeyRequest",
+    "VerifySignatureRequest",
+    "VerifySignatureResponse",
+]

apps/api/src/schemas/project/git_repository.py

@@ -0,0 +1,47 @@
+"""Git repository request/response schemas."""
+
+import uuid
+from datetime import datetime
+
+from pydantic import BaseModel, ConfigDict
+
+
+class GitRepositoryCreate(BaseModel):
+    name: str
+    remote_url: str | None = None
+    force_original_url: bool = False
+    ssh_key_id: str | None = None
+
+
+class URLParseRequest(BaseModel):
+    url: str
+
+
+class URLParseResponse(BaseModel):
+    original_url: str
+    base_url: str | None
+    is_valid_clone_url: bool
+    needs_parsing: bool
+    host: str | None
+    message: str
+    error_code: str | None
+
+
+class GitRepositoryResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    name: str
+    path: str
+    project_id: uuid.UUID | None
+    owner_id: uuid.UUID
+    is_mirror: bool
+    remote_url: str | None
+    last_push: datetime | None
+    ssh_key_id: uuid.UUID | None
+    created_at: datetime
+    updated_at: datetime
+
+
+class UpdateSSHKeyRequest(BaseModel):
+    ssh_key_id: str | None = None

apps/api/src/schemas/project/project.py

@@ -0,0 +1,29 @@
+"""Project request/response schemas."""
+
+import uuid
+
+from pydantic import BaseModel, ConfigDict
+
+
+class ProjectCreate(BaseModel):
+    name: str
+    description: str | None = None
+
+
+class ProjectUpdate(BaseModel):
+    name: str | None = None
+    description: str | None = None
+
+
+class ProjectResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    name: str
+    description: str | None
+    owner_id: uuid.UUID
+    default_ssh_key_id: uuid.UUID | None
+
+
+class SetDefaultSSHKeyRequest(BaseModel):
+    ssh_key_id: uuid.UUID

apps/api/src/schemas/project/ssh_key.py

@@ -0,0 +1,36 @@
+"""SSH key request/response schemas."""
+
+import uuid
+from datetime import datetime
+
+from pydantic import BaseModel, ConfigDict
+
+
+class SSHKeyCreate(BaseModel):
+    name: str
+
+
+class SSHKeyResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    name: str
+    public_key: str
+    created_at: datetime
+
+
+class SignPayloadRequest(BaseModel):
+    payload: str
+
+
+class SignatureResponse(BaseModel):
+    signature: str
+
+
+class VerifySignatureRequest(BaseModel):
+    payload: str
+    signature: str
+
+
+class VerifySignatureResponse(BaseModel):
+    valid: bool

apps/api/src/schemas/system/__init__.py

@@ -0,0 +1,17 @@
+"""System schemas module."""
+
+from src.schemas.system.health import (
+    DatabaseHealth,
+    DatabaseHealthResponse,
+    DiskHealth,
+    HealthChecks,
+    HealthResponse,
+)
+
+__all__ = [
+    "DatabaseHealth",
+    "DatabaseHealthResponse",
+    "DiskHealth",
+    "HealthChecks",
+    "HealthResponse",
+]

apps/api/src/schemas/system/health.py

@@ -0,0 +1,50 @@
+"""Health check response schemas."""
+
+from pydantic import BaseModel, Field
+
+
+class DatabaseHealth(BaseModel):
+    """Database health check result."""
+
+    status: str = Field(description="Database health status", examples=["healthy"])
+    response_time_ms: float = Field(
+        description="Query response time in milliseconds", examples=[5.2]
+    )
+
+
+class DiskHealth(BaseModel):
+    """Disk space health check result."""
+
+    status: str = Field(description="Disk health status", examples=["healthy"])
+    free_gb: float = Field(description="Free disk space in GB", examples=[45.2])
+    total_gb: float = Field(description="Total disk space in GB", examples=[100.0])
+
+
+class HealthChecks(BaseModel):
+    """Individual health checks."""
+
+    database: DatabaseHealth | None = None
+    disk: DiskHealth | None = None
+
+
+class HealthResponse(BaseModel):
+    """Overall health check response."""
+
+    status: str = Field(description="Overall health status", examples=["healthy"])
+    timestamp: str = Field(
+        description="ISO 8601 timestamp", examples=["2026-05-19T12:00:00Z"]
+    )
+    version: str = Field(description="API version", examples=["0.1.0"])
+    checks: HealthChecks = Field(description="Individual health checks")
+    uptime_seconds: float = Field(
+        description="Server uptime in seconds", examples=[3600.0]
+    )
+
+
+class DatabaseHealthResponse(BaseModel):
+    """Database-specific health check response."""
+
+    status: str = Field(description="Database health status", examples=["healthy"])
+    response_time_ms: float = Field(
+        description="Query response time in milliseconds", examples=[5.2]
+    )

apps/api/src/schemas/tool/__init__.py

@@ -0,0 +1,18 @@
+"""Tool schemas module."""
+
+from src.schemas.tool.tool_instance import CreateInstanceRequest, StartInstanceRequest
+from src.schemas.tool.tool_type import (
+    ToolTypeCreate,
+    ToolTypeResponse,
+    ToolTypeUpdate,
+    ToolTypeValidateRequest,
+)
+
+__all__ = [
+    "CreateInstanceRequest",
+    "StartInstanceRequest",
+    "ToolTypeCreate",
+    "ToolTypeResponse",
+    "ToolTypeUpdate",
+    "ToolTypeValidateRequest",
+]

apps/api/src/schemas/tool/tool_instance.py

@@ -0,0 +1,45 @@
+"""Tool instance request/response schemas."""
+
+from pydantic import BaseModel, Field
+
+
+class CreateInstanceRequest(BaseModel):
+    """Request body for creating a tool instance."""
+
+    model_config = {"extra": "ignore"}
+
+    tool_type_id: str = Field(description="UUID of the tool type to instantiate")
+    display_name: str | None = Field(
+        default=None, description="Optional display name for the instance"
+    )
+    workspace_id: str | None = Field(
+        default=None, description="UUID of workspace to mount (replaces clone_mode)"
+    )
+    clone_mode: str = Field(
+        default="mount", description="Repository access mode: 'mount' or 'clone'"
+    )
+    branch: str | None = Field(
+        default="main", description="Branch to clone (when clone_mode='clone')"
+    )
+    new_branch: str | None = Field(
+        default=None, description="Create a new local branch after cloning"
+    )
+    config_profile_id: str | None = Field(
+        default=None, description="Optional config profile ID for launch"
+    )
+    ssh_key_ids: list[str] = Field(
+        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
+    )
+
+
+class StartInstanceRequest(BaseModel):
+    """Request body for starting a tool instance."""
+
+    model_config = {"extra": "ignore"}
+
+    config_profile_id: str | None = Field(
+        default=None, description="Config profile ID to apply, or null for none"
+    )
+    ssh_key_ids: list[str] = Field(
+        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
+    )

apps/api/src/schemas/tool/tool_type.py

@@ -0,0 +1,230 @@
+"""Tool type request/response schemas."""
+
+import uuid
+
+from datetime import datetime
+
+from pydantic import BaseModel, ConfigDict, field_validator, model_validator
+
+from src.api.tool.tool_types_validation import (
+    check_port_exposed,
+    validate_compose_yaml,
+    validate_required_variables,
+)
+
+
+class ToolTypeCreate(BaseModel):
+    name: str
+    display_name: str
+    description: str | None = None
+    default_port: int = 0
+    definition_type: str = "compose"
+    manifest_id: uuid.UUID | None = None
+    compose_template: str | None = None
+    dockerfile_template: str | None = None
+    build_context: dict | None = None
+    readiness_probe: dict | None = None
+    startup_command: str | None = None
+    required_variables: list[str] = []
+    category: str = "other"
+    interface_type: str = "web"
+    requires_port: bool = True
+
+    @field_validator("definition_type")
+    @classmethod
+    def validate_definition_type(cls, v: str) -> str:
+        if v not in ("compose", "dockerfile", "manifest"):
+            raise ValueError(
+                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
+            )
+        return v
+
+    @field_validator("compose_template")
+    @classmethod
+    def validate_compose_template(cls, v: str | None, info) -> str | None:
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+
+        if v is None or not v.strip():
+            raise ValueError(
+                "compose_template is required when definition_type is 'compose'"
+            )
+
+        validate_compose_yaml(v)
+        return v
+
+    @field_validator("dockerfile_template")
+    @classmethod
+    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
+        data = info.data
+        if data.get("definition_type") != "dockerfile":
+            return v
+
+        if v is None or not v.strip():
+            raise ValueError(
+                "dockerfile_template is required when definition_type is 'dockerfile'"
+            )
+
+        if not v.strip().startswith("FROM"):
+            raise ValueError("Dockerfile must start with a FROM instruction")
+
+        return v
+
+    @field_validator("interface_type")
+    @classmethod
+    def validate_interface_type(cls, v: str) -> str:
+        if v not in ("web", "terminal"):
+            raise ValueError("interface_type must be 'web' or 'terminal'")
+        return v
+
+    @field_validator("default_port")
+    @classmethod
+    def validate_default_port(cls, v: int, info) -> int:
+        data = info.data
+        requires_port = data.get("requires_port", True)
+        if not requires_port:
+            return v
+        if v <= 0 or v > 65535:
+            raise ValueError("Port must be between 1 and 65535")
+        return v
+
+    @field_validator("required_variables")
+    @classmethod
+    def validate_required_variables(cls, v: list[str], info) -> list[str]:
+        if not v:
+            return v
+
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+
+        template = data.get("compose_template")
+        if not template:
+            return v
+
+        validate_required_variables(template, v)
+        return v
+
+    @model_validator(mode="after")
+    def validate_templates(self) -> "ToolTypeCreate":
+        if self.definition_type == "manifest":
+            if self.manifest_id is None:
+                raise ValueError(
+                    "manifest_id is required when definition_type is 'manifest'"
+                )
+            return self
+
+        if self.definition_type == "dockerfile" and (
+            self.dockerfile_template is None or not self.dockerfile_template.strip()
+        ):
+            raise ValueError(
+                "dockerfile_template is required when definition_type is 'dockerfile'"
+            )
+        if self.definition_type == "compose" and (
+            self.compose_template is None or not self.compose_template.strip()
+        ):
+            raise ValueError(
+                "compose_template is required when definition_type is 'compose'"
+            )
+
+        if (
+            self.requires_port
+            and self.definition_type == "compose"
+            and self.compose_template
+        ):
+            try:
+                parsed = validate_compose_yaml(self.compose_template)
+            except ValueError:
+                return self
+
+            if not check_port_exposed(parsed, self.default_port):
+                raise ValueError(
+                    f"Port {self.default_port} is not exposed in the compose template. Add it to the 'ports' section."
+                )
+
+        return self
+
+
+class ToolTypeUpdate(BaseModel):
+    display_name: str | None = None
+    description: str | None = None
+    default_port: int | None = None
+    definition_type: str | None = None
+    manifest_id: uuid.UUID | None = None
+    compose_template: str | None = None
+    dockerfile_template: str | None = None
+    build_context: dict | None = None
+    readiness_probe: dict | None = None
+    startup_command: str | None = None
+    required_variables: list[str] | None = None
+    category: str | None = None
+    interface_type: str | None = None
+    requires_port: bool | None = None
+
+    @field_validator("definition_type")
+    @classmethod
+    def validate_definition_type(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v not in ("compose", "dockerfile", "manifest"):
+            raise ValueError(
+                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
+            )
+        return v
+
+    @field_validator("interface_type")
+    @classmethod
+    def validate_interface_type(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v not in ("web", "terminal"):
+            raise ValueError("interface_type must be 'web' or 'terminal'")
+        return v
+
+    @field_validator("compose_template")
+    @classmethod
+    def validate_compose_template(cls, v: str | None, info) -> str | None:
+        if v is None:
+            return v
+        validate_compose_yaml(v)
+        return v
+
+    @field_validator("dockerfile_template")
+    @classmethod
+    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
+        if v is None:
+            return v
+        if not v.strip().startswith("FROM"):
+            raise ValueError("Dockerfile must start with a FROM instruction")
+        return v
+
+
+class ToolTypeResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    name: str
+    display_name: str
+    description: str | None
+    category: str
+    interface_type: str
+    requires_port: bool
+    default_port: int
+    definition_type: str
+    manifest_id: uuid.UUID | None
+    compose_template: str | None
+    dockerfile_template: str | None
+    build_context: dict | None
+    readiness_probe: dict | None
+    startup_command: str | None
+    required_variables: list[str]
+    created_by_id: uuid.UUID | None
+    created_at: datetime
+    updated_at: datetime
+
+
+class ToolTypeValidateRequest(BaseModel):
+    definition_type: str
+    compose_template: str | None = None
+    dockerfile_template: str | None = None

apps/api/src/schemas/user/__init__.py

@@ -0,0 +1,11 @@
+"""User schemas module."""
+
+from src.schemas.user.user import UserProfileResponse, UserProfileUpdate
+from src.schemas.user.user_config import UserConfigResponse, UserConfigUpdate
+
+__all__ = [
+    "UserConfigResponse",
+    "UserConfigUpdate",
+    "UserProfileResponse",
+    "UserProfileUpdate",
+]

apps/api/src/schemas/user/user.py

@@ -0,0 +1,19 @@
+"""User response schemas."""
+
+import uuid
+
+from pydantic import BaseModel, ConfigDict
+
+
+class UserProfileResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    email: str
+    name: str
+    avatar_url: str | None
+
+
+class UserProfileUpdate(BaseModel):
+    name: str | None = None
+    email: str | None = None

apps/api/src/schemas/user/user_config.py

@@ -0,0 +1,25 @@
+"""User config response schemas."""
+
+from pydantic import BaseModel, ConfigDict
+
+
+class UserConfigResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    default_editor: str | None = None
+    theme: str = "system"
+    git_user_name: str | None = None
+    git_user_email: str | None = None
+    last_session_id: str | None = None
+    notification_mute_categories: list[str] | None = None
+    notification_toast_level: str | None = None
+
+
+class UserConfigUpdate(BaseModel):
+    default_editor: str | None = None
+    theme: str | None = None
+    git_user_name: str | None = None
+    git_user_email: str | None = None
+    last_session_id: str | None = None
+    notification_mute_categories: list[str] | None = None
+    notification_toast_level: str | None = None

apps/api/src/seeds/__init__.py

@@ -0,0 +1 @@
+"""Database seeding utilities."""

apps/api/src/seeds/builtin_tool_types.py

@@ -0,0 +1,168 @@
+"""Seed built-in tool types into the database."""
+
+import logging
+
+from sqlalchemy import select, text
+
+from src.database import SessionLocal
+from src.models import ToolType
+
+logger = logging.getLogger(__name__)
+
+
+async def _table_exists(session, table_name: str) -> bool:
+    """Check if a table exists in the database."""
+    try:
+        result = await session.execute(
+            text(
+                """
+                SELECT EXISTS (
+                    SELECT FROM information_schema.tables
+                    WHERE table_schema = 'public'
+                    AND table_name = :table_name
+                )
+            """
+            ),
+            {"table_name": table_name},
+        )
+        return result.scalar() or False
+    except Exception:
+        return False
+
+
+async def seed_builtin_tool_types():
+    """Create or update built-in tool types in the database.
+
+    Built-in tool types have no creator (created_by_id=None) and provide
+    out-of-the-box tools for users without requiring manual tool creation.
+    """
+    async with SessionLocal() as session:
+        # Check if tool_types table exists before attempting to seed
+        if not await _table_exists(session, "tool_types"):
+            logger.warning(
+                "tool_types table does not exist. Skipping seeding. "
+                "Migrations may not have run yet."
+            )
+            return
+
+        builtin_types = [
+            {
+                "name": "code-server",
+                "display_name": "VS Code Server",
+                "description": "VS Code running in the browser via code-server",
+                "category": "editor",
+                "interface_type": "web",
+                "compose_template": """version: "3.8"
+services:
+  code-server:
+    image: lscr.io/linuxserver/code-server:latest
+    container_name: {{TOOL_NAME}}
+    environment:
+      - PUID=1000
+      - PGID=1000
+      - TZ=Europe/London
+    volumes:
+      - {{REPO_PATH}}:/config/workspace
+    ports:
+      - "8443:8443"
+    restart: unless-stopped""",
+                "default_port": 8443,
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+            {
+                "name": "jupyter-notebook",
+                "display_name": "Jupyter Notebook",
+                "description": "Jupyter Lab for interactive development",
+                "category": "notebook",
+                "interface_type": "web",
+                "default_port": 8888,
+                "compose_template": """version: "3.8"
+services:
+  jupyter:
+    image: jupyter/scipy-notebook:latest
+    container_name: {{TOOL_NAME}}
+    environment:
+      - JUPYTER_ENABLE_LAB=yes
+    volumes:
+      - {{REPO_PATH}}:/home/jovyan/work
+    ports:
+      - "8888:8888"
+    restart: unless-stopped""",
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+            {
+                "name": "opencode",
+                "display_name": "OpenCode",
+                "description": "AI coding assistant - run opencode in terminal",
+                "category": "ai-assistant",
+                "interface_type": "terminal",
+                "default_port": 3000,
+                "compose_template": """version: "3.8"
+services:
+  opencode:
+    image: node:20-slim
+    container_name: {{TOOL_NAME}}
+    working_dir: /workspace
+    environment:
+      - HOME=/tmp
+    volumes:
+      - {{REPO_PATH}}:/workspace
+      - opencode_home:/tmp
+    ports:
+      - "3000:3000"
+    command: >
+      sh -c "set -x &&
+             apt-get update && apt-get install -y git ca-certificates &&
+             echo 'Installing opencode...' &&
+             npm install -g opencode-ai 2>&1 || echo 'ERROR: npm install failed' &&
+             which opencode || echo 'ERROR: opencode not in PATH' &&
+             npm bin -g &&
+             ls -la $(npm bin -g) || echo 'ERROR: global bin dir not found' &&
+             echo 'export PATH=\"$(npm bin -g):\\$PATH\"' >> /root/.bashrc &&
+             echo 'cd /workspace' >> /root/.bashrc &&
+             echo 'OpenCode installation complete' &&
+             cd /workspace &&
+             exec tail -f /dev/null"
+    stdin_open: true
+    tty: true
+    restart: unless-stopped
+
+volumes:
+  opencode_home:""",
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+        ]
+
+        for tool_data in builtin_types:
+            existing = await session.scalar(
+                select(ToolType).where(ToolType.name == tool_data["name"])
+            )
+            if not existing:
+                tool_type = ToolType(
+                    name=tool_data["name"],
+                    display_name=tool_data["display_name"],
+                    description=tool_data["description"],
+                    category=tool_data["category"],
+                    interface_type=tool_data["interface_type"],
+                    definition_type="compose",
+                    compose_template=tool_data["compose_template"],
+                    required_variables=tool_data["required_variables"],
+                    default_port=tool_data.get("default_port", 0),
+                    created_by_id=None,
+                )
+                session.add(tool_type)
+                logger.info("Created built-in tool type: %s", tool_data["name"])
+            else:
+                # Update existing built-in tool types to reflect code changes
+                existing.display_name = tool_data["display_name"]
+                existing.description = tool_data["description"]
+                existing.category = tool_data["category"]
+                existing.interface_type = tool_data["interface_type"]
+                existing.definition_type = "compose"
+                existing.compose_template = tool_data["compose_template"]
+                existing.required_variables = tool_data["required_variables"]
+                existing.default_port = tool_data.get("default_port", 0)
+                logger.info("Updated built-in tool type: %s", tool_data["name"])
+
+        await session.commit()
+        logger.info("Built-in tool types seeded successfully.")

apps/api/src/services/config/__init__.py

@@ -0,0 +1,25 @@
+"""Config profile services module."""
+
+from src.services.config.config_profile_resolver import (
+    ConfigProfileCycleError,
+    ConfigProfileNotFoundError,
+    ResolvedMount,
+    ResolvedProfile,
+    apply_resolved_profile,
+    check_include_cycle,
+    expand_container_path,
+    resolve_profile,
+    resolved_profile_to_dict,
+)
+
+__all__ = [
+    "ConfigProfileCycleError",
+    "ConfigProfileNotFoundError",
+    "ResolvedMount",
+    "ResolvedProfile",
+    "apply_resolved_profile",
+    "check_include_cycle",
+    "expand_container_path",
+    "resolve_profile",
+    "resolved_profile_to_dict",
+]

apps/api/src/services/config/config_profile_resolver.py

@@ -13,7 +13,7 @@ from typing import Any
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models import ConfigProfile, ConfigProfileInclude
 
 logger = logging.getLogger(__name__)
 

apps/api/src/services/docker/__init__.py

@@ -0,0 +1,55 @@
+"""Docker services package for container and compose operations."""
+
+from src.services.docker.compose import (
+    execute_compose_command,
+    render_compose_template,
+    sort_volumes_by_specificity,
+    write_compose_file,
+)
+from src.services.docker.config_staging import (
+    ensure_instance_directory,
+    write_config_files,
+    write_env_file,
+)
+from src.services.docker.container import (
+    connect_container_to_network,
+    find_free_port,
+    get_backend_network_name,
+    get_container_id,
+    get_container_ip_on_network,
+    get_container_logs,
+    get_container_name,
+    get_container_status,
+    is_container_on_network,
+    wait_for_container_running,
+)
+from src.services.docker.tunnel import (
+    check_tunnel_health,
+    recreate_tunnel,
+    start_tunnel,
+    stop_tunnel,
+)
+
+__all__ = [
+    "check_tunnel_health",
+    "connect_container_to_network",
+    "ensure_instance_directory",
+    "execute_compose_command",
+    "find_free_port",
+    "get_backend_network_name",
+    "get_container_id",
+    "get_container_ip_on_network",
+    "get_container_logs",
+    "get_container_name",
+    "get_container_status",
+    "is_container_on_network",
+    "recreate_tunnel",
+    "render_compose_template",
+    "sort_volumes_by_specificity",
+    "start_tunnel",
+    "stop_tunnel",
+    "wait_for_container_running",
+    "write_compose_file",
+    "write_config_files",
+    "write_env_file",
+]

apps/api/src/services/docker/compose.py

@@ -0,0 +1,120 @@
+"""Docker Compose file generation and manipulation."""
+
+import logging
+import subprocess
+from collections import Counter
+from pathlib import Path
+from typing import Any
+
+logger = logging.getLogger(__name__)
+
+
+def sort_volumes_by_specificity(volumes: list[str]) -> list[str]:
+    """Sort volume strings so parent paths come before child paths.
+
+    Docker Compose mounts volumes in array order. A later mount at a parent
+    path hides earlier mounts at child paths. By sorting shallow paths first
+    and deep paths last, deeper (more specific) mounts overlay correctly.
+
+    Volume format: source:target or source:target:type
+
+    Args:
+        volumes: List of Docker volume mount strings.
+
+    Returns:
+        Sorted list with parent paths before child paths.
+    """
+
+    def _target_depth(vol: str) -> int:
+        parts = vol.split(":")
+        if len(parts) < 2:
+            return 0
+        target = parts[1].rstrip("/")
+        if not target or target == "/":
+            return 0
+        return target.count("/")
+
+    # Detect duplicate targets and warn
+    targets = []
+    for vol in volumes:
+        parts = vol.split(":")
+        targets.append(parts[1] if len(parts) > 1 else "")
+    dupes = [t for t, c in Counter(targets).items() if c > 1]
+    if dupes:
+        logger.warning("Duplicate mount targets detected: %s", dupes)
+
+    # Stable sort: parent paths first, child paths last
+    return sorted(volumes, key=_target_depth)
+
+
+def render_compose_template(template: str, variables: dict[str, Any]) -> str:
+    """Render a Docker Compose template with variable substitution.
+
+    Args:
+        template: The compose template string
+        variables: Dictionary of variable names to values
+
+    Returns:
+        Rendered compose file content
+    """
+    result = template
+    for key, value in variables.items():
+        placeholder = f"{{{{{key}}}}}"
+        result = result.replace(placeholder, str(value))
+    return result
+
+
+def write_compose_file(instance_dir: str, content: str) -> str:
+    """Write the rendered compose file to the instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+        content: Rendered compose content
+
+    Returns:
+        Path to the compose file
+    """
+    compose_path = Path(instance_dir) / "docker-compose.yml"
+    compose_path.write_text(content)
+    return str(compose_path)
+
+
+def execute_compose_command(
+    compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
+) -> tuple[int, str, str]:
+    """Execute a docker compose command.
+
+    Args:
+        compose_path: Path to docker-compose.yml
+        action: The compose action (up, down, start, stop, restart)
+        timeout: Command timeout in seconds
+        env_file: Optional path to .env file for environment variables
+
+    Returns:
+        Tuple of (returncode, stdout, stderr)
+    """
+    instance_dir = Path(compose_path).parent
+
+    cmd = ["docker", "compose", "-f", compose_path]
+
+    if env_file:
+        cmd.extend(["--env-file", env_file])
+
+    if action == "up":
+        cmd.extend(["up", "-d", "--force-recreate"])
+    elif action == "down":
+        cmd.extend(["down", "-v"])
+    elif action in ("start", "stop", "restart"):
+        cmd.append(action)
+    else:
+        raise ValueError(f"Unknown compose action: {action}")
+
+    result = subprocess.run(
+        cmd,
+        cwd=str(instance_dir),
+        capture_output=True,
+        text=True,
+        timeout=timeout,
+    )
+
+    return result.returncode, result.stdout, result.stderr

apps/api/src/services/docker/config_staging.py

@@ -0,0 +1,61 @@
+"""Staging configuration files into instance directories."""
+
+import logging
+from pathlib import Path
+
+logger = logging.getLogger(__name__)
+
+
+def ensure_instance_directory(instance_id: str, base_path: str | None = None) -> str:
+    """Create and return the instance directory path.
+
+    Args:
+        instance_id: Unique instance identifier
+        base_path: Base directory for all instances (defaults to Settings.instance_base_path)
+
+    Returns:
+        Absolute path to instance directory
+    """
+    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)
+    return str(instance_dir.absolute())
+
+
+def write_env_file(instance_dir: str, env_vars: dict[str, str]) -> str:
+    """Write environment variables to a .env file.
+
+    Args:
+        instance_dir: Path to instance directory
+        env_vars: Dictionary of env var names to values
+
+    Returns:
+        Path to the env file
+    """
+    env_path = Path(instance_dir) / ".env"
+    lines = [f'{key}="{value}"' for key, value in env_vars.items()]
+    env_path.write_text("\n".join(lines) + "\n")
+    return str(env_path)
+
+
+def write_config_files(instance_dir: str, files: dict[str, str]) -> None:
+    """Write config files to the instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+        files: Dictionary of file paths (relative to instance dir) to content
+    """
+    instance_path = Path(instance_dir)
+    for file_path, content in files.items():
+        # Ensure the path is within the instance directory (security)
+        full_path = instance_path / file_path
+        try:
+            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)

apps/api/src/services/docker/container.py

@@ -1,181 +1,13 @@
-"""Docker service for managing tool instances."""
+"""Docker container runtime queries and network management."""
 
 import logging
 import subprocess
 import time
-from collections import Counter
-from pathlib import Path
 from typing import Any
 
 logger = logging.getLogger(__name__)
 
 
-def sort_volumes_by_specificity(volumes: list[str]) -> list[str]:
-    """Sort volume strings so parent paths come before child paths.
-
-    Docker Compose mounts volumes in array order. A later mount at a parent
-    path hides earlier mounts at child paths. By sorting shallow paths first
-    and deep paths last, deeper (more specific) mounts overlay correctly.
-
-    Volume format: source:target or source:target:type
-
-    Args:
-        volumes: List of Docker volume mount strings.
-
-    Returns:
-        Sorted list with parent paths before child paths.
-    """
-
-    def _target_depth(vol: str) -> int:
-        parts = vol.split(":")
-        if len(parts) < 2:
-            return 0
-        target = parts[1].rstrip("/")
-        if not target or target == "/":
-            return 0
-        return target.count("/")
-
-    # Detect duplicate targets and warn
-    targets = []
-    for vol in volumes:
-        parts = vol.split(":")
-        targets.append(parts[1] if len(parts) > 1 else "")
-    dupes = [t for t, c in Counter(targets).items() if c > 1]
-    if dupes:
-        logger.warning("Duplicate mount targets detected: %s", dupes)
-
-    # Stable sort: parent paths first, child paths last
-    return sorted(volumes, key=_target_depth)
-
-
-def render_compose_template(template: str, variables: dict[str, Any]) -> str:
-    """Render a Docker Compose template with variable substitution.
-
-    Args:
-        template: The compose template string
-        variables: Dictionary of variable names to values
-
-    Returns:
-        Rendered compose file content
-    """
-    result = template
-    for key, value in variables.items():
-        placeholder = f"{{{{{key}}}}}"
-        result = result.replace(placeholder, str(value))
-    return result
-
-
-def ensure_instance_directory(instance_id: str, base_path: str | None = None) -> str:
-    """Create and return the instance directory path.
-
-    Args:
-        instance_id: Unique instance identifier
-        base_path: Base directory for all instances (defaults to Settings.instance_base_path)
-
-    Returns:
-        Absolute path to instance directory
-    """
-    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)
-    return str(instance_dir.absolute())
-
-
-def write_compose_file(instance_dir: str, content: str) -> str:
-    """Write the rendered compose file to the instance directory.
-
-    Args:
-        instance_dir: Path to instance directory
-        content: Rendered compose content
-
-    Returns:
-        Path to the compose file
-    """
-    compose_path = Path(instance_dir) / "docker-compose.yml"
-    compose_path.write_text(content)
-    return str(compose_path)
-
-
-def write_env_file(instance_dir: str, env_vars: dict[str, str]) -> str:
-    """Write environment variables to a .env file.
-
-    Args:
-        instance_dir: Path to instance directory
-        env_vars: Dictionary of env var names to values
-
-    Returns:
-        Path to the env file
-    """
-    env_path = Path(instance_dir) / ".env"
-    lines = [f'{key}="{value}"' for key, value in env_vars.items()]
-    env_path.write_text("\n".join(lines) + "\n")
-    return str(env_path)
-
-
-def write_config_files(instance_dir: str, files: dict[str, str]) -> None:
-    """Write config files to the instance directory.
-
-    Args:
-        instance_dir: Path to instance directory
-        files: Dictionary of file paths (relative to instance dir) to content
-    """
-    instance_path = Path(instance_dir)
-    for file_path, content in files.items():
-        # Ensure the path is within the instance directory (security)
-        full_path = instance_path / file_path
-        try:
-            full_path.resolve().relative_to(instance_path.resolve())
-        except ValueError:
-            raise ValueError(f"File path '{file_path}' escapes instance directory")
-
-        full_path.parent.mkdir(parents=True, exist_ok=True)
-        full_path.write_text(content)
-
-
-def execute_compose_command(
-    compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
-) -> tuple[int, str, str]:
-    """Execute a docker compose command.
-
-    Args:
-        compose_path: Path to docker-compose.yml
-        action: The compose action (up, down, start, stop, restart)
-        timeout: Command timeout in seconds
-        env_file: Optional path to .env file for environment variables
-
-    Returns:
-        Tuple of (returncode, stdout, stderr)
-    """
-    instance_dir = Path(compose_path).parent
-
-    cmd = ["docker", "compose", "-f", compose_path]
-
-    if env_file:
-        cmd.extend(["--env-file", env_file])
-
-    if action == "up":
-        cmd.extend(["up", "-d", "--force-recreate"])
-    elif action == "down":
-        cmd.extend(["down", "-v"])
-    elif action in ("start", "stop", "restart"):
-        cmd.append(action)
-    else:
-        raise ValueError(f"Unknown compose action: {action}")
-
-    result = subprocess.run(
-        cmd,
-        cwd=str(instance_dir),
-        capture_output=True,
-        text=True,
-        timeout=timeout,
-    )
-
-    return result.returncode, result.stdout, result.stderr
-
-
 def get_container_id(instance_name: str) -> str | None:
     """Get the container ID for a compose service.
 

apps/api/src/services/docker/tunnel.py

@@ -1,10 +1,8 @@
-"""Clean tunnel service using cloudflared containers on the backend network.
+"""Cloudflare tunnel management using cloudflared Docker containers.
 
-Design:
+Each tunnel runs as a Docker container on the same 'backend' network as the API.
-- Each tunnel runs as a Docker container on the same 'backend' network as the API.
+cloudflared connects to the tool container by its Docker Compose service name
-- cloudflared connects to the tool container by its Docker Compose service name
+(e.g. http://code-server-headquarter-34837cd3:8443).
-  (e.g. http://code-server-headquarter-34837cd3:8443).
-- This avoids host port conflicts and DNS resolution issues.
 """
 
 import logging
@@ -12,7 +10,7 @@ import re
 import subprocess
 from typing import Any
 
-from src.services.docker import get_backend_network_name
+from src.services.docker.container import get_backend_network_name
 
 logger = logging.getLogger(__name__)
 
@@ -55,7 +53,7 @@ def _cleanup_stale_tunnel(tunnel_name: str) -> None:
     )
 
 
-def _get_container_logs(tunnel_name: str) -> tuple[str, str]:
+def _get_tunnel_logs(tunnel_name: str) -> tuple[str, str]:
     """Get stdout and stderr logs from a container."""
     result = subprocess.run(
         ["docker", "logs", tunnel_name],
@@ -65,7 +63,7 @@ def _get_container_logs(tunnel_name: str) -> tuple[str, str]:
     return result.stdout, result.stderr
 
 
-def _get_container_exit_code(tunnel_name: str) -> int | None:
+def _get_tunnel_exit_code(tunnel_name: str) -> int | None:
     """Get exit code of a container if it has exited."""
     result = subprocess.run(
         ["docker", "inspect", "-f", "{{.State.ExitCode}}", tunnel_name],
@@ -133,13 +131,15 @@ def start_tunnel(
     logger.debug("Tunnel container started: %s", container_id)
 
     # Wait for URL to appear in logs
-    url_pattern = re.compile(r"https://[a-z0-9-]+\.trycloudflare\.com")
+    # Exclude api.trycloudflare.com which is the Cloudflare API endpoint,
+    # not a tunnel URL. Real tunnel URLs have random subdomains (10+ chars).
+    url_pattern = re.compile(r"https://(?!api\.)[a-z0-9-]{10,}\.trycloudflare\.com")
     start_time = __import__("time").time()
     url: str | None = None
     combined_logs = ""
 
     while __import__("time").time() - start_time < timeout:
-        stdout, stderr = _get_container_logs(tunnel_name)
+        stdout, stderr = _get_tunnel_logs(tunnel_name)
         combined_logs = stdout + "\n" + stderr
 
         match = url_pattern.search(combined_logs)
@@ -148,7 +148,7 @@ def start_tunnel(
             break
 
         # Check if container exited early
-        exit_code = _get_container_exit_code(tunnel_name)
+        exit_code = _get_tunnel_exit_code(tunnel_name)
         if exit_code is not None and exit_code != 0:
             _cleanup_stale_tunnel(tunnel_name)
             raise RuntimeError(
@@ -159,9 +159,9 @@ def start_tunnel(
         __import__("time").sleep(0.5)
 
     if not url:
-        stdout, stderr = _get_container_logs(tunnel_name)
+        stdout, stderr = _get_tunnel_logs(tunnel_name)
         combined_logs = stdout + "\n" + stderr
-        exit_code = _get_container_exit_code(tunnel_name)
+        exit_code = _get_tunnel_exit_code(tunnel_name)
 
         _cleanup_stale_tunnel(tunnel_name)
         raise RuntimeError(

apps/api/src/services/git/__init__.py

@@ -0,0 +1,19 @@
+"""Git services module."""
+
+from src.services.git.clone import (
+    check_dirty_state,
+    clone_repository,
+    remove_clone_directory,
+)
+from src.services.git.git_operations import Commit, GitOperations, GitStatus
+from src.services.git.git_service import GitService
+
+__all__ = [
+    "check_dirty_state",
+    "clone_repository",
+    "remove_clone_directory",
+    "Commit",
+    "GitOperations",
+    "GitStatus",
+    "GitService",
+]

apps/api/src/services/git/git_operations.py

@@ -4,7 +4,7 @@ import asyncio
 import logging
 from dataclasses import dataclass
 
-from src.models.workspace import Workspace
+from src.models import Workspace
 
 logger = logging.getLogger(__name__)
 

apps/api/src/services/instance/__init__.py

@@ -0,0 +1,7 @@
+"""Instance lifecycle services module."""
+
+from src.services.instance.event_bus import InstanceEventBus
+from src.services.instance.health_monitor import HealthMonitor
+from src.services.instance.lifecycle_hooks import publish_lifecycle_event
+
+__all__ = ["InstanceEventBus", "HealthMonitor", "publish_lifecycle_event"]

apps/api/src/services/instance/health_monitor.py

@@ -10,13 +10,13 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.database import SessionLocal
-from src.models.health_check import HealthCheck
+from src.models import HealthCheck
-from src.models.tool_instance import ToolInstance
+from src.models import ToolInstance
-from src.services.correlation import get_correlation_id
+from src.services.shared.correlation import get_correlation_id
 from src.services.docker import get_container_status
-from src.services.tunnel import check_tunnel_health
+from src.services.shared.tunnel import check_tunnel_health
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
+from src.services.instance.event_bus import InstanceEventBus, InstanceEventPayload
-from src.services.notification_service import notification_service
+from src.services.shared.notification_service import notification_service
 
 logger = logging.getLogger(__name__)
 

apps/api/src/services/instance/lifecycle_hooks.py

@@ -6,11 +6,11 @@ from datetime import datetime, timezone
 
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.models.instance_event import InstanceEvent
+from src.models import InstanceEvent
-from src.models.tool_instance import ToolInstance
+from src.models import ToolInstance
-from src.services.correlation import get_correlation_id
+from src.services.shared.correlation import get_correlation_id
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
+from src.services.instance.event_bus import InstanceEventBus, InstanceEventPayload
-from src.services.notification_service import notification_service
+from src.services.shared.notification_service import notification_service
 
 logger = logging.getLogger(__name__)
 

apps/api/src/services/shared/__init__.py

@@ -0,0 +1,51 @@
+"""Shared services module."""
+
+from src.services.shared.correlation import CorrelationIdMiddleware, get_correlation_id
+from src.services.shared.file_service import FileEntry, FileService
+from src.services.shared.notification_service import NotificationService
+from src.services.shared.permission_fixer import (
+    PermissionFixError,
+    apply_mount_permissions,
+    apply_ssh_permissions,
+    check_root_user_available,
+)
+from src.services.shared.readiness_probe import execute_probe
+from src.services.shared.ssh_keys import (
+    cleanup_ssh_key_files,
+    prepare_ssh_key_files,
+    write_ssh_config,
+)
+from src.services.shared.tunnel import (
+    check_tunnel_health,
+    recreate_tunnel,
+    start_tunnel,
+    stop_tunnel,
+)
+from src.services.shared.workspace_manager import (
+    SyncResult,
+    WorkspaceHasInstancesError,
+    WorkspaceManager,
+)
+
+__all__ = [
+    "CorrelationIdMiddleware",
+    "FileEntry",
+    "FileService",
+    "NotificationService",
+    "PermissionFixError",
+    "SyncResult",
+    "WorkspaceHasInstancesError",
+    "WorkspaceManager",
+    "apply_mount_permissions",
+    "apply_ssh_permissions",
+    "check_root_user_available",
+    "check_tunnel_health",
+    "cleanup_ssh_key_files",
+    "execute_probe",
+    "get_correlation_id",
+    "prepare_ssh_key_files",
+    "recreate_tunnel",
+    "start_tunnel",
+    "stop_tunnel",
+    "write_ssh_config",
+]

apps/api/src/services/shared/file_service.py

@@ -4,7 +4,7 @@ import logging
 import os
 from dataclasses import dataclass
 
-from src.models.workspace import Workspace
+from src.models import Workspace
 
 logger = logging.getLogger(__name__)
 

apps/api/src/services/shared/notification_service.py

@@ -8,7 +8,7 @@ from sqlalchemy import func, select, update
 from sqlalchemy.engine import CursorResult
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.models.notification import Notification
+from src.models import Notification
 
 
 class NotificationService:

apps/api/src/services/shared/tunnel.py

@@ -0,0 +1,8 @@
+"""Tunnel service — re-exported from docker.tunnel for backward compatibility."""
+
+from src.services.docker.tunnel import (  # noqa: F401
+    check_tunnel_health,
+    recreate_tunnel,
+    start_tunnel,
+    stop_tunnel,
+)

apps/api/src/services/shared/workspace_manager.py

@@ -14,15 +14,15 @@ from typing import TYPE_CHECKING
 
 from sqlalchemy import select
 
-from src.models.workspace import Workspace
+from src.models import Workspace
-from src.services.git_service import GitService
+from src.services.git.git_service import GitService
-from src.services.ssh_keys import _get_fernet
+from src.services.shared.ssh_keys import _get_fernet
 
 if TYPE_CHECKING:
     from sqlalchemy.ext.asyncio import AsyncSession
 
-    from src.models.git_repository import GitRepository
+    from src.models import GitRepository
-    from src.models.tool_instance import ToolInstance
+    from src.models import ToolInstance
 
 logger = logging.getLogger(__name__)
 
@@ -96,7 +96,7 @@ class WorkspaceManager:
         # Load SSH key if repo has one
         ssh_key = None
         if getattr(repo, "ssh_key_id", None) and session is not None:
-            from src.models.ssh_key import SSHKey
+            from src.models import SSHKey
 
             result = await session.execute(
                 select(SSHKey).where(SSHKey.id == repo.ssh_key_id)
@@ -181,8 +181,8 @@ class WorkspaceManager:
         # Load SSH key if repo has one
         ssh_key = None
         if session is not None:
-            from src.models.git_repository import GitRepository
+            from src.models import GitRepository
-            from src.models.ssh_key import SSHKey
+            from src.models import SSHKey
 
             repo = await session.get(GitRepository, workspace.repo_id)
             if repo and getattr(repo, "ssh_key_id", None):
@@ -241,7 +241,7 @@ class WorkspaceManager:
         session: AsyncSession,
     ) -> list[ToolInstance]:
         """Get all tool instances associated with this workspace."""
-        from src.models.tool_instance import ToolInstance
+        from src.models import ToolInstance
 
         result = await session.execute(
             select(ToolInstance).where(ToolInstance.workspace_id == workspace.id)

apps/api/src/services/terminal/__init__.py

@@ -0,0 +1,9 @@
+"""Terminal services module."""
+
+from src.services.terminal.terminal_manager import (
+    MaxSessionsExceededError,
+    TerminalManager,
+)
+from src.services.terminal.terminal_session import TerminalSession
+
+__all__ = ["MaxSessionsExceededError", "TerminalManager", "TerminalSession"]

apps/api/src/services/terminal/terminal_manager.py

@@ -9,8 +9,8 @@ from fastapi import WebSocket
 from sqlalchemy.dialects.postgresql import insert as pg_insert
 
 from src.database import SessionLocal
-from src.models.terminal_session import TerminalSessionModel
+from src.models import TerminalSessionModel
-from src.services.terminal_session import TerminalSession
+from src.services.terminal.terminal_session import TerminalSession
 
 logger = logging.getLogger(__name__)