fix: mobile terminal back and X buttons navigate to /sessions

Terminal sessions are opened in a new tab via window.open with
noopener,noreferrer. In a new tab, window.history has no previous
entry, so navigate(-1) silently does nothing. Both the back arrow
and the X button in the mobile terminal overlay called navigate(-1),
which made them appear broken.

Change both buttons to navigate('/sessions') so they always exit
to a sensible page regardless of how the terminal was opened.

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

.gitignore

@@ -48,8 +48,9 @@ apps/web/dist/
 # OS
 .DS_Store
 Thumbs.db
-
-# Local runtime state
-.atl/
+/.stoneforge/.worktrees/
+# Pi / agent cache
 .pi/
-swap-pane
+.atl/
+.sisyphus/
+.pi-lens/

AGENTS.md

@@ -90,13 +90,6 @@ Before completion, report:
 
 Do not claim completion without verification evidence.
 
-## Git branch policy
-
-- **Default working branch:** `dev` — all commits and pushes target `dev` unless the user explicitly requests otherwise.
-- `main` is the stable/production branch; merge to `main` only when explicitly instructed.
-- After committing, push to `origin/dev`.
-- If `dev` does not exist locally, create it from `main` or fetch it from origin.
-
 ## Git workflow
 
 ### Branching strategy

CHANGELOG.md

@@ -21,7 +21,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **User Settings** - Theme selection, git identity, and preference management
 - **SSH Key Management** - Ed25519 key generation with secure storage
 - **Tool Types** - Built-in development tools (code-server, jupyter-notebook) with custom type support
-- **Config Profiles** - User-owned profile CRUD with includes, mounts, path validation, cycle detection, and default profile selection
 - **Comprehensive Documentation** - Architecture, API, deployment, and development guides
 
 ### Changed

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/src/api/__init__.py

@@ -1,6 +1 @@
-from src.api.auth import router as auth_router
-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"]
+"""API routers package."""

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

@@ -0,0 +1,842 @@
+"""Config profile API endpoints."""
+
+import logging
+import os
+import subprocess
+import uuid
+from typing import Any
+
+from fastapi import APIRouter, Depends, HTTPException, Query, status
+from sqlalchemy import select
+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 import ConfigProfile, ConfigProfileInclude
+from src.models.project import Project
+from src.models import ToolType
+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,
+    resolved_profile_to_dict,
+)
+from src.utils.git_url_parser import parse_git_url
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
+
+MAX_PROFILE_SIZE_MB = 10
+MAX_PROFILE_SIZE_BYTES = MAX_PROFILE_SIZE_MB * 1024 * 1024
+
+
+def _calculate_profile_size(data: dict) -> int:
+    """Calculate approximate serialized size of profile data."""
+    total = 0
+    for key, value in data.get("env_vars", {}).items():
+        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
+    for key, value in data.get("runtime_hints", {}).items():
+        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
+    for mount in data.get("mounts", []):
+        total += len(str(mount.get("target", "")).encode("utf-8"))
+        total += len(str(mount.get("mode", "")).encode("utf-8"))
+        for path, content in mount.get("files", {}).items():
+            total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
+    for path, content in data.get("files", {}).items():
+        total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
+    return total
+
+
+async def _get_profile_with_includes(
+    session: AsyncSession, profile_id: uuid.UUID
+) -> ConfigProfile | None:
+    """Fetch a profile with includes eagerly loaded."""
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile_id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    return result.scalar_one_or_none()
+
+
+async def _check_access(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    project_id: uuid.UUID | None = None,
+    tool_type_id: uuid.UUID | None = None,
+) -> None:
+    """Verify user has access to referenced project and tool type."""
+    if project_id is not None:
+        project = await session.get(Project, project_id)
+        if project is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND, detail="Project not found"
+            )
+        # Add ownership check if needed; for now just verify existence
+    if tool_type_id is not None:
+        tool_type = await session.get(ToolType, tool_type_id)
+        if tool_type is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND, detail="Tool type not found"
+            )
+
+
+async def _validate_git_mounts(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    git_mounts: list[Any],
+    project_id: uuid.UUID | None = None,
+) -> None:
+    """Validate git mount URLs.
+
+    Simply checks that remote_url looks like a valid git URL.
+    Actual clone validation happens at instance startup time.
+    """
+    for mount in git_mounts:
+        remote_url = mount.get("remote_url")
+        if not remote_url:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="Git mount missing remote_url",
+            )
+
+        if not remote_url.startswith(("http://", "https://", "git@", "ssh://")):
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail=f"Invalid git URL: {remote_url}",
+            )
+
+
+def _profile_to_response(
+    profile: ConfigProfile, includes: list[ConfigProfileInclude] | None = None
+) -> dict:
+    return {
+        "id": str(profile.id),
+        "user_id": str(profile.user_id),
+        "name": profile.name,
+        "description": profile.description,
+        "project_id": str(profile.project_id) if profile.project_id else None,
+        "tool_type_id": str(profile.tool_type_id) if profile.tool_type_id else None,
+        "env_vars": profile.env_vars or {},
+        "runtime_hints": profile.runtime_hints or {},
+        "mounts": profile.mounts or [],
+        "git_mounts": profile.git_mounts or [],
+        "files": profile.files or {},
+        "is_default": profile.is_default,
+        "includes": [
+            {
+                "id": str(inc.id),
+                "included_profile_id": str(inc.included_profile_id),
+                "order_index": inc.order_index,
+            }
+            for inc in (includes or profile.includes)
+        ],
+        "created_at": profile.created_at.isoformat() if profile.created_at else None,
+        "updated_at": profile.updated_at.isoformat() if profile.updated_at else None,
+    }
+
+
+@router.get("", response_model=list[ConfigProfileResponse])
+async def list_config_profiles(
+    project_id: str | None = Query(None, description="Filter by project compatibility"),
+    tool_type_id: str | None = Query(
+        None, description="Filter by tool type compatibility"
+    ),
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """List config profiles, optionally filtered by compatibility."""
+    user_uuid = current_user_id
+    query = (
+        select(ConfigProfile)
+        .where(ConfigProfile.user_id == user_uuid)
+        .options(selectinload(ConfigProfile.includes))
+    )
+
+    if project_id or tool_type_id:
+        # Compatibility filter: include portable profiles and matching scoped profiles
+        project_uuid = uuid.UUID(project_id) if project_id else None
+        tool_uuid = uuid.UUID(tool_type_id) if tool_type_id else None
+
+        from sqlalchemy import or_
+
+        conditions: list = []
+        # Portable profiles (no project, no tool)
+        conditions.append(
+            (ConfigProfile.project_id.is_(None))
+            & (ConfigProfile.tool_type_id.is_(None))
+        )
+        if project_uuid:
+            # Profiles matching this project (with or without tool)
+            conditions.append(ConfigProfile.project_id == project_uuid)
+        if tool_uuid:
+            # Profiles matching this tool (with or without project)
+            conditions.append(ConfigProfile.tool_type_id == tool_uuid)
+        if project_uuid and tool_uuid:
+            # Exact match
+            conditions.append(
+                (ConfigProfile.project_id == project_uuid)
+                & (ConfigProfile.tool_type_id == tool_uuid)
+            )
+
+        query = query.where(or_(*conditions))
+
+    result = await session.execute(query)
+    profiles = result.scalars().all()
+    return [_profile_to_response(p) for p in profiles]
+
+
+@router.post(
+    "", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED
+)
+async def create_config_profile(
+    data: ConfigProfileCreate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Create a new config profile."""
+    user_uuid = current_user_id
+
+    # Check for duplicate name
+    existing = await session.execute(
+        select(ConfigProfile)
+        .where(
+            ConfigProfile.user_id == user_uuid,
+            ConfigProfile.name == data.name,
+        )
+        .options(selectinload(ConfigProfile.includes))
+    )
+    if existing.scalar_one_or_none() is not None:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"Profile with name '{data.name}' already exists",
+        )
+
+    # Validate references
+    project_uuid = uuid.UUID(data.project_id) if data.project_id else None
+    tool_uuid = uuid.UUID(data.tool_type_id) if data.tool_type_id else None
+    await _check_access(session, user_uuid, project_uuid, tool_uuid)
+
+    # Validate git mounts reference existing repositories
+    if data.git_mounts:
+        git_mounts_data = [
+            m.model_dump() if hasattr(m, "model_dump") else m for m in data.git_mounts
+        ]
+        await _validate_git_mounts(session, user_uuid, git_mounts_data, project_uuid)
+
+    # Check size
+    size = _calculate_profile_size(data.model_dump())
+    if size > MAX_PROFILE_SIZE_BYTES:
+        raise HTTPException(
+            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
+        )
+
+    profile = ConfigProfile(
+        user_id=user_uuid,
+        name=data.name,
+        description=data.description,
+        project_id=project_uuid,
+        tool_type_id=tool_uuid,
+        env_vars=data.env_vars,
+        runtime_hints=data.runtime_hints,
+        mounts=[m.model_dump() for m in data.mounts],
+        git_mounts=[m.model_dump() for m in data.git_mounts],
+        files=data.files,
+        is_default=data.is_default,
+    )
+    session.add(profile)
+    await session.commit()
+
+    # Re-fetch with includes to avoid lazy loading issues
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile.id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    profile = result.scalar_one()
+
+    logger.debug("Created config profile %s for user %s", profile.id, user_uuid)
+    return _profile_to_response(profile)
+
+
+@router.get("/{profile_id}", response_model=ConfigProfileResponse)
+async def get_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Get a config profile by ID."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+    return _profile_to_response(profile)
+
+
+@router.put("/{profile_id}", response_model=ConfigProfileResponse)
+async def update_config_profile(
+    profile_id: str,
+    data: ConfigProfileUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    update_data = data.model_dump(exclude_unset=True)
+
+    # Handle name uniqueness
+    if "name" in update_data:
+        existing = await session.execute(
+            select(ConfigProfile).where(
+                ConfigProfile.user_id == profile.user_id,
+                ConfigProfile.name == update_data["name"],
+                ConfigProfile.id != profile.id,
+            )
+        )
+        if existing.scalar_one_or_none() is not None:
+            raise HTTPException(
+                status_code=status.HTTP_409_CONFLICT,
+                detail=f"Profile with name '{update_data['name']}' already exists",
+            )
+
+    # Validate references
+    project_uuid = (
+        uuid.UUID(update_data["project_id"])
+        if "project_id" in update_data and update_data["project_id"]
+        else (profile.project_id if "project_id" not in update_data else None)
+    )
+    tool_uuid = (
+        uuid.UUID(update_data["tool_type_id"])
+        if "tool_type_id" in update_data and update_data["tool_type_id"]
+        else (profile.tool_type_id if "tool_type_id" not in update_data else None)
+    )
+    await _check_access(session, profile.user_id, project_uuid, tool_uuid)
+
+    # Validate git mounts reference existing repositories
+    if "git_mounts" in update_data and update_data["git_mounts"] is not None:
+        git_mounts_data = [
+            m.model_dump() if hasattr(m, "model_dump") else m
+            for m in update_data["git_mounts"]
+        ]
+        await _validate_git_mounts(
+            session, profile.user_id, git_mounts_data, project_uuid
+        )
+
+    # Check size
+    current_data = _profile_to_response(profile)
+    merged = {**current_data, **update_data}
+    size = _calculate_profile_size(merged)
+    if size > MAX_PROFILE_SIZE_BYTES:
+        raise HTTPException(
+            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
+        )
+
+    # Apply updates
+    for field_name, value in update_data.items():
+        if field_name in ("project_id", "tool_type_id"):
+            value = uuid.UUID(value) if value else None
+        elif field_name == "mounts" and value is not None:
+            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
+        elif field_name == "git_mounts" and value is not None:
+            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
+        setattr(profile, field_name, value)
+
+    await session.commit()
+
+    # Re-fetch with includes to avoid lazy loading issues
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile.id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    profile = result.scalar_one()
+
+    logger.debug("Updated config profile %s", profile.id)
+    return _profile_to_response(profile)
+
+
+@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Delete a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    await session.delete(profile)
+    await session.commit()
+
+    logger.debug("Deleted config profile %s", profile_id)
+    return None
+
+
+@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
+async def update_profile_includes(
+    profile_id: str,
+    data: ConfigProfileIncludeUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update the ordered includes for a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    # Validate all included profiles exist and belong to the user
+    included_uuids = [uuid.UUID(inc_id) for inc_id in data.includes]
+    for inc_uuid in included_uuids:
+        inc_profile = await session.get(ConfigProfile, inc_uuid)
+        if inc_profile is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Included profile not found: {inc_uuid}",
+            )
+        if inc_profile.user_id != current_user_id:
+            raise HTTPException(
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail=f"Not authorized to include profile: {inc_uuid}",
+            )
+        if inc_uuid == profile.id:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="Profile cannot include itself",
+            )
+
+    # Check for cycles
+    cycle = await check_include_cycle(session, profile.id, None)
+    if cycle is None and included_uuids:
+        # Check each new include would not create a cycle
+        for inc_uuid in included_uuids:
+            cycle = await check_include_cycle(session, profile.id, inc_uuid)
+            if cycle is not None:
+                break
+
+    if cycle is not None:
+        cycle_str = " -> ".join(str(c) for c in cycle)
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"Include cycle detected: {cycle_str}",
+        )
+
+    # Remove existing includes
+    result = await session.execute(
+        select(ConfigProfileInclude).where(
+            ConfigProfileInclude.profile_id == profile.id
+        )
+    )
+    for existing in result.scalars().all():
+        await session.delete(existing)
+    await session.flush()
+
+    # Add new includes
+    for order_index, inc_uuid in enumerate(included_uuids):
+        include = ConfigProfileInclude(
+            profile_id=profile.id,
+            included_profile_id=inc_uuid,
+            order_index=order_index,
+        )
+        session.add(include)
+    await session.flush()
+
+    await session.commit()
+
+    # Re-fetch profile (includes loaded separately due to SQLite async issue)
+    result = await session.execute(
+        select(ConfigProfile).where(ConfigProfile.id == profile.id)
+    )
+    profile = result.scalar_one()
+
+    inc_result = await session.execute(
+        select(ConfigProfileInclude).where(
+            ConfigProfileInclude.profile_id == profile.id
+        )
+    )
+    direct_includes = inc_result.scalars().all()
+
+    logger.debug("Updated includes for config profile %s", profile.id)
+    return _profile_to_response(profile, list(direct_includes))
+
+
+@router.get("/{profile_id}/preview")
+async def preview_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Preview the resolved output of a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    try:
+        resolved = await resolve_profile(session, profile.id)
+    except ConfigProfileCycleError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=str(exc),
+        )
+
+    return resolved_profile_to_dict(resolved)
+
+
+@router.get("/defaults/resolve")
+async def resolve_default_profile(
+    project_id: str = Query(..., description="Project ID"),
+    tool_type_id: str = Query(..., description="Tool type ID"),
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Resolve the default config profile for a project/tool combination.
+
+    Selects by specificity:
+    1. project+tool explicit default
+    2. project explicit default
+    3. tool explicit default
+    4. global/user explicit default
+    5. first created compatible profile
+    6. none (returns null)
+    """
+    user_uuid = current_user_id
+    project_uuid = uuid.UUID(project_id)
+    tool_uuid = uuid.UUID(tool_type_id)
+
+    # Fetch all compatible profiles ordered by created_at
+    query = (
+        select(ConfigProfile)
+        .where(ConfigProfile.user_id == user_uuid)
+        .where(
+            (ConfigProfile.project_id.is_(None) & ConfigProfile.tool_type_id.is_(None))
+            | (ConfigProfile.project_id == project_uuid)
+            | (ConfigProfile.tool_type_id == tool_uuid)
+            | (
+                (ConfigProfile.project_id == project_uuid)
+                & (ConfigProfile.tool_type_id == tool_uuid)
+            )
+        )
+        .order_by(ConfigProfile.created_at)
+    )
+    result = await session.execute(query)
+    profiles = result.scalars().all()
+
+    if not profiles:
+        return {"profile_id": None, "profile_name": None}
+
+    # Check explicit defaults by specificity
+    explicit_defaults = [p for p in profiles if p.is_default]
+
+    # Most specific: project+tool
+    for p in explicit_defaults:
+        if p.project_id == project_uuid and p.tool_type_id == tool_uuid:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: project only
+    for p in explicit_defaults:
+        if p.project_id == project_uuid and p.tool_type_id is None:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: tool only
+    for p in explicit_defaults:
+        if p.project_id is None and p.tool_type_id == tool_uuid:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: global/user (no project, no tool)
+    for p in explicit_defaults:
+        if p.project_id is None and p.tool_type_id is None:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Fall back to first created compatible profile
+    first = profiles[0]
+    return {"profile_id": str(first.id), "profile_name": first.name}
+
+
+# ---------------------------------------------------------------------------
+# Default profile management
+# ---------------------------------------------------------------------------
+
+
+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
+
+
+async def _validate_default_profiles(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    default_profiles: dict[str, str],
+) -> None:
+    """Validate that all profile IDs in default_profiles belong to the user."""
+    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)
+async def validate_git_url(
+    data: ValidateGitUrlRequest,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> ValidateGitUrlResponse:
+    """Validate a git remote URL and list available branches.
+
+    Parses the URL, suggests corrections for browser URLs, and runs
+    git ls-remote to verify reachability and enumerate branches.
+    """
+    parse_result = parse_git_url(data.url)
+    original_url = data.url.strip()
+    url_to_check = parse_result.get("base_url") or original_url
+
+    if not url_to_check:
+        return ValidateGitUrlResponse(
+            valid=False,
+            error=parse_result.get("message", "Invalid URL"),
+            error_code=parse_result.get("error_code", "INVALID_URL"),
+        )
+
+    # If the URL needed parsing, return suggestion without checking remote
+    if parse_result.get("needs_parsing") and url_to_check != original_url:
+        return ValidateGitUrlResponse(
+            valid=False,
+            suggested_url=url_to_check,
+            error=parse_result.get("message"),
+            error_code=parse_result.get("error_code", "URL_NEEDS_PARSING"),
+        )
+
+    # Optional SSH key for private repos
+    env = None
+    key_path = None
+    if data.ssh_key_id:
+        from src.models import SSHKey
+        from src.services.shared.ssh_keys import _get_fernet
+
+        try:
+            ssh_key_uuid = uuid.UUID(data.ssh_key_id)
+        except ValueError:
+            return ValidateGitUrlResponse(
+                valid=False,
+                error="Invalid SSH key ID format",
+                error_code="INVALID_SSH_KEY",
+            )
+
+        ssh_key = await session.get(SSHKey, ssh_key_uuid)
+        if ssh_key is None or ssh_key.user_id != current_user_id:
+            return ValidateGitUrlResponse(
+                valid=False,
+                error="SSH key not found or not authorized",
+                error_code="SSH_KEY_NOT_FOUND",
+            )
+
+        import tempfile
+
+        fernet = _get_fernet()
+        private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
+        fd, key_path = tempfile.mkstemp(prefix="ssh_key_")
+        try:
+            os.write(fd, private_key.encode())
+        finally:
+            os.close(fd)
+        os.chmod(key_path, 0o600)
+        env = {
+            "GIT_SSH_COMMAND": f"ssh -i {key_path} -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
+        }
+
+    try:
+        result = subprocess.run(
+            ["git", "ls-remote", "--heads", url_to_check],
+            capture_output=True,
+            text=True,
+            timeout=30,
+            env={**os.environ, **env} if env else None,
+        )
+    except subprocess.TimeoutExpired:
+        if key_path and os.path.exists(key_path):
+            os.unlink(key_path)
+        return ValidateGitUrlResponse(
+            valid=False,
+            error="Remote repository check timed out",
+            error_code="TIMEOUT",
+        )
+    except FileNotFoundError:
+        if key_path and os.path.exists(key_path):
+            os.unlink(key_path)
+        return ValidateGitUrlResponse(
+            valid=False,
+            error="git command not found on server",
+            error_code="GIT_NOT_FOUND",
+        )
+    finally:
+        if key_path and os.path.exists(key_path):
+            os.unlink(key_path)
+
+    if result.returncode != 0:
+        stderr = result.stderr.strip()
+        if (
+            "could not resolve" in stderr.lower()
+            or "unable to access" in stderr.lower()
+        ):
+            error_msg = "Could not reach repository. Check the URL and network access."
+            error_code = "UNREACHABLE"
+        elif (
+            "authentication" in stderr.lower() or "permission denied" in stderr.lower()
+        ):
+            error_msg = (
+                "Authentication failed. Provide an SSH key for private repositories."
+            )
+            error_code = "AUTH_FAILED"
+        else:
+            error_msg = f"Repository not accessible: {stderr[:200]}"
+            error_code = "REMOTE_ERROR"
+        return ValidateGitUrlResponse(
+            valid=False,
+            error=error_msg,
+            error_code=error_code,
+        )
+
+    # Parse branches from ls-remote output
+    branches: list[str] = []
+    default_branch = "main"
+    for line in result.stdout.strip().split("\n"):
+        if not line.strip():
+            continue
+        parts = line.split()
+        if len(parts) == 2:
+            ref = parts[1]
+            # refs/heads/branch-name
+            if ref.startswith("refs/heads/"):
+                branch_name = ref[len("refs/heads/") :]
+                branches.append(branch_name)
+                if branch_name in ("main", "master"):
+                    default_branch = branch_name
+
+    if not branches:
+        return ValidateGitUrlResponse(
+            valid=False,
+            error="No branches found in remote repository",
+            error_code="NO_BRANCHES",
+        )
+
+    return ValidateGitUrlResponse(
+        valid=True,
+        suggested_url=url_to_check if url_to_check != original_url else None,
+        branches=branches,
+        default_branch=default_branch,
+    )

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

@@ -1,20 +1,22 @@
 import logging
 import uuid
 
-from fastapi import APIRouter, Depends, HTTPException, status
+from fastapi import APIRouter, Depends
 from sqlalchemy import select
 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.schemas.user_config import UserConfigResponse, UserConfigUpdate
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
+from src.models import UserConfig
+from src.schemas.user import UserConfigResponse, UserConfigUpdate
+
+logger = logging.getLogger(__name__)
 
 router = APIRouter(prefix="/users/me", tags=["user-config"])
 
 
-
-async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> UserConfig:
+async def _get_or_create_config(
+    session: AsyncSession, user_id: uuid.UUID
+) -> UserConfig:
     """Get or create user config record.
 
     Args:
@@ -24,10 +26,12 @@ async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> Us
     Returns:
         The user's config, creating a new one if it doesn't exist.
     """
-    result = await session.execute(select(UserConfig).where(UserConfig.user_id == user.id))
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
+    )
     config = result.scalar_one_or_none()
     if config is None:
-        config = UserConfig(user_id=user.id, config={})
+        config = UserConfig(user_id=user_id, config={})
         session.add(config)
         await session.commit()
         await session.refresh(config)
@@ -41,7 +45,7 @@ async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> Us
     description="Get the current user's configuration settings.",
 )
 async def get_user_config(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
     """Get the current user's configuration.
@@ -53,7 +57,8 @@ async def get_user_config(
     Returns:
         The user's configuration settings.
     """
-    config = await _get_or_create_config(session, user.id)
+    _user = await _get_user(session, user_id)
+    config = await _get_or_create_config(session, user_id)
     return UserConfigResponse.model_validate(config.config)
 
 
@@ -65,7 +70,7 @@ async def get_user_config(
 )
 async def update_user_config(
     data: UserConfigUpdate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
     """Update the current user's configuration.
@@ -78,15 +83,16 @@ async def update_user_config(
     Returns:
         The updated user configuration.
     """
-    config = await _get_or_create_config(session, user.id)
+    _user = await _get_user(session, user_id)
+    config = await _get_or_create_config(session, user_id)
 
     # Merge updates
     update_data = data.model_dump(exclude_unset=True)
-    logger.info("Updating user config for user %s: %s", user.id, update_data)
+    logger.debug("Updating user config for user %s: %s", user_id, update_data)
     # SQLAlchemy JSON doesn't track dict mutations, so we replace the whole dict
     config.config = {**config.config, **update_data}
 
     await session.commit()
     await session.refresh(config)
-    logger.info("Updated config: %s", config.config)
+    logger.debug("Updated config: %s", config.config)
     return UserConfigResponse.model_validate(config.config)

apps/api/src/api/config_profiles.py

@@ -1,299 +0,0 @@
-"""Config profile API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, status
-from sqlalchemy import select
-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.config_include import ConfigInclude
-from src.models.config_mount import ConfigMount
-from src.models.config_profile import ConfigProfile
-from src.models.tool_type import ToolType
-from src.models.user_config import UserConfig
-from src.schemas.config_profile import (
-    ConfigIncludeCreate,
-    ConfigIncludeUpdate,
-    ConfigMountCreate,
-    ConfigMountUpdate,
-    ConfigProfileCreate,
-    ConfigProfileUpdate,
-    DefaultProfilesUpdate,
-)
-from src.services.config_profiles import (
-    check_duplicate_include,
-    check_duplicate_mount_path,
-    check_duplicate_name,
-    get_default_profile_for_tool_type,
-    get_default_profiles,
-    get_owned_profile,
-    include_to_dict,
-    list_includes_for_profile,
-    list_mounts_for_profile,
-    mount_to_dict,
-    profile_to_dict,
-    set_default_profiles,
-    validate_includes_no_cycle,
-)
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
-
-
-
-@router.get("")
-async def list_config_profiles(
-    tool_type_id: str | None = None,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    query = select(ConfigProfile).where(ConfigProfile.user_id == user_id)
-    if tool_type_id:
-        tool_type = await session.get(ToolType, uuid.UUID(tool_type_id))
-        if tool_type is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    result = await session.execute(query.order_by(ConfigProfile.name))
-    return {"profiles": [profile_to_dict(p) for p in result.scalars().all()]}
-
-
-@router.post("", status_code=status.HTTP_201_CREATED)
-async def create_config_profile(
-    data: ConfigProfileCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await check_duplicate_name(session, user_id, data.name)
-    profile = ConfigProfile(user_id=user_id, name=data.name, description=data.description)
-    session.add(profile)
-    await session.commit()
-    await session.refresh(profile)
-    return profile_to_dict(profile)
-
-
-@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:
-    return await get_default_profiles(session, user_id)
-
-
-@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:
-    return await set_default_profiles(session, user_id, data.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:
-    return await get_default_profile_for_tool_type(session, user_id, tool_type_id)
-
-
-@router.get("/{profile_id}")
-async def get_config_profile(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    profile = await session.get(
-        ConfigProfile,
-        profile_id,
-        options=[selectinload(ConfigProfile.includes), selectinload(ConfigProfile.mounts)],
-    )
-    if profile is None or profile.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config profile not found")
-    includes_data = []
-    for inc in profile.includes:
-        included_profile = await session.get(ConfigProfile, inc.included_profile_id)
-        includes_data.append(include_to_dict(inc, included_profile.name if included_profile else None))
-    return {
-        **profile_to_dict(profile),
-        "includes": includes_data,
-        "mounts": [mount_to_dict(m) for m in profile.mounts],
-    }
-
-
-@router.put("/{profile_id}")
-async def update_config_profile(
-    profile_id: uuid.UUID,
-    data: ConfigProfileUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    profile = await get_owned_profile(profile_id, user_id, session)
-    if data.name is not None:
-        await check_duplicate_name(session, user_id, data.name, exclude_id=profile_id)
-        profile.name = data.name
-    if data.description is not None:
-        profile.description = data.description
-    await session.commit()
-    await session.refresh(profile)
-    return profile_to_dict(profile)
-
-
-@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_config_profile(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    profile = await get_owned_profile(profile_id, user_id, session)
-    await session.delete(profile)
-    await session.commit()
-
-
-
-@router.get("/{profile_id}/includes")
-async def list_profile_includes(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await get_owned_profile(profile_id, user_id, session)
-    return await list_includes_for_profile(session, profile_id)
-
-
-@router.post("/{profile_id}/includes", status_code=status.HTTP_201_CREATED)
-async def add_profile_include(
-    profile_id: uuid.UUID,
-    data: ConfigIncludeCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    profile = await get_owned_profile(profile_id, user_id, session)
-    included_profile_id = uuid.UUID(data.included_profile_id)
-    if included_profile_id == profile_id:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="a profile cannot include itself")
-    included_profile = await session.get(ConfigProfile, included_profile_id)
-    if included_profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="included profile not found")
-    if included_profile.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="included profile does not belong to user")
-    await check_duplicate_include(session, profile_id, included_profile_id)
-    await validate_includes_no_cycle(session, profile_id, included_profile_id)
-    include = ConfigInclude(
-        profile_id=profile_id,
-        included_profile_id=included_profile_id,
-        order_index=data.order_index,
-    )
-    session.add(include)
-    await session.commit()
-    await session.refresh(include)
-    return include_to_dict(include, included_profile.name)
-
-
-@router.put("/{profile_id}/includes/{include_id}")
-async def update_profile_include(
-    profile_id: uuid.UUID,
-    include_id: uuid.UUID,
-    data: ConfigIncludeUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await get_owned_profile(profile_id, user_id, session)
-    include = await session.get(ConfigInclude, include_id)
-    if include is None or include.profile_id != profile_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="include not found")
-    include.order_index = data.order_index
-    await session.commit()
-    await session.refresh(include)
-    included_profile = await session.get(ConfigProfile, include.included_profile_id)
-    return include_to_dict(include, included_profile.name if included_profile else None)
-
-
-@router.delete("/{profile_id}/includes/{include_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def remove_profile_include(
-    profile_id: uuid.UUID,
-    include_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    await get_owned_profile(profile_id, user_id, session)
-    include = await session.get(ConfigInclude, include_id)
-    if include is None or include.profile_id != profile_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="include not found")
-    await session.delete(include)
-    await session.commit()
-
-
-
-@router.get("/{profile_id}/mounts")
-async def list_profile_mounts(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await get_owned_profile(profile_id, user_id, session)
-    return await list_mounts_for_profile(session, profile_id)
-
-
-@router.post("/{profile_id}/mounts", status_code=status.HTTP_201_CREATED)
-async def add_profile_mount(
-    profile_id: uuid.UUID,
-    data: ConfigMountCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    profile = await get_owned_profile(profile_id, user_id, session)
-    await check_duplicate_mount_path(session, profile_id, data.target_path)
-    mount = ConfigMount(
-        profile_id=profile_id,
-        target_path=data.target_path,
-        mode=data.mode,
-        files=data.files,
-        order_index=data.order_index,
-    )
-    session.add(mount)
-    await session.commit()
-    await session.refresh(mount)
-    return mount_to_dict(mount)
-
-
-@router.put("/{profile_id}/mounts/{mount_id}")
-async def update_profile_mount(
-    profile_id: uuid.UUID,
-    mount_id: uuid.UUID,
-    data: ConfigMountUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await get_owned_profile(profile_id, user_id, session)
-    mount = await session.get(ConfigMount, mount_id)
-    if mount is None or mount.profile_id != profile_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="mount not found")
-    if data.target_path is not None:
-        await check_duplicate_mount_path(session, profile_id, data.target_path, exclude_id=mount_id)
-        mount.target_path = data.target_path
-    if data.files is not None:
-        mount.files = data.files
-    if data.order_index is not None:
-        mount.order_index = data.order_index
-    await session.commit()
-    await session.refresh(mount)
-    return mount_to_dict(mount)
-
-
-@router.delete("/{profile_id}/mounts/{mount_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def remove_profile_mount(
-    profile_id: uuid.UUID,
-    mount_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    await get_owned_profile(profile_id, user_id, session)
-    mount = await session.get(ConfigMount, mount_id)
-    if mount is None or mount.profile_id != profile_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="mount not found")
-    await session.delete(mount)
-    await session.commit()

apps/api/src/api/git_repositories.py

@@ -1,290 +0,0 @@
-"""Git repository API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, Response, status
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user, get_db_session, get_owned_project
-from src.models.project import Project
-from src.models.user import User
-from src.schemas.git_repository import (
-    BranchCreateRequest,
-    CheckoutRequest,
-    CommitRequest,
-    CommitResponse,
-    FetchResponse,
-    FileContentResponse,
-    FileListResponse,
-    FileUpdateRequest,
-    FileUpdateResponse,
-    GitRepositoryCreate,
-    GitRepositoryResponse,
-    MergeRequest,
-    MergeResponse,
-    PullResponse,
-    PushResponse,
-    StatusResponse,
-    URLParseRequest,
-    URLParseResponse,
-)
-from src.services.git import control as git_control
-from src.services.git import files as git_files
-from src.services.git.repository import create_repository, delete_repository, list_repositories
-from src.utils.git_url_parser import parse_git_url
-
-router = APIRouter(prefix="/projects", tags=["git-repositories"])
-logger = logging.getLogger(__name__)
-
-
-@router.get("/{project_id}/repositories", response_model=list[GitRepositoryResponse])
-async def list_repositories_endpoint(
-    project_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-):
-    return await list_repositories(session, project_id)
-
-
-@router.post("/{project_id}/repositories", response_model=GitRepositoryResponse, status_code=status.HTTP_201_CREATED)
-async def create_repository_endpoint(
-    project_id: uuid.UUID,
-    data: GitRepositoryCreate,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-):
-    return await create_repository(session, project_id, data, user)
-
-
-@router.delete("/{project_id}/repositories/{repo_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_repository_endpoint(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-):
-    await delete_repository(session, repo_id, project_id)
-    return Response(status_code=status.HTTP_204_NO_CONTENT)
-
-
-@router.post("/repositories/parse-url", response_model=URLParseResponse)
-async def parse_repository_url(data: URLParseRequest) -> URLParseResponse:
-    return URLParseResponse(**parse_git_url(data.url))
-
-
-# History
-
-@router.get("/{project_id}/repositories/{repo_id}/history")
-async def get_repository_history(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    view: str = "graph",
-    branch: str | None = None,
-    limit: int = 100,
-    offset: int = 0,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    from src.utils.git_history import get_commit_history
-    from src.services.git.repository import get_repo_and_validate, ensure_repo_on_disk
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        return get_commit_history(repo.path, branch=branch, limit=limit, offset=offset)
-    except RuntimeError as e:
-        logger.warning("Git history failed for %s: %s", repo.path, str(e))
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"Git history unavailable: {str(e)}",
-        ) from e
-
-
-@router.get("/{project_id}/repositories/{repo_id}/commits/{commit_hash}")
-async def get_repository_commit(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    commit_hash: str,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    from src.utils.git_history import get_commit_detail
-    from src.services.git.repository import get_repo_and_validate, ensure_repo_on_disk
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        return get_commit_detail(repo.path, commit_hash)
-    except RuntimeError as e:
-        logger.warning("Git commit detail failed for %s %s: %s", repo.path, commit_hash, str(e))
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"Commit detail unavailable: {str(e)}",
-        ) from e
-
-
-# File browsing
-
-@router.get("/{project_id}/repositories/{repo_id}/files", response_model=FileListResponse)
-async def list_repository_files(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str = "main",
-    path: str = "",
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileListResponse:
-    return await git_files.list_files(session, project_id, repo_id, branch, path)
-
-
-@router.get("/{project_id}/repositories/{repo_id}/files/content", response_model=FileContentResponse)
-async def get_repository_file_content(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str,
-    path: str,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileContentResponse:
-    return await git_files.get_file(session, project_id, repo_id, branch, path)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/files/content", response_model=FileUpdateResponse)
-async def update_repository_file(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: FileUpdateRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileUpdateResponse:
-    return await git_files.update_file(session, project_id, repo_id, data, user)
-
-
-# Branches
-
-@router.get("/{project_id}/repositories/{repo_id}/branches")
-async def get_repository_branches(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    return await git_files.list_branches_with_validation(session, project_id, repo_id)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/branches")
-async def create_repository_branch(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: BranchCreateRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    return await git_control.create_branch_with_validation(session, project_id, repo_id, data)
-
-
-@router.delete("/{project_id}/repositories/{repo_id}/branches/{branch_name}")
-async def delete_repository_branch(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch_name: str,
-    force: bool = False,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    return await git_control.delete_branch_with_validation(session, project_id, repo_id, branch_name, force)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/checkout")
-async def checkout_repository_branch(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CheckoutRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    return await git_control.checkout_branch_with_validation(session, project_id, repo_id, data)
-
-
-# Git control
-
-@router.get("/{project_id}/repositories/{repo_id}/status", response_model=StatusResponse)
-async def get_repository_status(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> StatusResponse:
-    return await git_control.get_status_with_validation(session, project_id, repo_id)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/commit", response_model=CommitResponse)
-async def commit_repository_changes(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CommitRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> CommitResponse:
-    result = await git_control.commit_changes_with_validation(session, project_id, repo_id, data, user)
-    return CommitResponse(commit_hash=result["commit_hash"], message=result["message"])
-
-
-@router.post("/{project_id}/repositories/{repo_id}/fetch", response_model=FetchResponse)
-async def fetch_repository(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> FetchResponse:
-    return await git_control.fetch_with_validation(session, project_id, repo_id)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/pull", response_model=PullResponse)
-async def pull_repository(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str | None = None,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> PullResponse:
-    return await git_control.pull_with_validation(session, project_id, repo_id, branch)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/push", response_model=PushResponse)
-async def push_repository(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str | None = None,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> PushResponse:
-    return await git_control.push_with_validation(session, project_id, repo_id, branch)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/merge", response_model=MergeResponse)
-async def merge_repository_branches(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: MergeRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> MergeResponse:
-    return await git_control.merge_with_validation(session, project_id, repo_id, data)

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/projects.py

@@ -3,25 +3,29 @@ import shutil
 import uuid
 
 from fastapi import APIRouter, Depends, HTTPException, Response, status
-from sqlalchemy import select
+from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import get_current_user, get_db_session, get_owned_project
-from src.models.git_repository import GitRepository
+from src.auth.dependencies import (
+    _get_owned_project,
+    _get_user,
+    get_current_user_id,
+    get_db_session,
+)
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
-from src.models.user import User
+from src.models import SSHKey
+from src.models import ToolInstance
 from src.schemas.project import (
     ProjectCreate,
-    ProjectUpdate,
     ProjectResponse,
+    ProjectUpdate,
     SetDefaultSSHKeyRequest,
 )
 
 router = APIRouter(prefix="/projects", tags=["projects"])
 
 
-
 @router.post(
     "",
     response_model=ProjectResponse,
@@ -31,7 +35,7 @@ router = APIRouter(prefix="/projects", tags=["projects"])
 )
 async def create_project(
     data: ProjectCreate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
     """Create a new project.
@@ -44,6 +48,7 @@ async def create_project(
     Returns:
         The newly created project.
     """
+    user = await _get_user(session, user_id)
     project = Project(
         name=data.name,
         description=data.description,
@@ -58,25 +63,77 @@ async def create_project(
 
 @router.get(
     "",
-    response_model=list[ProjectResponse],
     summary="List all projects",
-    description="Retrieve all projects owned by the authenticated user.",
+    description="Retrieve all projects owned by the authenticated user with repositories and workspaces.",
 )
 async def list_projects(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
-) -> list[Project]:
+) -> list[dict]:
     """List all projects for the authenticated user.
 
-    Args:
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        List of projects owned by the user.
+    Returns projects with nested repositories and workspaces for inline display.
     """
-    result = await session.execute(select(Project).where(Project.owner_id == user.id))
-    return list(result.scalars().all())
+    user = await _get_user(session, user_id)
+    result = await session.execute(
+        select(Project)
+        .where(Project.owner_id == user.id)
+        .order_by(Project.created_at.desc())
+    )
+    projects = result.scalars().all()
+
+    from src.models import Workspace
+
+    enriched = []
+    for project in projects:
+        repos_result = await session.execute(
+            select(GitRepository).where(GitRepository.project_id == project.id)
+        )
+        repositories = []
+        for repo in repos_result.scalars().all():
+            ws_result = await session.execute(
+                select(Workspace).where(Workspace.repo_id == repo.id)
+            )
+            workspaces = []
+            for ws in ws_result.scalars().all():
+                # Count instances
+                inst_result = await session.execute(
+                    select(func.count()).where(ToolInstance.workspace_id == ws.id)
+                )
+                instance_count = inst_result.scalar() or 0
+                workspaces.append(
+                    {
+                        "id": str(ws.id),
+                        "name": ws.name,
+                        "branch": ws.branch,
+                        "status": ws.status,
+                        "instance_count": instance_count,
+                    }
+                )
+
+            repositories.append(
+                {
+                    "id": str(repo.id),
+                    "name": repo.name,
+                    "remote_url": repo.remote_url,
+                    "workspaces": workspaces,
+                }
+            )
+
+        enriched.append(
+            {
+                "id": str(project.id),
+                "name": project.name,
+                "description": project.description,
+                "owner_id": str(project.owner_id),
+                "repositories": repositories,
+                "created_at": project.created_at.isoformat()
+                if project.created_at
+                else None,
+            }
+        )
+
+    return enriched
 
 
 @router.get(
@@ -87,8 +144,7 @@ async def list_projects(
 )
 async def get_project(
     project_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
     """Get a specific project by ID.
@@ -101,8 +157,8 @@ async def get_project(
     Returns:
         The requested project.
     """
-    return project
-
+    await _get_user(session, user_id)
+    return await _get_owned_project(project_id, user_id, session)
 
 
 @router.patch(
@@ -114,8 +170,7 @@ async def get_project(
 async def update_project(
     project_id: uuid.UUID,
     data: ProjectUpdate,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
     """Update a project.
@@ -129,6 +184,8 @@ async def update_project(
     Returns:
         The updated project.
     """
+    await _get_user(session, user_id)
+    project = await _get_owned_project(project_id, user_id, session)
 
     if data.name is not None:
         project.name = data.name
@@ -148,8 +205,7 @@ async def update_project(
 )
 async def delete_project(
     project_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Response:
     """Delete a project and all its repositories.
@@ -162,9 +218,13 @@ async def delete_project(
     Returns:
         Empty response with 204 status code.
     """
+    await _get_user(session, user_id)
+    project = await _get_owned_project(project_id, user_id, session)
 
     # Delete repositories from disk and database
-    result = await session.execute(select(GitRepository).where(GitRepository.project_id == project_id))
+    result = await session.execute(
+        select(GitRepository).where(GitRepository.project_id == project_id)
+    )
     repositories = result.scalars().all()
     for repo in repositories:
         if os.path.exists(repo.path):
@@ -185,8 +245,7 @@ async def delete_project(
 async def set_default_ssh_key(
     project_id: uuid.UUID,
     data: SetDefaultSSHKeyRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
     """Set the default SSH key for a project.
@@ -200,6 +259,8 @@ async def set_default_ssh_key(
     Returns:
         The updated project.
     """
+    user = await _get_user(session, user_id)
+    project = await _get_owned_project(project_id, user_id, session)
 
     ssh_key = await session.get(SSHKey, data.ssh_key_id)
     if ssh_key is None or ssh_key.user_id != user.id:

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

@@ -4,12 +4,11 @@ import time
 from datetime import datetime, timezone
 from typing import Any
 
-from fastapi import APIRouter, status
+from fastapi import APIRouter
 from sqlalchemy import text
 
-from src.config import Settings
 from src.database import SessionLocal
-from src.schemas.health import (
+from src.schemas.system import (
     DatabaseHealth,
     DatabaseHealthResponse,
     DiskHealth,

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.tool_type import ToolType
+from src.models import ToolInstance
+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.services.notification_service import notification_service
+from src.models import UserConfig
+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.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.services.terminal_manager import MaxSessionsExceededError, terminal_manager
+from src.models import TerminalSessionModel
+from src.models import ToolInstance
+from src.models import ToolType
+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.tool_type import ToolType
-from src.services.manifest_compiler import (
+from src.models import ToolDefinitionManifest
+from src.models import ToolType
+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_types.py

@@ -1,14 +1,18 @@
 import uuid
 
-import yaml
 from fastapi import APIRouter, Depends, HTTPException, status
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import get_current_user, get_db_session
-from src.models.tool_type import ToolType
+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 import ToolType
 from src.models.user import User
-from src.schemas.tool_type import (
+from src.schemas.tool import (
     ToolTypeCreate,
     ToolTypeResponse,
     ToolTypeUpdate,
@@ -38,7 +42,7 @@ async def _require_admin(user: User) -> None:
 )
 async def create_tool_type(
     data: ToolTypeCreate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Create a new tool type.
@@ -51,6 +55,7 @@ async def create_tool_type(
     Returns:
         The newly created tool type.
     """
+    user = await _get_user(session, user_id)
     await _require_admin(user)
 
     # Check for duplicate name
@@ -67,13 +72,16 @@ async def create_tool_type(
         description=data.description,
         default_port=data.default_port,
         definition_type=data.definition_type,
+        manifest_id=data.manifest_id,
         compose_template=data.compose_template,
         dockerfile_template=data.dockerfile_template,
         build_context=data.build_context,
         readiness_probe=data.readiness_probe,
+        startup_command=data.startup_command,
         required_variables=data.required_variables,
         category=data.category,
-        interfaces=data.interfaces,
+        interface_type=data.interface_type,
+        requires_port=data.requires_port,
         created_by_id=user.id,
     )
     session.add(tool_type)
@@ -89,7 +97,7 @@ async def create_tool_type(
     description="List all available tool types including built-in and custom ones.",
 )
 async def list_tool_types(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[ToolType]:
     """List all tool types.
@@ -101,6 +109,7 @@ async def list_tool_types(
     Returns:
         List of all tool types ordered by name.
     """
+    await _get_user(session, user_id)
     result = await session.execute(select(ToolType).order_by(ToolType.name))
     return list(result.scalars().all())
 
@@ -113,7 +122,7 @@ async def list_tool_types(
 )
 async def get_tool_type(
     tool_type_id: uuid.UUID,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Get a specific tool type by ID.
@@ -126,6 +135,7 @@ async def get_tool_type(
     Returns:
         The requested tool type.
     """
+    await _get_user(session, user_id)
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
         raise HTTPException(
@@ -143,7 +153,7 @@ async def get_tool_type(
 async def update_tool_type(
     tool_type_id: uuid.UUID,
     data: ToolTypeUpdate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Update a tool type.
@@ -157,6 +167,7 @@ async def update_tool_type(
     Returns:
         The updated tool type.
     """
+    user = await _get_user(session, user_id)
     await _require_admin(user)
 
     tool_type = await session.get(ToolType, tool_type_id)
@@ -165,16 +176,13 @@ async def update_tool_type(
             status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
         )
 
-    if tool_type.is_builtin:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN,
-            detail="cannot modify built-in tool types",
-        )
+    # Built-in tool types can now be modified
 
     update_data = data.model_dump(exclude_unset=True)
 
     # Validate port if being updated
-    if "default_port" in update_data:
+    requires_port = update_data.get("requires_port", tool_type.requires_port)
+    if "default_port" in update_data and requires_port:
         new_port = update_data["default_port"]
         if new_port <= 0 or new_port > 65535:
             raise HTTPException(
@@ -188,62 +196,35 @@ async def update_tool_type(
             template = update_data.get("compose_template", tool_type.compose_template)
             if template:
                 try:
-                    parsed = yaml.safe_load(template)
-                except yaml.YAMLError:
-                    parsed = None
-
-                if parsed and isinstance(parsed, dict) and "services" in parsed:
-                    port_str = str(new_port)
-                    port_exposed = False
-                    for service_config in parsed["services"].values():
-                        if (
-                            isinstance(service_config, dict)
-                            and "ports" in service_config
-                        ):
-                            for port_mapping in service_config["ports"]:
-                                if (
-                                    isinstance(port_mapping, str)
-                                    and port_str in port_mapping
-                                ):
-                                    port_exposed = True
-                                    break
-                                elif (
-                                    isinstance(port_mapping, int)
-                                    and port_mapping == new_port
-                                ):
-                                    port_exposed = True
-                                    break
-                        if port_exposed:
-                            break
-
-                    if not port_exposed:
+                    parsed = validate_compose_yaml(template)
+                    if not check_port_exposed(parsed, new_port):
                         raise HTTPException(
                             status_code=status.HTTP_400_BAD_REQUEST,
                             detail=f"Port {new_port} is not exposed in the compose template",
                         )
+                except ValueError as e:
+                    raise HTTPException(
+                        status_code=status.HTTP_400_BAD_REQUEST, detail=str(e)
+                    )
 
     # Validate required variables for compose definitions
     definition_type = update_data.get("definition_type", tool_type.definition_type)
     if definition_type == "compose":
         if "required_variables" in update_data and "compose_template" in update_data:
-            template = update_data["compose_template"]
-            for var in update_data["required_variables"]:
-                placeholder = f"{{{{{var}}}}}"
-                if placeholder not in template:
-                    raise HTTPException(
-                        status_code=status.HTTP_400_BAD_REQUEST,
-                        detail=f"Required variable '{var}' not found in compose template",
-                    )
+            validate_required_variables(
+                update_data["compose_template"], update_data["required_variables"]
+            )
         elif "required_variables" in update_data:
             template = tool_type.compose_template
             if template:
-                for var in update_data["required_variables"]:
-                    placeholder = f"{{{{{var}}}}}"
-                    if placeholder not in template:
-                        raise HTTPException(
-                            status_code=status.HTTP_400_BAD_REQUEST,
-                            detail=f"Required variable '{var}' not found in compose template",
-                        )
+                validate_required_variables(template, update_data["required_variables"])
+
+    # When switching to manifest, clear legacy templates
+    if definition_type == "manifest":
+        if "manifest_id" in update_data:
+            tool_type.manifest_id = update_data["manifest_id"]
+        tool_type.compose_template = None
+        tool_type.dockerfile_template = None
 
     for field, value in update_data.items():
         setattr(tool_type, field, value)
@@ -260,7 +241,7 @@ async def update_tool_type(
 )
 async def validate_tool_type_template(
     data: ToolTypeValidateRequest,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict:
     """Validate a tool type template syntax.
@@ -273,6 +254,7 @@ async def validate_tool_type_template(
     Returns:
         Validation result with success status and any errors.
     """
+    await _get_user(session, user_id)
 
     errors = []
 
@@ -281,15 +263,9 @@ async def validate_tool_type_template(
             errors.append("Compose template is required")
         else:
             try:
-                parsed = yaml.safe_load(data.compose_template)
-                if not isinstance(parsed, dict):
-                    errors.append("Compose template must be a YAML mapping")
-                elif "services" not in parsed:
-                    errors.append("Compose template must contain 'services' key")
-                elif not parsed["services"]:
-                    errors.append("Compose template must define at least one service")
-            except yaml.YAMLError as e:
-                errors.append(f"Invalid YAML: {e}")
+                validate_compose_yaml(data.compose_template)
+            except ValueError as e:
+                errors.append(str(e))
 
     elif data.definition_type == "dockerfile":
         if not data.dockerfile_template:
@@ -297,8 +273,11 @@ async def validate_tool_type_template(
         elif not data.dockerfile_template.strip().startswith("FROM"):
             errors.append("Dockerfile must start with a FROM instruction")
 
+    elif data.definition_type == "manifest":
+        pass  # Manifest validation is handled separately
+
     else:
-        errors.append("definition_type must be 'compose' or 'dockerfile'")
+        errors.append("definition_type must be 'compose', 'dockerfile', or 'manifest'")
 
     return {
         "valid": len(errors) == 0,
@@ -313,7 +292,7 @@ async def validate_tool_type_template(
 )
 async def validate_tool_type(
     tool_type_id: uuid.UUID,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict:
     """Validate a tool type's template syntax.
@@ -326,6 +305,7 @@ async def validate_tool_type(
     Returns:
         Validation result with success status and any errors.
     """
+    await _get_user(session, user_id)
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
         raise HTTPException(
@@ -339,15 +319,9 @@ async def validate_tool_type(
             errors.append("Compose template is empty")
         else:
             try:
-                parsed = yaml.safe_load(tool_type.compose_template)
-                if not isinstance(parsed, dict):
-                    errors.append("Compose template must be a YAML mapping")
-                elif "services" not in parsed:
-                    errors.append("Compose template must contain 'services' key")
-                elif not parsed["services"]:
-                    errors.append("Compose template must define at least one service")
-            except yaml.YAMLError as e:
-                errors.append(f"Invalid YAML: {e}")
+                validate_compose_yaml(tool_type.compose_template)
+            except ValueError as e:
+                errors.append(str(e))
 
     elif tool_type.definition_type == "dockerfile":
         if not tool_type.dockerfile_template:
@@ -355,6 +329,10 @@ async def validate_tool_type(
         elif not tool_type.dockerfile_template.strip().startswith("FROM"):
             errors.append("Dockerfile must start with a FROM instruction")
 
+    elif tool_type.definition_type == "manifest":
+        if not tool_type.manifest_id:
+            errors.append("Manifest reference is missing")
+
     return {
         "valid": len(errors) == 0,
         "errors": errors,
@@ -369,7 +347,7 @@ async def validate_tool_type(
 )
 async def delete_tool_type(
     tool_type_id: uuid.UUID,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> None:
     """Delete a tool type.
@@ -382,6 +360,7 @@ async def delete_tool_type(
     Returns:
         None with 204 status code.
     """
+    user = await _get_user(session, user_id)
     await _require_admin(user)
 
     tool_type = await session.get(ToolType, tool_type_id)
@@ -390,11 +369,7 @@ async def delete_tool_type(
             status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
         )
 
-    if tool_type.is_builtin:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN,
-            detail="cannot delete built-in tool types",
-        )
+    # Built-in tool types can now be deleted
 
     await session.delete(tool_type)
     await session.commit()

apps/api/src/api/tool_instances.py

@@ -1,286 +0,0 @@
-"""Tool instance API endpoints."""
-
-import logging
-import uuid
-
-import httpx
-from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user, get_db_session, get_owned_project
-from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.models.user import User
-from src.schemas.tool_instance import CreateInstanceRequest
-from src.services import instance_lifecycle as lifecycle
-from src.services.docker import container as container_svc
-from src.services.docker import tunnel as tunnel_svc
-
-logger = logging.getLogger(__name__)
-router = APIRouter(prefix="/projects", tags=["tool-instances"])
-async def _get_instance(session: AsyncSession, instance_id: uuid.UUID, repo_id: uuid.UUID) -> ToolInstance:
-    instance = await session.get(ToolInstance, instance_id)
-    if instance is None or instance.repository_id != repo_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="instance not found")
-    return instance
-async def _get_repo(session: AsyncSession, repo_id: uuid.UUID, project_id: uuid.UUID) -> GitRepository:
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-    return repo
-# ── Endpoints ──────────────────────────────────────────────────────────────
-
-@router.post("/{project_id}/repositories/{repo_id}/instances")
-async def create_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CreateInstanceRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a new tool instance."""
-    repo = await _get_repo(session, repo_id, project_id)
-    tool_type = await session.get(ToolType, uuid.UUID(data.tool_type_id))
-    if tool_type is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-
-    selected_profile = None
-    if data.config_profile_id:
-        from src.models.config_profile import ConfigProfile
-        selected_profile = await session.get(ConfigProfile, uuid.UUID(data.config_profile_id))
-        if selected_profile is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config profile not found")
-        if selected_profile.user_id != user.id:
-            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="config profile does not belong to user")
-
-    instance = await lifecycle.create_new_instance(
-        session, project, repo, tool_type, user, data.display_name, selected_profile,
-        ssh_key_ids=data.ssh_key_ids or None,
-    )
-    return {
-        "id": str(instance.id),
-        "name": instance.name,
-        "display_name": instance.display_name,
-        "tool_type_id": str(instance.tool_type_id),
-        "status": instance.status,
-        "config_profile_id": str(instance.selected_profile_id) if instance.selected_profile_id else None,
-        "ssh_key_ids": instance.ssh_key_ids or [],
-        "created_at": instance.created_at.isoformat(),
-    }
-@router.get("/{project_id}/repositories/{repo_id}/instances")
-async def list_instances(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """List all tool instances for a repository."""
-    await _get_repo(session, repo_id, project_id)
-    from sqlalchemy import select
-    result = await session.execute(
-        select(ToolInstance)
-        .where(ToolInstance.repository_id == repo_id, ToolInstance.owner_id == user.id)
-        .order_by(ToolInstance.created_at.desc())
-    )
-    instances = []
-    for i in result.scalars().all():
-        tt = await session.get(ToolType, i.tool_type_id)
-        instances.append({
-            "id": str(i.id), "name": i.name, "display_name": i.display_name,
-            "tool_type_id": str(i.tool_type_id), "tool_type_name": tt.name if tt else "unknown",
-            "tool_type_interfaces": tt.interfaces if tt else [],
-            "status": i.status, "url": i.url, "port": i.port,
-            "config_profile_id": str(i.selected_profile_id) if i.selected_profile_id else None,
-            "created_at": i.created_at.isoformat(),
-        })
-    return {"instances": instances}
-@router.get("/{project_id}/repositories/{repo_id}/instances/{instance_id}")
-async def get_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get a specific instance with real-time Docker status."""
-    from datetime import datetime
-    instance = await _get_instance(session, instance_id, repo_id)
-    if instance.container_id:
-        docker_status = container_svc.get_container_status(instance.container_id)
-        if docker_status == "running" and instance.status != "running":
-            instance.status = "running"
-            await session.commit()
-        elif docker_status == "exited" and instance.status == "running":
-            instance.status = "stopped"
-            instance.last_stopped_at = datetime.now()
-            await session.commit()
-    return {
-        "id": str(instance.id), "name": instance.name, "display_name": instance.display_name,
-        "tool_type_id": str(instance.tool_type_id), "status": instance.status,
-        "container_id": instance.container_id, "compose_path": instance.compose_path,
-        "url": instance.url, "port": instance.port,
-        "config_profile_id": str(instance.selected_profile_id) if instance.selected_profile_id else None,
-        "last_started_at": instance.last_started_at.isoformat() if instance.last_started_at else None,
-        "last_stopped_at": instance.last_stopped_at.isoformat() if instance.last_stopped_at else None,
-        "created_at": instance.created_at.isoformat(),
-    }
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/start")
-async def start_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Start a tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    return await lifecycle.start_existing_instance(session, instance, user, project_id)
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/stop")
-async def stop_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Stop a running tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    await lifecycle.stop_existing_instance(session, instance)
-    return {"status": instance.status}
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/restart")
-async def restart_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Restart a tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    return await lifecycle.restart_existing_instance(session, instance, user, project_id)
-@router.delete("/{project_id}/repositories/{repo_id}/instances/{instance_id}")
-async def delete_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Delete a tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    await lifecycle.delete_existing_instance(session, instance)
-@router.get("/{project_id}/repositories/{repo_id}/instances/{instance_id}/logs")
-async def get_instance_logs(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    tail: int = 100,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get container logs for an instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    if not instance.container_id:
-        return {"logs": "No container running"}
-    return {"logs": container_svc.get_container_logs(instance.container_id, tail)}
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/recreate-tunnel")
-async def recreate_tunnel_endpoint(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Recreate the temporary tunnel for an instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    if instance.status != "running":
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="instance must be running")
-
-    tool_type = await session.get(ToolType, instance.tool_type_id)
-    instance_port = tool_type.default_port if tool_type and tool_type.default_port else 8080
-
-    try:
-        tunnel_info = tunnel_svc.recreate_tunnel(
-            container_name=instance.container_name or instance.name,
-            port=instance_port,
-            old_pid=instance.tunnel_id,
-        )
-        instance.tunnel_id = tunnel_info["pid"]
-        instance.public_url = tunnel_info["url"]
-        instance.url = tunnel_info["url"]
-        await session.commit()
-        return {"status": "healthy", "url": instance.url}
-    except Exception as exc:
-        logger.exception("Failed to recreate tunnel")
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=f"Failed to recreate tunnel: {exc}")
-@router.get("/{project_id}/repositories/{repo_id}/instances/{instance_id}/health")
-async def check_instance_tunnel_health(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Check tunnel health for an instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    if not instance.url or instance.status != "running":
-        return {"healthy": False, "status_code": None, "error": "instance not running"}
-    return tunnel_svc.check_tunnel_health(instance.url)
-@router.api_route(
-    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/proxy/{path:path}",
-    methods=["GET", "POST", "PUT", "DELETE", "PATCH", "HEAD", "OPTIONS"],
-)
-async def proxy_to_instance(
-    request: Request,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    path: str = "",
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> Response:
-    """Proxy HTTP requests to a running tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    if instance.owner_id != user.id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not authorized")
-    if instance.status != "running" or not instance.container_name:
-        raise HTTPException(status_code=status.HTTP_503_SERVICE_UNAVAILABLE, detail="instance is not running")
-
-    target_url = f"http://{instance.container_name}:{instance.port}"
-    if path:
-        target_url += f"/{path}"
-    query = str(request.query_params)
-    if query:
-        target_url += f"?{query}"
-
-    headers = dict(request.headers)
-    headers.pop("host", None)
-    headers.pop("cookie", None)
-
-    try:
-        async with httpx.AsyncClient() as client:
-            body = await request.body()
-            response = await client.request(
-                method=request.method, url=target_url, headers=headers,
-                content=body, follow_redirects=False, timeout=30.0,
-            )
-    except Exception as exc:
-        logger.error("Proxy error: %s", exc)
-        raise HTTPException(status_code=status.HTTP_502_BAD_GATEWAY, detail=f"failed to reach instance: {exc}")
-
-    resp_headers = dict(response.headers)
-    for h in ["content-encoding", "transfer-encoding", "connection"]:
-        resp_headers.pop(h, None)
-    return Response(content=response.content, status_code=response.status_code, headers=resp_headers)

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

@@ -1,5 +1,5 @@
+import base64
 import uuid
-from datetime import datetime
 
 from cryptography.fernet import Fernet
 from cryptography.hazmat.primitives import serialization
@@ -8,21 +8,26 @@ from fastapi import APIRouter, Depends, HTTPException, status
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import get_current_user, get_db_session
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.config import Settings
-from src.models.ssh_key import SSHKey
-from src.models.user import User
-from src.schemas.ssh_key import SSHKeyCreate, SSHKeyResponse
+from src.models import SSHKey
+from src.schemas.project import (
+    SSHKeyCreate,
+    SSHKeyResponse,
+    SignPayloadRequest,
+    SignatureResponse,
+    VerifySignatureRequest,
+    VerifySignatureResponse,
+)
 
 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
 
 
-
 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()
@@ -63,7 +68,7 @@ def generate_ssh_key_pair() -> tuple[str, str]:
 )
 async def create_ssh_key(
     data: SSHKeyCreate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> SSHKey:
     """Create a new SSH key pair.
@@ -76,6 +81,7 @@ async def create_ssh_key(
     Returns:
         The newly created SSH key with public key exposed.
     """
+    user = await _get_user(session, user_id)
     private_key, public_key = generate_ssh_key_pair()
 
     fernet = _get_fernet()
@@ -100,7 +106,7 @@ async def create_ssh_key(
     description="List all SSH keys for the authenticated user.",
 )
 async def list_ssh_keys(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[SSHKey]:
     """List all SSH keys for the authenticated user.
@@ -112,6 +118,7 @@ async def list_ssh_keys(
     Returns:
         List of SSH keys owned by the user.
     """
+    user = await _get_user(session, user_id)
     result = await session.execute(select(SSHKey).where(SSHKey.user_id == user.id))
     return list(result.scalars().all())
 
@@ -124,7 +131,7 @@ async def list_ssh_keys(
 )
 async def delete_ssh_key(
     key_id: uuid.UUID,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> None:
     """Delete an SSH key.
@@ -137,9 +144,93 @@ async def delete_ssh_key(
     Returns:
         None with 204 status code.
     """
+    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()
+
+
+@router.post(
+    "/{key_id}/sign",
+    response_model=SignatureResponse,
+    summary="Sign payload",
+    description="Sign a payload using the SSH private key.",
+)
+async def sign_payload(
+    key_id: uuid.UUID,
+    data: SignPayloadRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> SignatureResponse:
+    """Sign a payload with an SSH key.
+
+    Args:
+        key_id: UUID of the SSH key to use for signing.
+        data: Sign request containing the payload string.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Base64-encoded Ed25519 signature.
+    """
+    user = await _get_user(session, user_id)
+    ssh_key = await session.get(SSHKey, key_id)
+    if ssh_key is None or ssh_key.user_id != user.id:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+        )
+
+    fernet = _get_fernet()
+    private_key_pem = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
+
+    private_key = serialization.load_ssh_private_key(
+        private_key_pem.encode(), password=None
+    )
+
+    signature = private_key.sign(data.payload.encode())
+    return SignatureResponse(signature=base64.b64encode(signature).decode())
+
+
+@router.post(
+    "/{key_id}/verify",
+    response_model=VerifySignatureResponse,
+    summary="Verify signature",
+    description="Verify a signature against a payload using the SSH public key.",
+)
+async def verify_signature(
+    key_id: uuid.UUID,
+    data: VerifySignatureRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> VerifySignatureResponse:
+    """Verify a signature with an SSH key's public key.
+
+    Args:
+        key_id: UUID of the SSH key to use for verification.
+        data: Verify request containing payload and base64-encoded signature.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Whether the signature is valid.
+    """
+    user = await _get_user(session, user_id)
+    ssh_key = await session.get(SSHKey, key_id)
+    if ssh_key is None or ssh_key.user_id != user.id:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+        )
+
+    public_key = serialization.load_ssh_public_key(ssh_key.public_key.encode())
+
+    try:
+        signature = base64.b64decode(data.signature)
+        public_key.verify(signature, data.payload.encode())
+        return VerifySignatureResponse(valid=True)
+    except Exception:
+        return VerifySignatureResponse(valid=False)

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

@@ -2,13 +2,10 @@ import uuid
 from pathlib import Path
 
 from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
-from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import get_current_user, get_db_session
-from src.models.tool_instance import ToolInstance
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.user import User
-from src.schemas.tool_instance import SessionItemResponse, SessionListResponse
 from src.schemas.user import UserProfileResponse, UserProfileUpdate
 
 router = APIRouter(prefix="/users", tags=["users"])
@@ -26,7 +23,7 @@ MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
     description="Retrieve the profile of the currently authenticated user.",
 )
 async def get_profile(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Get the current user's profile.
@@ -38,7 +35,7 @@ async def get_profile(
     Returns:
         The user's profile information.
     """
-    return user
+    return await _get_user(session, user_id)
 
 
 @router.put(
@@ -49,7 +46,7 @@ async def get_profile(
 )
 async def update_profile(
     data: UserProfileUpdate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Update the current user's profile.
@@ -62,6 +59,7 @@ async def update_profile(
     Returns:
         The updated user profile.
     """
+    user = await _get_user(session, user_id)
 
     if data.name is not None:
         if len(data.name.strip()) == 0:
@@ -90,7 +88,7 @@ async def update_profile(
 )
 async def upload_avatar(
     file: UploadFile,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Upload a profile avatar image.
@@ -103,6 +101,7 @@ async def upload_avatar(
     Returns:
         The updated user profile with new avatar URL.
     """
+    user = await _get_user(session, user_id)
 
     if file.content_type not in ALLOWED_CONTENT_TYPES:
         raise HTTPException(
@@ -137,41 +136,3 @@ async def upload_avatar(
     await session.commit()
     await session.refresh(user)
     return user
-
-
-@router.get(
-    "/me/sessions",
-    response_model=SessionListResponse,
-    summary="Get current user sessions",
-    description="Retrieve all tool instances (sessions) for the authenticated user.",
-)
-async def get_user_sessions(
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> SessionListResponse:
-    """Return all tool instances for the current user with related names."""
-    result = await session.execute(
-        select(ToolInstance)
-        .where(ToolInstance.owner_id == user.id)
-        .order_by(ToolInstance.created_at.desc())
-    )
-    instances = result.scalars().all()
-
-    sessions = [
-        SessionItemResponse(
-            id=str(inst.id),
-            display_name=inst.display_name,
-            tool_type_name=inst.tool_type.display_name if inst.tool_type else "Unknown",
-            tool_icon=None,
-            tool_type_interfaces=inst.tool_type.interfaces if inst.tool_type else [],
-            repository_name=inst.repository.name if inst.repository else "Unknown",
-            repository_id=str(inst.repository_id),
-            project_name=inst.project.name if inst.project else "Unknown",
-            project_id=str(inst.project_id),
-            status=inst.status,
-            url=inst.url,
-        )
-        for inst in instances
-    ]
-
-    return SessionListResponse(sessions=sessions)

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.services.file_service import FileService
+from src.models import Workspace
+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.services.git_operations import GitOperations
+from src.models import Workspace
+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.workspace import Workspace
+from src.models import ToolInstance
+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.tool_instance import ToolInstance
-from src.models.workspace import Workspace
-from src.services.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
+from src.models import GitRepository
+from src.models import ToolInstance
+from src.models import Workspace
+from src.services.shared.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
 
 logger = logging.getLogger(__name__)
 

apps/api/src/auth/dependencies.py

@@ -50,17 +50,25 @@ async def get_current_user(
     return user
 
 
-async def get_owned_project(
+async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+    """Fetch a user by ID or raise 401 if not found."""
+    user = await session.get(User, user_id)
+    if user is None:
+        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
+    return user
+
+
+async def _get_owned_project(
     project_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    db_session: AsyncSession = Depends(get_db_session),
-) -> Project:
+    user_id: uuid.UUID,
+    session: AsyncSession,
+) -> "Project":
     """Fetch a project and verify ownership.
 
     Args:
-        project_id: UUID of the project (injected from path parameter).
-        user: The currently authenticated user.
-        db_session: Database session.
+        project_id: UUID of the project.
+        user_id: ID of the authenticated user.
+        session: Database session.
 
     Returns:
         The project if found and owned by the user.
@@ -68,9 +76,11 @@ async def get_owned_project(
     Raises:
         HTTPException: 404 if project not found, 403 if user is not the owner.
     """
-    project = await db_session.get(Project, project_id)
+    from src.models.project import Project
+
+    project = await session.get(Project, project_id)
     if project is None:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="project not found")
-    if project.owner_id != user.id:
+    if project.owner_id != user_id:
         raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not project owner")
     return project

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

@@ -6,20 +6,34 @@ from fastapi.exceptions import RequestValidationError
 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.dashboard import router as dashboard_router
-from src.api.git_repositories import router as git_repositories_router
-from src.api.health import router as health_router
-from src.api.projects import router as projects_router
-from src.api.ssh_keys import router as ssh_keys_router
-from src.api.terminal import router as terminal_router
-from src.api.instance_proxy import router as instance_proxy_router
-from src.api.config_profiles import router as config_profiles_router
-from src.api.tool_instances import router as tool_instances_router
-from src.api.tool_types import router as tool_types_router
-from src.api.user_config import router as user_config_router
-from src.api.users import router as users_router
+
+from src.api.config import config_profiles_router, user_config_router
+from src.api.project import git_repositories_router, projects_router
+from src.api.system import (
+    dashboard_router,
+    events_router,
+    health_router,
+    instance_proxy_router,
+    notifications_router,
+    terminal_router,
+)
+from src.api.tool import (
+    sessions_router,
+    tool_definitions_router,
+    tool_instances_router,
+    tool_types_router,
+)
+from src.api.user import auth_router, ssh_keys_router, users_router
+from src.api.workspace import (
+    all_workspaces_router,
+    workspace_files_router,
+    workspace_git_router,
+    workspace_instances_router,
+    workspaces_router,
+)
 from src.config import Settings
+from src.models import Notification  # 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,
@@ -27,6 +41,8 @@ from src.logging_config import (
     configure_logging,
 )
 from src.seeds.builtin_tool_types import seed_builtin_tool_types
+from src.services.instance import InstanceEventBus, HealthMonitor
+from src.services.shared import CorrelationIdMiddleware
 
 # Configure logging early
 log_level = os.getenv("LOG_LEVEL", "INFO").upper()
@@ -51,6 +67,7 @@ app.add_middleware(
     allow_headers=["*"],
 )
 
+app.add_middleware(CorrelationIdMiddleware)
 app.add_middleware(RequestLoggingMiddleware)
 app.add_middleware(ExceptionLoggingMiddleware)
 
@@ -100,6 +117,11 @@ async def validation_exception_handler(request: Request, exc: RequestValidationE
     )
 
 
+# Global services
+_event_bus = InstanceEventBus()
+_health_monitor = HealthMonitor(_event_bus)
+
+
 @app.on_event("startup")
 async def on_startup():
     logger.info("Starting up Headquarter API...")
@@ -112,11 +134,25 @@ async def on_startup():
 
         sys.exit(1)
 
-    # Seed built-in data
+    # Start background health monitor
+    _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.")
 
 
+@app.on_event("shutdown")
+async def on_shutdown():
+    logger.info("Shutting down Headquarter API...")
+    _health_monitor.stop()
+    logger.info("Health monitor stopped")
+    logger.info("Shutdown complete.")
+
+
 app.include_router(health_router)
 app.include_router(auth_router)
 app.include_router(dashboard_router)
@@ -126,8 +162,17 @@ app.include_router(ssh_keys_router)
 app.include_router(git_repositories_router)
 app.include_router(user_config_router)
 app.include_router(tool_types_router)
+app.include_router(tool_definitions_router)
 app.include_router(config_profiles_router)
 app.include_router(tool_instances_router)
+app.include_router(sessions_router)
 app.include_router(instance_proxy_router)
 app.include_router(terminal_router)
+app.include_router(events_router)
+app.include_router(notifications_router)
+app.include_router(all_workspaces_router)
+app.include_router(workspaces_router)
+app.include_router(workspace_files_router)
+app.include_router(workspace_git_router)
+app.include_router(workspace_instances_router)
 app.mount("/uploads", StaticFiles(directory="uploads"), name="uploads")

apps/api/src/models/__init__.py

@@ -1,25 +1,34 @@
 from src.models.base import Base
-from src.models.config_include import ConfigInclude
-from src.models.config_mount import ConfigMount
-from src.models.config_profile import ConfigProfile
-from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.ssh_key import SSHKey
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.models.user import User
-from src.models.user_config import UserConfig
+from src.models.config.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models.project.git_repository import GitRepository
+from src.models.project.project import Project
+from src.models.project.workspace import Workspace
+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
+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
+from src.models.user.ssh_key import SSHKey
+from src.models.user.user import User
+from src.models.user.user_config import UserConfig
 
 __all__ = [
     "Base",
-    "ConfigInclude",
-    "ConfigMount",
     "ConfigProfile",
+    "ConfigProfileInclude",
     "GitRepository",
+    "HealthCheck",
+    "InstanceEvent",
+    "Notification",
     "Project",
     "SSHKey",
+    "TerminalSessionModel",
+    "ToolDefinitionManifest",
     "ToolInstance",
     "ToolType",
     "User",
     "UserConfig",
+    "Workspace",
 ]

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

@@ -0,0 +1,88 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import (
+    Boolean,
+    ForeignKey,
+    JSON,
+    Integer,
+    String,
+    Text,
+    UniqueConstraint,
+)
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.project import Project
+    from src.models 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
+    )
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    description: Mapped[str | None] = mapped_column(Text, nullable=True)
+    project_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("projects.id", ondelete="CASCADE"), nullable=True
+    )
+    tool_type_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("tool_types.id", ondelete="CASCADE"), nullable=True
+    )
+    env_vars: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"VAR_NAME": "value", ...}
+    runtime_hints: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"start_command": "...", "working_dir": "...", ...}
+    mounts: Mapped[list] = mapped_column(
+        JSON, default=list, nullable=False
+    )  # [{"target": "/path", "mode": "rw", "files": {"rel/path": "content"}}, ...]
+    files: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"rel/path": "content", ...}
+    git_mounts: Mapped[list] = mapped_column(
+        JSON, default=list, nullable=False
+    )  # [{"remote_url": "https://github.com/user/repo.git", "source_path": ".", "target_path": "/path", "branch": "main"}, ...]
+    is_default: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
+
+    user: Mapped["User"] = relationship()
+    project: Mapped["Project | None"] = relationship()
+    tool_type: Mapped["ToolType | None"] = relationship()
+    includes: Mapped[list["ConfigProfileInclude"]] = relationship(
+        "ConfigProfileInclude",
+        foreign_keys="ConfigProfileInclude.profile_id",
+        order_by="ConfigProfileInclude.order_index",
+        cascade="all, delete-orphan",
+    )
+
+
+class ConfigProfileInclude(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_profile_includes"
+
+    profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    included_profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
+
+    profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[profile_id],
+        back_populates="includes",
+    )
+    included_profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[included_profile_id],
+    )

apps/api/src/models/config_include.py

@@ -1,36 +0,0 @@
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import ForeignKey, Integer, UniqueConstraint
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.config_profile import ConfigProfile
-
-
-class ConfigInclude(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    __tablename__ = "config_includes"
-    __table_args__ = (
-        UniqueConstraint("profile_id", "included_profile_id", name="uq_config_includes_pair"),
-    )
-
-    profile_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
-    )
-    included_profile_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
-    )
-    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
-
-    profile: Mapped["ConfigProfile"] = relationship(
-        "ConfigProfile",
-        foreign_keys=[profile_id],
-        back_populates="includes",
-    )
-    included_profile: Mapped["ConfigProfile"] = relationship(
-        "ConfigProfile",
-        foreign_keys=[included_profile_id],
-    )

apps/api/src/models/config_mount.py

@@ -1,31 +0,0 @@
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import ForeignKey, Integer, JSON, String
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.config_profile import ConfigProfile
-
-
-class ConfigMount(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    __tablename__ = "config_mounts"
-
-    profile_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
-    )
-    target_path: Mapped[str] = mapped_column(String(1024), nullable=False)
-    mode: Mapped[str] = mapped_column(String(10), nullable=False, default="rw")
-    files: Mapped[dict[str, str] | None] = mapped_column(
-        JSON, default=dict, nullable=True
-    )
-    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
-
-    profile: Mapped["ConfigProfile"] = relationship(
-        "ConfigProfile",
-        foreign_keys=[profile_id],
-        back_populates="mounts",
-    )

apps/api/src/models/config_profile.py

@@ -1,59 +0,0 @@
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import ForeignKey, Integer, JSON, String, Text, UniqueConstraint
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.config_include import ConfigInclude
-    from src.models.config_mount import ConfigMount
-    from src.models.project import Project
-    from src.models.tool_type import ToolType
-    from src.models.user import User
-
-
-class ConfigProfile(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    __tablename__ = "config_profiles"
-    __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
-    )
-    project_id: Mapped[uuid.UUID | None] = mapped_column(
-        UUID(), ForeignKey("projects.id", ondelete="CASCADE"), nullable=True
-    )
-    tool_type_id: Mapped[uuid.UUID | None] = mapped_column(
-        UUID(), ForeignKey("tool_types.id", ondelete="CASCADE"), nullable=True
-    )
-    name: Mapped[str] = mapped_column(String(255), nullable=False)
-    description: Mapped[str | None] = mapped_column(Text, nullable=True)
-    environment_variables: Mapped[dict[str, str] | None] = mapped_column(
-        JSON, default=dict, nullable=True
-    )
-    start_command: Mapped[str | None] = mapped_column(Text, nullable=True)
-    working_directory: Mapped[str | None] = mapped_column(Text, nullable=True)
-    port: Mapped[int | None] = mapped_column(Integer, nullable=True)
-    is_default: Mapped[bool] = mapped_column(default=False, nullable=False)
-
-    user: Mapped["User"] = relationship()
-    project: Mapped["Project | None"] = relationship()
-    tool_type: Mapped["ToolType | None"] = relationship()
-    includes: Mapped[list["ConfigInclude"]] = relationship(
-        "ConfigInclude",
-        primaryjoin="ConfigProfile.id == ConfigInclude.profile_id",
-        back_populates="profile",
-        cascade="all, delete-orphan",
-        order_by="ConfigInclude.order_index",
-    )
-    mounts: Mapped[list["ConfigMount"]] = relationship(
-        "ConfigMount",
-        primaryjoin="ConfigProfile.id == ConfigMount.profile_id",
-        back_populates="profile",
-        cascade="all, delete-orphan",
-        order_by="ConfigMount.order_index",
-    )

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.ssh_key import SSHKey
+    from src.models import GitRepository
+    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

@@ -9,11 +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.git_repository import GitRepository
+    from src.models import ConfigProfile
+    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 import Workspace
 
 
 class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
@@ -33,45 +34,40 @@ class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     owner_id: Mapped[uuid.UUID] = mapped_column(
         UUID(), ForeignKey("users.id"), nullable=False
     )
-    status: Mapped[str] = mapped_column(
-        String(50), nullable=False, default="pending"
-    )
-    container_id: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    container_name: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    compose_path: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    url: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    public_url: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    tunnel_id: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    port: Mapped[int | None] = mapped_column(
-        Integer, nullable=True
-    )
+    status: Mapped[str] = mapped_column(String(50), nullable=False, default="pending")
+    container_id: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    container_name: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    compose_path: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    public_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    tunnel_id: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    port: Mapped[int | None] = mapped_column(Integer, nullable=True)
     last_started_at: Mapped[datetime | None] = mapped_column(
         DateTime(timezone=True), nullable=True
     )
     last_stopped_at: Mapped[datetime | None] = mapped_column(
         DateTime(timezone=True), nullable=True
     )
-    selected_profile_id: Mapped[uuid.UUID | None] = mapped_column(
+    manifest_compiled_at: Mapped[datetime | None] = mapped_column(
+        DateTime(timezone=True), nullable=True
+    )
+    image_tag: Mapped[str | None] = mapped_column(String(256), nullable=True)
+    probe_result: Mapped[dict | None] = mapped_column(JSON, nullable=True)
+    clone_mode: Mapped[str] = mapped_column(String(20), nullable=False, default="mount")
+    branch: Mapped[str | None] = mapped_column(
+        String(255), nullable=True, default="main"
+    )
+    selected_config_profile_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True
     )
-    ssh_key_ids: Mapped[list[str] | None] = mapped_column(
-        JSON, nullable=True
+    ssh_key_ids: Mapped[list[str] | None] = mapped_column(JSON, nullable=True)
+    workspace_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("workspaces.id", ondelete="SET NULL"), nullable=True
     )
 
     tool_type: Mapped["ToolType"] = relationship()
+    workspace: Mapped["Workspace | None"] = relationship()
     repository: Mapped["GitRepository"] = relationship()
     project: Mapped["Project"] = relationship()
     owner: Mapped["User"] = relationship()
-    selected_profile: Mapped["ConfigProfile | None"] = relationship()
+    selected_config_profile: Mapped["ConfigProfile | None"] = relationship()

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

@@ -1,12 +1,12 @@
 import uuid
 from typing import TYPE_CHECKING
 
-from sqlalchemy import Boolean, ForeignKey, JSON, String, Text, Uuid as UUID
+from sqlalchemy import Boolean, ForeignKey, JSON, String, Text
+from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-from src.models.tool_definition_manifest import ToolDefinitionManifest
+from src.models.tool.tool_definition_manifest import ToolDefinitionManifest
 
 if TYPE_CHECKING:
     from src.models.user import User
@@ -52,21 +52,3 @@ class ToolType(UUIDPrimaryKeyMixin, TimestampMixin, Base):
         foreign_keys=[manifest_id],
     )
     created_by: Mapped["User | None"] = relationship()
-
-    @property
-    def interfaces(self) -> list[str]:
-        """Backward-compatible API view for the single interface type."""
-        return [self.interface_type]
-
-    @interfaces.setter
-    def interfaces(self, value: list[str] | str) -> None:
-        """Accept legacy interface lists and store the first interface type."""
-        if isinstance(value, str):
-            self.interface_type = value
-            return
-        self.interface_type = value[0] if value else "web"
-
-    @property
-    def is_builtin(self) -> bool:
-        """Built-in tools are seeded system tools without a creating user."""
-        return self.created_by_id is None

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.user_config import UserConfig
+    from src.models import SSHKey
+    from src.models import UserConfig
 
 
 class User(UUIDPrimaryKeyMixin, TimestampMixin, Base):

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

@@ -1,8 +1,8 @@
 import uuid
 from typing import TYPE_CHECKING
 
-from sqlalchemy import ForeignKey
-from sqlalchemy import JSON, Uuid as UUID
+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
@@ -14,15 +14,22 @@ if TYPE_CHECKING:
 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_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")
-        return uuid.UUID(profile_id) if profile_id else None
+        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:
@@ -33,7 +40,11 @@ class UserConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
 
     @property
     def default_profiles(self) -> dict[str, str]:
-        return self.config.get("default_profiles", {})
+        """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:

apps/api/src/schemas/__init__.py

@@ -1 +0,0 @@
-"""Pydantic request/response schemas."""

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/config_profile.py

@@ -1,131 +0,0 @@
-"""Config profile request/response schemas."""
-
-from typing import Any
-
-from pydantic import BaseModel, Field, field_validator
-
-MAX_MOUNT_PATH_LENGTH = 1024
-
-
-class ConfigProfileCreate(BaseModel):
-    name: str = Field(description="Profile name (unique per user)")
-    description: str | None = Field(default=None, description="Optional description")
-
-    @field_validator("name")
-    @classmethod
-    def validate_name(cls, v: str) -> str:
-        v = v.strip()
-        if not v:
-            raise ValueError("Profile name cannot be empty")
-        if len(v) > 255:
-            raise ValueError("Profile name must be 255 characters or less")
-        return v
-
-
-class ConfigProfileUpdate(BaseModel):
-    name: str | None = Field(default=None, description="Profile name")
-    description: str | None = Field(default=None, description="Optional description")
-
-    @field_validator("name")
-    @classmethod
-    def validate_name(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        v = v.strip()
-        if not v:
-            raise ValueError("Profile name cannot be empty")
-        if len(v) > 255:
-            raise ValueError("Profile name must be 255 characters or less")
-        return v
-
-
-class ConfigProfileResponse(BaseModel):
-    id: str
-    user_id: str
-    name: str
-    description: str | None
-    created_at: str
-    updated_at: str
-
-
-class ConfigProfileDetailResponse(ConfigProfileResponse):
-    includes: list[dict[str, Any]]
-    mounts: list[dict[str, Any]]
-
-
-class ConfigIncludeCreate(BaseModel):
-    included_profile_id: str = Field(description="UUID of the profile to include")
-    order_index: int = Field(default=0, description="Order index for include resolution")
-
-
-class ConfigIncludeUpdate(BaseModel):
-    order_index: int = Field(description="Order index for include resolution")
-
-
-class ConfigIncludeResponse(BaseModel):
-    id: str
-    profile_id: str
-    included_profile_id: str
-    included_profile_name: str | None
-    order_index: int
-    created_at: str
-    updated_at: str
-
-
-class ConfigMountCreate(BaseModel):
-    target_path: str = Field(description="Absolute target path in container")
-    mode: str = Field(default="rw", description="Mount mode (rw or ro)")
-    files: dict[str, str] | None = Field(
-        default=None, description="Files as {path: content}"
-    )
-    order_index: int = Field(default=0, description="Order index for mount resolution")
-
-    @field_validator("target_path")
-    @classmethod
-    def validate_target_path(cls, v: str) -> str:
-        if not v.startswith("/"):
-            raise ValueError("Target path must be absolute (start with /)")
-        if ".." in v:
-            raise ValueError("Target path cannot contain parent directory references (..)")
-        if len(v) > MAX_MOUNT_PATH_LENGTH:
-            raise ValueError(f"Target path must be {MAX_MOUNT_PATH_LENGTH} characters or less")
-        return v
-
-
-class ConfigMountUpdate(BaseModel):
-    target_path: str | None = Field(default=None, description="Absolute target path in container")
-    mode: str | None = Field(default=None, description="Mount mode (rw or ro)")
-    files: dict[str, str] | None = Field(
-        default=None, description="Files as {path: content}"
-    )
-    order_index: int | None = Field(default=None, description="Order index for mount resolution")
-
-    @field_validator("target_path")
-    @classmethod
-    def validate_target_path(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if not v.startswith("/"):
-            raise ValueError("Target path must be absolute (start with /)")
-        if ".." in v:
-            raise ValueError("Target path cannot contain parent directory references (..)")
-        if len(v) > MAX_MOUNT_PATH_LENGTH:
-            raise ValueError(f"Target path must be {MAX_MOUNT_PATH_LENGTH} characters or less")
-        return v
-
-
-class ConfigMountResponse(BaseModel):
-    id: str
-    profile_id: str
-    target_path: str
-    mode: str
-    files: dict[str, str] | None
-    order_index: int
-    created_at: str
-    updated_at: str
-
-
-class DefaultProfilesUpdate(BaseModel):
-    default_profiles: dict[str, str] = Field(
-        description="Mapping of tool_type_id to profile_id"
-    )

apps/api/src/schemas/git_repository.py

@@ -1,129 +0,0 @@
-"""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
-
-
-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
-    owner_id: uuid.UUID
-    is_mirror: bool
-    remote_url: str | None
-    last_push: datetime | None
-    created_at: datetime
-    updated_at: datetime
-
-
-class FileListResponse(BaseModel):
-    path: str
-    branch: str
-    entries: list[dict]
-
-
-class FileContentResponse(BaseModel):
-    path: str
-    branch: str
-    content: str
-    size: int
-    encoding: str
-    language: str | None
-    is_binary: bool
-    last_commit: dict | None
-
-
-class BranchesResponse(BaseModel):
-    branches: list[dict]
-    default_branch: str
-
-
-class FileUpdateRequest(BaseModel):
-    path: str
-    branch: str
-    content: str
-    commit_message: str
-
-
-class FileUpdateResponse(BaseModel):
-    commit_hash: str
-    message: str
-    branch: str
-
-
-class StatusResponse(BaseModel):
-    branch: str
-    modified: list[str]
-    added: list[str]
-    deleted: list[str]
-    untracked: list[str]
-    renamed: list[str]
-    ahead: int
-    behind: int
-
-
-class BranchCreateRequest(BaseModel):
-    name: str
-    base_branch: str = "HEAD"
-
-
-class CheckoutRequest(BaseModel):
-    branch: str
-
-
-class CommitRequest(BaseModel):
-    message: str
-    files: list[str] | None = None
-
-
-class CommitResponse(BaseModel):
-    commit_hash: str
-    message: str
-
-
-class FetchResponse(BaseModel):
-    message: str
-
-
-class PullResponse(BaseModel):
-    message: str
-
-
-class PushResponse(BaseModel):
-    message: str
-
-
-class MergeRequest(BaseModel):
-    source_branch: str
-    target_branch: str | None = None
-    message: str | None = None
-
-
-class MergeResponse(BaseModel):
-    commit_hash: str
-    message: str

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

@@ -1,6 +1,8 @@
 """Project request/response schemas."""
 
-from pydantic import BaseModel
+import uuid
+
+from pydantic import BaseModel, ConfigDict
 
 
 class ProjectCreate(BaseModel):
@@ -14,12 +16,14 @@ class ProjectUpdate(BaseModel):
 
 
 class ProjectResponse(BaseModel):
-    id: str
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
     name: str
     description: str | None
-    created_at: str
-    updated_at: str
+    owner_id: uuid.UUID
+    default_ssh_key_id: uuid.UUID | None
 
 
 class SetDefaultSSHKeyRequest(BaseModel):
-    ssh_key_id: str
+    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/ssh_key.py

@@ -1,16 +0,0 @@
-"""SSH key request/response schemas."""
-
-from pydantic import BaseModel
-
-
-class SSHKeyCreate(BaseModel):
-    name: str
-    public_key: str
-
-
-class SSHKeyResponse(BaseModel):
-    id: str
-    name: str
-    public_key: str
-    fingerprint: str
-    created_at: str

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/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

@@ -1,31 +1,42 @@
 """Tool type request/response schemas."""
 
 import uuid
+
 from datetime import datetime
 
-import yaml
 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
+    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"
-    interfaces: list[str] = ["web"]
+    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"):
-            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
+        if v not in ("compose", "dockerfile", "manifest"):
+            raise ValueError(
+                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
+            )
         return v
 
     @field_validator("compose_template")
@@ -34,18 +45,13 @@ class ToolTypeCreate(BaseModel):
         data = info.data
         if data.get("definition_type") != "compose":
             return v
-        if v is None:
-            raise ValueError("compose_template is required when definition_type is 'compose'")
-        try:
-            parsed = yaml.safe_load(v)
-        except yaml.YAMLError as e:
-            raise ValueError(f"Invalid YAML: {e}")
-        if not isinstance(parsed, dict):
-            raise ValueError("Compose template must be a YAML mapping")
-        if "services" not in parsed:
-            raise ValueError("Compose template must contain 'services' key")
-        if not parsed["services"]:
-            raise ValueError("Compose template must define at least one service")
+
+        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")
@@ -54,43 +60,33 @@ class ToolTypeCreate(BaseModel):
         data = info.data
         if data.get("definition_type") != "dockerfile":
             return v
-        if v is None:
-            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
+
+        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")
-        data = info.data
-        if data.get("definition_type") != "compose":
-            return v
-        template = data.get("compose_template")
-        if not template:
-            return v
-        try:
-            parsed = yaml.safe_load(template)
-        except yaml.YAMLError:
-            return v
-        port_str = str(v)
-        port_exposed = False
-        if isinstance(parsed, dict) and "services" in parsed:
-            for service_config in parsed["services"].values():
-                if isinstance(service_config, dict) and "ports" in service_config:
-                    for port_mapping in service_config["ports"]:
-                        if isinstance(port_mapping, str) and port_str in port_mapping:
-                            port_exposed = True
-                            break
-                        elif isinstance(port_mapping, int) and port_mapping == v:
-                            port_exposed = True
-                            break
-                if port_exposed:
-                    break
-        if not port_exposed:
-            raise ValueError(f"Port {v} is not exposed in the compose template. Add it to the 'ports' section.")
         return v
 
     @field_validator("required_variables")
@@ -98,24 +94,55 @@ class ToolTypeCreate(BaseModel):
     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")
+
+        validate_required_variables(template, v)
         return v
 
     @model_validator(mode="after")
     def validate_templates(self) -> "ToolTypeCreate":
-        if self.definition_type == "dockerfile" and self.dockerfile_template is None:
-            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
-        if self.definition_type == "compose" and self.compose_template is None:
-            raise ValueError("compose_template is required when definition_type is 'compose'")
+        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
 
 
@@ -124,21 +151,35 @@ class ToolTypeUpdate(BaseModel):
     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
-    interfaces: list[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"):
-            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
+        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")
@@ -146,20 +187,7 @@ class ToolTypeUpdate(BaseModel):
     def validate_compose_template(cls, v: str | None, info) -> str | None:
         if v is None:
             return v
-        data = info.data
-        definition_type = data.get("definition_type")
-        if definition_type and definition_type != "compose":
-            return v
-        try:
-            parsed = yaml.safe_load(v)
-        except yaml.YAMLError as e:
-            raise ValueError(f"Invalid YAML: {e}")
-        if not isinstance(parsed, dict):
-            raise ValueError("Compose template must be a YAML mapping")
-        if "services" not in parsed:
-            raise ValueError("Compose template must contain 'services' key")
-        if not parsed["services"]:
-            raise ValueError("Compose template must define at least one service")
+        validate_compose_yaml(v)
         return v
 
     @field_validator("dockerfile_template")
@@ -167,10 +195,6 @@ class ToolTypeUpdate(BaseModel):
     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
@@ -184,15 +208,17 @@ class ToolTypeResponse(BaseModel):
     display_name: str
     description: str | None
     category: str
-    interfaces: list[str]
+    interface_type: str
+    requires_port: bool
     default_port: int
     definition_type: str
+    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]
-    is_builtin: bool
     created_by_id: uuid.UUID | None
     created_at: datetime
     updated_at: datetime

apps/api/src/schemas/tool_instance.py

@@ -1,44 +0,0 @@
-"""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"
-    )
-    config_profile_id: str | None = Field(
-        default=None, description="Optional config profile ID to apply to the instance"
-    )
-    ssh_key_ids: list[str] = Field(
-        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
-    )
-
-
-class SessionItemResponse(BaseModel):
-    """Lightweight session summary for sidebar and dashboard."""
-
-    model_config = {"extra": "ignore"}
-
-    id: str = Field(description="Session (tool instance) ID")
-    display_name: str = Field(description="Display name of the session")
-    tool_type_name: str = Field(description="Name of the tool type")
-    tool_icon: str | None = Field(default=None, description="Icon URL for the tool type")
-    tool_type_interfaces: list[str] = Field(default_factory=list, description="Supported interfaces")
-    repository_name: str = Field(description="Name of the repository")
-    repository_id: str = Field(description="Repository ID")
-    project_name: str = Field(description="Name of the project")
-    project_id: str = Field(description="Project ID")
-    status: str = Field(description="Current status")
-    url: str | None = Field(default=None, description="Access URL")
-
-
-class SessionListResponse(BaseModel):
-    """Response wrapping a list of session summaries."""
-
-    sessions: list[SessionItemResponse]

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

@@ -1,4 +1,4 @@
-"""User request/response schemas."""
+"""User response schemas."""
 
 import uuid
 

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

@@ -1,4 +1,4 @@
-"""User config request/response schemas."""
+"""User config response schemas."""
 
 from pydantic import BaseModel, ConfigDict
 
@@ -11,6 +11,8 @@ class UserConfigResponse(BaseModel):
     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):
@@ -19,3 +21,5 @@ class UserConfigUpdate(BaseModel):
     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

@@ -1,17 +1,17 @@
+"""Seed built-in tool types into the database."""
+
 import logging
 
-from sqlalchemy import select
+from sqlalchemy import select, text
 
 from src.database import SessionLocal
-from src.models.tool_type import ToolType
+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."""
-    from sqlalchemy import text
-
     try:
         result = await session.execute(
             text(
@@ -31,6 +31,11 @@ async def _table_exists(session, table_name: str) -> bool:
 
 
 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"):
@@ -142,7 +147,8 @@ volumes:
                     definition_type="compose",
                     compose_template=tool_data["compose_template"],
                     required_variables=tool_data["required_variables"],
-                    default_port=tool_data["default_port"],
+                    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"])
@@ -155,7 +161,7 @@ volumes:
                 existing.definition_type = "compose"
                 existing.compose_template = tool_data["compose_template"]
                 existing.required_variables = tool_data["required_variables"]
-                existing.default_port = tool_data["default_port"]
+                existing.default_port = tool_data.get("default_port", 0)
                 logger.info("Updated built-in tool type: %s", tool_data["name"])
 
         await session.commit()

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/config_profiles.py

@@ -1,299 +0,0 @@
-"""Config profile business logic."""
-
-import logging
-import uuid
-
-from fastapi import HTTPException, status
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-from sqlalchemy.orm import selectinload
-
-from src.models.config_include import ConfigInclude
-from src.models.config_mount import ConfigMount
-from src.models.config_profile import ConfigProfile
-from src.models.tool_type import ToolType
-from src.models.user_config import UserConfig
-
-logger = logging.getLogger(__name__)
-
-MAX_INCLUDES_DEPTH = 10
-
-
-async def get_owned_profile(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID,
-    session: AsyncSession,
-) -> ConfigProfile:
-    """Fetch a config profile and verify ownership."""
-    profile = await session.get(ConfigProfile, profile_id)
-    if profile is None or profile.user_id != user_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail="config profile not found",
-        )
-    return profile
-
-
-async def _detect_cycle(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-    visited: set[uuid.UUID] | None = None,
-    depth: int = 0,
-) -> bool:
-    """Detect cycles in profile includes using DFS.
-
-    Returns True if a cycle is detected.
-    """
-    if depth > MAX_INCLUDES_DEPTH:
-        return True
-
-    if visited is None:
-        visited = set()
-
-    if profile_id in visited:
-        return True
-
-    visited.add(profile_id)
-
-    result = await session.execute(
-        select(ConfigInclude.included_profile_id).where(
-            ConfigInclude.profile_id == profile_id
-        )
-    )
-    included_ids = result.scalars().all()
-
-    for included_id in included_ids:
-        if await _detect_cycle(session, included_id, visited.copy(), depth + 1):
-            return True
-
-    return False
-
-
-async def validate_includes_no_cycle(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-    new_included_id: uuid.UUID | None = None,
-) -> None:
-    """Validate that adding an include wouldn't create a cycle."""
-    if new_included_id and await _detect_cycle(session, new_included_id, {profile_id}):
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="adding this include would create a circular reference",
-        )
-
-
-# ---------------------------------------------------------------------------
-# Profile CRUD helpers
-# ---------------------------------------------------------------------------
-
-async def check_duplicate_name(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    name: str,
-    exclude_id: uuid.UUID | None = None,
-) -> None:
-    """Raise 409 if a profile with the given name already exists."""
-    query = select(ConfigProfile).where(
-        ConfigProfile.user_id == user_id,
-        ConfigProfile.name == name,
-    )
-    if exclude_id:
-        query = query.where(ConfigProfile.id != exclude_id)
-    existing = await session.scalar(query)
-    if existing:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"config profile with name '{name}' already exists",
-        )
-
-
-def profile_to_dict(profile: ConfigProfile) -> dict:
-    """Serialize a ConfigProfile to a dict."""
-    return {
-        "id": str(profile.id),
-        "user_id": str(profile.user_id),
-        "name": profile.name,
-        "description": profile.description,
-        "created_at": profile.created_at.isoformat() if profile.created_at else None,
-        "updated_at": profile.updated_at.isoformat() if profile.updated_at else None,
-    }
-
-
-# ---------------------------------------------------------------------------
-# Include helpers
-# ---------------------------------------------------------------------------
-
-async def check_duplicate_include(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-    included_profile_id: uuid.UUID,
-) -> None:
-    """Raise 409 if the include already exists."""
-    existing = await session.scalar(
-        select(ConfigInclude).where(
-            ConfigInclude.profile_id == profile_id,
-            ConfigInclude.included_profile_id == included_profile_id,
-        )
-    )
-    if existing:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail="this include already exists",
-        )
-
-
-def include_to_dict(inc: ConfigInclude, included_name: str | None) -> dict:
-    """Serialize a ConfigInclude to a dict."""
-    return {
-        "id": str(inc.id),
-        "profile_id": str(inc.profile_id),
-        "included_profile_id": str(inc.included_profile_id),
-        "included_profile_name": included_name,
-        "order_index": inc.order_index,
-        "created_at": inc.created_at.isoformat() if inc.created_at else None,
-        "updated_at": inc.updated_at.isoformat() if inc.updated_at else None,
-    }
-
-
-# ---------------------------------------------------------------------------
-# Mount helpers
-# ---------------------------------------------------------------------------
-
-async def check_duplicate_mount_path(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-    target_path: str,
-    exclude_id: uuid.UUID | None = None,
-) -> None:
-    """Raise 409 if a mount with the given path already exists."""
-    query = select(ConfigMount).where(
-        ConfigMount.profile_id == profile_id,
-        ConfigMount.target_path == target_path,
-    )
-    if exclude_id:
-        query = query.where(ConfigMount.id != exclude_id)
-    existing = await session.scalar(query)
-    if existing:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"mount with path '{target_path}' already exists",
-        )
-
-
-def mount_to_dict(mount: ConfigMount) -> dict:
-    """Serialize a ConfigMount to a dict."""
-    return {
-        "id": str(mount.id),
-        "profile_id": str(mount.profile_id),
-        "target_path": mount.target_path,
-        "files": mount.files,
-        "mode": mount.mode,
-        "order_index": mount.order_index,
-        "created_at": mount.created_at.isoformat() if mount.created_at else None,
-        "updated_at": mount.updated_at.isoformat() if mount.updated_at else None,
-    }
-
-
-# ---------------------------------------------------------------------------
-# Default profile helpers
-# ---------------------------------------------------------------------------
-
-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
-
-
-async def validate_default_profiles(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    default_profiles: dict[str, str],
-) -> None:
-    """Validate that all profile IDs in default_profiles belong to the user."""
-    for tool_type_id, profile_id_str in default_profiles.items():
-        profile = await session.get(ConfigProfile, uuid.UUID(profile_id_str))
-        if profile is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=f"profile {profile_id_str} not found")
-        if profile.user_id != user_id:
-            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail=f"profile {profile_id_str} does not belong to user")
-
-
-async def get_default_profiles(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-) -> dict:
-    """Get default profiles for a 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 {}}
-
-
-async def set_default_profiles(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    default_profiles: dict[str, str],
-) -> dict:
-    """Set default profiles for a user."""
-    user_config = await get_or_create_user_config(session, user_id)
-    await validate_default_profiles(session, user_id, default_profiles)
-    user_config.config = {**user_config.config, "default_profiles": default_profiles}
-    await session.commit()
-    await session.refresh(user_config)
-    return {"default_profiles": user_config.default_profiles}
-
-
-async def get_default_profile_for_tool_type(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    tool_type_id: str,
-) -> dict:
-    """Get default profile 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}
-
-
-# ---------------------------------------------------------------------------
-# Include list helper
-# ---------------------------------------------------------------------------
-
-async def list_includes_for_profile(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-) -> dict:
-    """List all includes for a profile."""
-    result = await session.execute(
-        select(ConfigInclude)
-        .where(ConfigInclude.profile_id == profile_id)
-        .order_by(ConfigInclude.order_index)
-    )
-    includes_data = []
-    for inc in result.scalars().all():
-        included_profile = await session.get(ConfigProfile, inc.included_profile_id)
-        includes_data.append(include_to_dict(inc, included_profile.name if included_profile else None))
-    return {"includes": includes_data}
-
-
-# ---------------------------------------------------------------------------
-# Mount list helper
-# ---------------------------------------------------------------------------
-
-async def list_mounts_for_profile(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-) -> dict:
-    """List all mounts for a profile."""
-    result = await session.execute(
-        select(ConfigMount)
-        .where(ConfigMount.profile_id == profile_id)
-        .order_by(ConfigMount.order_index)
-    )
-    return {"mounts": [mount_to_dict(m) for m in result.scalars().all()]}

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

@@ -1,43 +1,55 @@
-"""Docker services for container and tunnel management."""
+"""Docker services package for container and compose operations."""
 
-from .compose import (
-    ensure_instance_directory,
+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 .config_staging import write_config_files
-from .container import (
+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 .tunnel import (
+from src.services.docker.tunnel import (
     check_tunnel_health,
     recreate_tunnel,
-    start_cloudflared_tunnel,
-    stop_cloudflared_tunnel,
+    start_tunnel,
+    stop_tunnel,
 )
 
 __all__ = [
-    "render_compose_template",
-    "ensure_instance_directory",
-    "write_compose_file",
-    "write_env_file",
-    "execute_compose_command",
-    "write_config_files",
-    "get_container_id",
-    "get_container_name",
-    "connect_container_to_network",
-    "get_container_status",
-    "get_container_logs",
-    "find_free_port",
-    "start_cloudflared_tunnel",
-    "stop_cloudflared_tunnel",
-    "recreate_tunnel",
     "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

@@ -1,133 +1,50 @@
-"""Docker Compose file generation and command execution."""
+"""Docker Compose file generation and manipulation."""
 
-import re
+import logging
 import subprocess
-import uuid
+from collections import Counter
 from pathlib import Path
 from typing import Any
 
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.config_profile import ConfigProfile
-from src.models.tool_instance import ToolInstance
-from src.services.profile_resolver import resolve_profile
+logger = logging.getLogger(__name__)
 
 
-def _sanitize_name(name: str) -> str:
-    """Sanitize a string for use in Docker/container names."""
-    sanitized = re.sub(r"[^a-z0-9-]", "-", name.lower())
-    sanitized = re.sub(r"-+", "-", sanitized)
-    return sanitized.strip("-")
+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.
 
-async def _generate_instance_name(
-    session: AsyncSession,
-    project_name: str,
-    tool_type_name: str,
-) -> str:
-    """Generate a unique instance name: project-tool-NUM."""
-    base = f"{_sanitize_name(project_name)}-{_sanitize_name(tool_type_name)}"
-    base = base.strip("-") or "instance"
-    result = await session.execute(
-        select(ToolInstance.name).where(ToolInstance.name.like(f"{base}-%"))
-    )
-    names = result.scalars().all()
-    max_num = 0
-    for name in names:
-        parts = name.rsplit("-", 1)
-        if len(parts) == 2 and parts[0] == base and parts[1].isdigit():
-            max_num = max(max_num, int(parts[1]))
-    return f"{base}-{max_num + 1:03d}"
+    Volume format: source:target or source:target:type
 
+    Args:
+        volumes: List of Docker volume mount strings.
 
-def _modify_compose_file(
-    compose_path: str,
-    port_override: int | None = None,
-    start_command: str | None = None,
-    working_directory: str | None = None,
-    extra_volumes: list[dict] | None = None,
-) -> None:
-    """Modify compose file with runtime overrides."""
-    import yaml
+    Returns:
+        Sorted list with parent paths before child paths.
+    """
 
-    compose_file = Path(compose_path)
-    content = compose_file.read_text()
-    compose_data = yaml.safe_load(content)
+    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("/")
 
-    if not compose_data or "services" not in compose_data:
-        return
+    # 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)
 
-    for service_name, service_config in compose_data["services"].items():
-        if port_override and "ports" in service_config:
-            for i, port_mapping in enumerate(service_config["ports"]):
-                if isinstance(port_mapping, str) and ":" in port_mapping:
-                    _host_port, container_port = port_mapping.split(":", 1)
-                    service_config["ports"][i] = f"{port_override}:{container_port}"
-                    break
-
-        if start_command:
-            service_config["command"] = start_command
-
-        if working_directory:
-            service_config["working_dir"] = working_directory
-
-        if extra_volumes:
-            if "volumes" not in service_config:
-                service_config["volumes"] = []
-            for vol in extra_volumes:
-                source = vol.get("source", "")
-                target = vol.get("target", "")
-                vol_type = vol.get("type", "bind")
-                if vol_type == "bind":
-                    service_config["volumes"].append(f"{source}:{target}")
-                else:
-                    service_config["volumes"].append(f"{source}:{target}:{vol_type}")
-
-        break
-
-    compose_file.write_text(yaml.dump(compose_data, default_flow_style=False))
-
-
-async def _apply_resolved_profile(
-    profile: ConfigProfile,
-    instance_dir: str,
-    env_vars: dict[str, str],
-    port_override: int | None,
-    start_command: str | None,
-    working_directory: str | None,
-    extra_volumes: list[dict],
-) -> tuple[dict[str, str], int | None, str | None, str | None, list[dict]]:
-    """Resolve a profile and apply its output to instance configuration."""
-    resolved = resolve_profile(profile)
-
-    if resolved.environment_variables:
-        env_vars.update(resolved.environment_variables)
-
-    if resolved.runtime_hints.start_command is not None:
-        start_command = resolved.runtime_hints.start_command
-    if resolved.runtime_hints.working_directory is not None:
-        working_directory = resolved.runtime_hints.working_directory
-    if resolved.runtime_hints.port is not None:
-        port_override = resolved.runtime_hints.port
-
-    for target_path, mount in resolved.mounts.items():
-        safe_name = target_path.strip("/").replace("/", "_")
-        mount_dir = Path(instance_dir) / "mounts" / safe_name
-        mount_dir.mkdir(parents=True, exist_ok=True)
-
-        for rel_path, content in mount.files.items():
-            file_path = mount_dir / rel_path
-            file_path.parent.mkdir(parents=True, exist_ok=True)
-            file_path.write_text(content)
-
-        extra_volumes.append({
-            "source": str(mount_dir),
-            "target": target_path,
-            "type": mount.mode,
-        })
-
-    return env_vars, port_override, start_command, working_directory, extra_volumes
+    # 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:
@@ -147,24 +64,6 @@ def render_compose_template(template: str, variables: dict[str, Any]) -> str:
     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.
 
@@ -180,22 +79,6 @@ def write_compose_file(instance_dir: str, content: str) -> str:
     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 execute_compose_command(
     compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
 ) -> tuple[int, str, str]:
@@ -218,7 +101,7 @@ def execute_compose_command(
         cmd.extend(["--env-file", env_file])
 
     if action == "up":
-        cmd.extend(["up", "-d"])
+        cmd.extend(["up", "-d", "--force-recreate"])
     elif action == "down":
         cmd.extend(["down", "-v"])
     elif action in ("start", "stop", "restart"):

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

@@ -1,7 +1,46 @@
-"""Config file staging for Docker instances."""
+"""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.
 

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

@@ -1,59 +1,123 @@
-"""Docker container lifecycle and query operations."""
+"""Docker container runtime queries and network management."""
 
-import socket
+import logging
 import subprocess
+import time
+from typing import Any
+
+logger = logging.getLogger(__name__)
 
 
 def get_container_id(instance_name: str) -> str | None:
     """Get the container ID for a compose service.
 
+    Uses exact name matching to avoid substring collisions with tunnel
+    containers (e.g. tunnel-code-server-... matching code-server-...).
+    Falls back to case-insensitive matching since Docker DNS is case-
+    insensitive but docker inspect is case-sensitive.
+
     Args:
-        instance_name: The service name in compose
+        instance_name: The expected container name.
 
     Returns:
-        Container ID or None if not found
+        Container ID or None if not found.
     """
+    expected = instance_name.lower()
+
+    # Fast path: exact match via docker inspect
     result = subprocess.run(
-        ["docker", "ps", "-q", "--filter", f"name={instance_name}"],
+        ["docker", "inspect", "-f", "{{.Id}}", expected],
         capture_output=True,
         text=True,
     )
-
     if result.returncode == 0 and result.stdout.strip():
-        return result.stdout.strip().split("\n")[0]
+        return result.stdout.strip()
+
+    # Fallback: list all containers and do case-insensitive exact match
+    ps_result = subprocess.run(
+        ["docker", "ps", "-a", "--format", "{{.Names}}\t{{.ID}}"],
+        capture_output=True,
+        text=True,
+    )
+    if ps_result.returncode == 0:
+        for line in ps_result.stdout.strip().splitlines():
+            parts = line.split("\t")
+            if len(parts) == 2:
+                name, cid = parts
+                if name.lower() == expected:
+                    return cid
     return None
 
 
 def get_container_name(instance_name: str) -> str | None:
     """Get the full container name for a compose service.
 
+    Uses exact name matching via docker inspect to avoid substring collisions.
+
     Args:
-        instance_name: The service name in compose
+        instance_name: The exact container name (case-insensitive for Docker).
 
     Returns:
-        Container name or None if not found
+        Container name or None if not found.
     """
     result = subprocess.run(
-        ["docker", "ps", "--format", "{{.Names}}", "--filter", f"name={instance_name}"],
+        ["docker", "inspect", "-f", "{{.Name}}", instance_name.lower()],
         capture_output=True,
         text=True,
     )
-
     if result.returncode == 0 and result.stdout.strip():
-        return result.stdout.strip().split("\n")[0]
+        return result.stdout.strip().lstrip("/")
     return None
 
 
-def connect_container_to_network(container_name: str, network_name: str = "backend") -> bool:
+def get_backend_network_name() -> str:
+    """Auto-detect the actual Docker network name for the backend network.
+
+    Docker Compose prefixes network names with the project directory name
+    (e.g. 'headquarter_backend' instead of 'backend'). We inspect the API
+    container itself to find the real network name it's connected to.
+
+    Returns:
+        The actual Docker network name, or 'backend' as fallback.
+    """
+    # Try to find the API container by its known name
+    api_container = "hq-api"
+    result = subprocess.run(
+        [
+            "docker",
+            "inspect",
+            "-f",
+            "{{range $k, $v := .NetworkSettings.Networks}}{{$k}} {{end}}",
+            api_container,
+        ],
+        capture_output=True,
+        text=True,
+    )
+    if result.returncode == 0 and result.stdout.strip():
+        networks = result.stdout.strip().split()
+        for net in networks:
+            if "backend" in net.lower():
+                return net
+        # API container is on some network — return the first one
+        return networks[0]
+    return "backend"
+
+
+def connect_container_to_network(
+    container_name: str, network_name: str | None = None
+) -> bool:
     """Connect a Docker container to an existing network.
 
     Args:
         container_name: Name or ID of the container
-        network_name: Name of the Docker network (default: backend)
+        network_name: Name of the Docker network. If None, auto-detects
+            from the API container's own network membership.
 
     Returns:
         True if successful, False otherwise
     """
+    if network_name is None:
+        network_name = get_backend_network_name()
     result = subprocess.run(
         ["docker", "network", "connect", network_name, container_name],
         capture_output=True,
@@ -62,24 +126,153 @@ def connect_container_to_network(container_name: str, network_name: str = "backe
     return result.returncode == 0
 
 
-def get_container_status(container_id: str) -> str:
+def get_container_ip_on_network(
+    container_id: str, network_name: str | None = None
+) -> str | None:
+    """Get a container's IP address on a specific Docker network.
+
+    Args:
+        container_id: Docker container ID or name.
+        network_name: Network name. If None, auto-detects from the API container.
+
+    Returns:
+        IP address string, or None if the container is not on that network.
+    """
+    if network_name is None:
+        network_name = get_backend_network_name()
+    result = subprocess.run(
+        [
+            "docker",
+            "inspect",
+            "-f",
+            f"{{{{.NetworkSettings.Networks.{network_name}.IPAddress}}}}",
+            container_id,
+        ],
+        capture_output=True,
+        text=True,
+    )
+    if result.returncode == 0:
+        ip = result.stdout.strip()
+        if ip and ip != "<no value>":
+            return ip
+    return None
+
+
+def is_container_on_network(container_id: str, network_name: str | None = None) -> bool:
+    """Check whether a container is already attached to a Docker network.
+
+    Args:
+        container_id: Docker container ID or name.
+        network_name: Network name. If None, auto-detects from the API container.
+
+    Returns:
+        True if the container is on the network.
+    """
+    if network_name is None:
+        network_name = get_backend_network_name()
+    result = subprocess.run(
+        [
+            "docker",
+            "inspect",
+            "-f",
+            f"{{{{.NetworkSettings.Networks.{network_name}}}}}",
+            container_id,
+        ],
+        capture_output=True,
+        text=True,
+    )
+    return result.returncode == 0 and "<no value>" not in result.stdout
+
+
+def get_container_status(container_id: str) -> dict[str, Any]:
     """Get the status of a Docker container.
 
     Args:
         container_id: Docker container ID
 
     Returns:
-        Container status string (running, exited, etc.)
+        Dict with 'status' (running, exited, restarting, not_found),
+        'exit_code' (int or None), and 'health' (health status or None)
     """
     result = subprocess.run(
-        ["docker", "inspect", "-f", "{{.State.Status}}", container_id],
+        [
+            "docker",
+            "inspect",
+            "-f",
+            "{{.State.Status}}|{{.State.ExitCode}}|{{if .State.Health}}{{.State.Health.Status}}{{else}}none{{end}}",
+            container_id,
+        ],
         capture_output=True,
         text=True,
     )
 
-    if result.returncode == 0:
-        return result.stdout.strip()
-    return "unknown"
+    if result.returncode != 0:
+        return {"status": "not_found", "exit_code": None, "health": None}
+
+    parts = result.stdout.strip().split("|")
+    status = parts[0] if parts else "unknown"
+    exit_code = int(parts[1]) if len(parts) > 1 and parts[1].isdigit() else None
+    health = parts[2] if len(parts) > 2 and parts[2] != "none" else None
+
+    return {"status": status, "exit_code": exit_code, "health": health}
+
+
+def wait_for_container_running(
+    container_id: str, timeout: int = 30, interval: float = 2.0
+) -> dict[str, Any]:
+    """Wait for a container to reach the running state.
+
+    Polls docker inspect until the container status is "running" or timeout.
+
+    Args:
+        container_id: Docker container ID
+        timeout: Maximum seconds to wait
+        interval: Seconds between polls
+
+    Returns:
+        Dict with 'success' (bool), 'status' (str), 'exit_code' (int or None),
+        and 'waited_seconds' (float)
+    """
+
+    start_time = time.time()
+
+    while time.time() - start_time < timeout:
+        info = get_container_status(container_id)
+
+        if info["status"] == "running":
+            return {
+                "success": True,
+                "status": "running",
+                "exit_code": None,
+                "waited_seconds": time.time() - start_time,
+            }
+
+        if info["status"] == "exited":
+            return {
+                "success": False,
+                "status": "exited",
+                "exit_code": info["exit_code"],
+                "waited_seconds": time.time() - start_time,
+            }
+
+        if info["status"] == "not_found":
+            return {
+                "success": False,
+                "status": "not_found",
+                "exit_code": None,
+                "waited_seconds": time.time() - start_time,
+            }
+
+        time.sleep(interval)
+
+    # Timeout reached
+    info = get_container_status(container_id)
+    return {
+        "success": False,
+        "status": info["status"],
+        "exit_code": info["exit_code"],
+        "waited_seconds": time.time() - start_time,
+    }
 
 
 def get_container_logs(container_id: str, tail: int = 100) -> str:
@@ -113,6 +306,8 @@ def find_free_port(start: int = 10000, end: int = 20000) -> int:
     Returns:
         Free port number
     """
+    import socket
+
     for port in range(start, end):
         with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
             if s.connect_ex(("localhost", port)) != 0:

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

@@ -1,146 +1,281 @@
-"""Cloudflare tunnel management for Docker instances."""
+"""Cloudflare tunnel management using cloudflared Docker containers.
+
+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
+(e.g. http://code-server-headquarter-34837cd3:8443).
+"""
 
 import logging
-import os
 import re
-import signal
 import subprocess
-import time
 from typing import Any
 
+from src.services.docker.container import get_backend_network_name
+
 logger = logging.getLogger(__name__)
 
+TUNNEL_IMAGE = "cloudflare/cloudflared:latest"
 
-def start_cloudflared_tunnel(
-    container_name: str, port: int, timeout: int = 30
-) -> dict[str, str]:
-    """Start a temporary Cloudflare tunnel for a container.
 
-    Uses 'cloudflared tunnel --url' to create a temporary tunnel
-    with a random trycloudflare.com URL.
+def _tunnel_container_name(instance_name: str) -> str:
+    return f"tunnel-{instance_name.lower()}"
 
-    Args:
-        container_name: Name of the Docker container to tunnel to
-        port: Port number the container listens on
-        timeout: Maximum seconds to wait for tunnel URL
 
-    Returns:
-        Dict with 'url' (the public tunnel URL) and 'pid' (process ID)
-    """
-    import select as sel
-
-    # First verify the container is accessible
-    logger.info("Checking connectivity to %s:%d...", container_name, port)
-    for attempt in range(10):
-        check = subprocess.run(
-            ["curl", "-s", "-o", "/dev/null", "-w", "%{http_code}",
-             f"http://{container_name}:{port}"],
+def _ensure_image() -> None:
+    """Pull cloudflared image if not already present."""
+    result = subprocess.run(
+        ["docker", "images", "-q", TUNNEL_IMAGE],
+        capture_output=True,
+        text=True,
+    )
+    if not result.stdout.strip():
+        logger.info("Pulling %s ...", TUNNEL_IMAGE)
+        pull = subprocess.run(
+            ["docker", "pull", TUNNEL_IMAGE],
             capture_output=True,
             text=True,
-            timeout=5,
         )
-        logger.info("Connectivity check %d: http_code=%s", attempt + 1, check.stdout.strip())
-        if check.returncode == 0:
-            break
-        time.sleep(1)
-    else:
-        logger.warning("Container %s:%d not responding to curl checks", container_name, port)
+        if pull.returncode != 0:
+            logger.warning("Failed to pull %s: %s", TUNNEL_IMAGE, pull.stderr)
 
-    # Run cloudflared in background, capture output
-    logger.info("Starting cloudflared tunnel to http://%s:%d", container_name, port)
-    proc = subprocess.Popen(
-        ["cloudflared", "tunnel", "--url", f"http://{container_name}:{port}"],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
+
+def _cleanup_stale_tunnel(tunnel_name: str) -> None:
+    """Remove any existing tunnel container with this name."""
+    subprocess.run(
+        ["docker", "stop", "-t", "3", tunnel_name],
+        capture_output=True,
+        text=True,
+    )
+    subprocess.run(
+        ["docker", "rm", "-f", tunnel_name],
+        capture_output=True,
         text=True,
     )
 
-    # Wait for the URL to appear in output
-    url_pattern = re.compile(r"https://[a-z0-9-]+\.trycloudflare\.com")
-    start_time = time.time()
-    url = None
 
-    while time.time() - start_time < timeout:
-        # Read available output
-        readable, _, _ = sel.select([proc.stdout], [], [], 1.0)
-        if readable:
-            line = proc.stdout.readline()
-            if line:
-                match = url_pattern.search(line)
-                if match:
-                    url = match.group(0)
-                    break
-
-    if not url:
-        proc.terminate()
-        proc.wait(timeout=5)
-        raise RuntimeError(
-            f"Failed to get tunnel URL within {timeout}s. "
-            f"cloudflared output may contain errors."
-        )
-
-    return {"url": url, "pid": str(proc.pid)}
+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],
+        capture_output=True,
+        text=True,
+    )
+    return result.stdout, result.stderr
 
 
-def stop_cloudflared_tunnel(pid: str) -> None:
-    """Stop a cloudflared tunnel process.
+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],
+        capture_output=True,
+        text=True,
+    )
+    if result.returncode == 0:
+        try:
+            return int(result.stdout.strip())
+        except ValueError:
+            pass
+    return None
+
+
+def start_tunnel(
+    instance_name: str,
+    container_port: int,
+    timeout: int = 30,
+    target_url: str | None = None,
+) -> dict[str, str]:
+    """Start a temporary Cloudflare tunnel for an instance.
 
     Args:
-        pid: Process ID of the cloudflared tunnel
+        instance_name: The tool instance name (used for tunnel naming).
+        container_port: The port the tool container listens on internally.
+        timeout: Seconds to wait for the tunnel URL.
+        target_url: Optional explicit URL to proxy to. If omitted, derives
+            http://{instance_name.lower()}:{container_port}.
+
+    Returns:
+        Dict with 'url' and 'container_name'.
     """
-    try:
-        os.kill(int(pid), signal.SIGTERM)
-    except ProcessLookupError:
-        pass  # Already stopped
+    _ensure_image()
+
+    tunnel_name = _tunnel_container_name(instance_name)
+    _cleanup_stale_tunnel(tunnel_name)
+
+    # Target the tool container by name on the backend network
+    if target_url is None:
+        target_url = f"http://{instance_name.lower()}:{container_port}"
+
+    cmd = [
+        "docker",
+        "run",
+        "-d",
+        "--network",
+        get_backend_network_name(),
+        "--name",
+        tunnel_name,
+        TUNNEL_IMAGE,
+        "tunnel",
+        "--no-autoupdate",
+        "--url",
+        target_url,
+    ]
+
+    logger.debug("Running: %s", " ".join(cmd))
+    proc = subprocess.run(cmd, capture_output=True, text=True)
+    if proc.returncode != 0:
+        raise RuntimeError(
+            f"Failed to start tunnel container {tunnel_name}: {proc.stderr}"
+        )
+
+    container_id = proc.stdout.strip()
+    logger.debug("Tunnel container started: %s", container_id)
+
+    # Wait for URL to appear in logs
+    # 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_tunnel_logs(tunnel_name)
+        combined_logs = stdout + "\n" + stderr
+
+        match = url_pattern.search(combined_logs)
+        if match:
+            url = match.group(0)
+            break
+
+        # Check if container exited early
+        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(
+                f"Tunnel container {tunnel_name} exited with code {exit_code}. "
+                f"Logs:\n{combined_logs[-3000:]}"
+            )
+
+        __import__("time").sleep(0.5)
+
+    if not url:
+        stdout, stderr = _get_tunnel_logs(tunnel_name)
+        combined_logs = stdout + "\n" + stderr
+        exit_code = _get_tunnel_exit_code(tunnel_name)
+
+        _cleanup_stale_tunnel(tunnel_name)
+        raise RuntimeError(
+            f"Tunnel {tunnel_name} did not produce a URL within {timeout}s. "
+            f"Exit code: {exit_code}. Logs:\n{combined_logs[-3000:]}"
+        )
+
+    # Wait a moment for Cloudflare DNS edge to propagate the new tunnel subdomain
+    __import__("time").sleep(2)
+
+    logger.info(
+        "Tunnel %s started for %s → %s (%s)",
+        tunnel_name,
+        instance_name,
+        target_url,
+        url,
+    )
+    return {"url": url, "container_name": tunnel_name}
+
+
+def stop_tunnel(instance_name: str) -> None:
+    """Stop and remove the tunnel container for an instance."""
+    tunnel_name = _tunnel_container_name(instance_name)
+    _cleanup_stale_tunnel(tunnel_name)
+    logger.debug("Stopped and removed tunnel container %s", tunnel_name)
 
 
 def recreate_tunnel(
-    container_name: str, port: int, old_pid: str | None = None
+    instance_name: str, container_port: int, target_url: str | None = None
 ) -> dict[str, str]:
-    """Recreate a temporary Cloudflare tunnel.
-
-    Stops the old tunnel (if pid provided) and starts a new one.
+    """Recreate a tunnel for an instance.
 
     Args:
-        container_name: Name of the Docker container to tunnel to
-        port: Port number the container listens on
-        old_pid: Optional PID of the old tunnel process to stop
-
-    Returns:
-        Dict with 'url' and 'pid' for the new tunnel
+        instance_name: The tool instance name.
+        container_port: The port the tool container listens on internally.
+        target_url: Optional explicit origin URL. If omitted, derives
+            http://{instance_name.lower()}:{container_port}.
     """
-    if old_pid:
-        stop_cloudflared_tunnel(old_pid)
-
-    return start_cloudflared_tunnel(container_name, port)
+    stop_tunnel(instance_name)
+    return start_tunnel(instance_name, container_port, target_url=target_url)
 
 
 def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
     """Check if a tunnel URL is healthy.
 
-    Args:
-        url: The tunnel URL to check
-        timeout: Request timeout in seconds
-
     Returns:
-        Dict with 'healthy' (bool) and 'status_code' (int or None)
+        Dict with 'tunnel_status', 'status_code', 'healthy', 'error'.
     """
     try:
         result = subprocess.run(
-            ["curl", "-s", "-o", "/dev/null", "-w", "%{http_code}",
-             "--max-time", str(timeout), url],
+            [
+                "curl",
+                "-s",
+                "-o",
+                "/dev/null",
+                "-w",
+                "%{http_code}",
+                "--max-time",
+                str(timeout),
+                url,
+            ],
             capture_output=True,
             text=True,
             timeout=timeout + 5,
         )
         status_code = int(result.stdout.strip())
+
+        if 200 <= status_code < 400:
+            return {
+                "tunnel_status": "healthy",
+                "status_code": status_code,
+                "healthy": True,
+                "error": None,
+            }
+        if status_code in (502, 503, 504):
+            return {
+                "tunnel_status": "error_response",
+                "status_code": status_code,
+                "healthy": False,
+                "error": f"Application returned HTTP {status_code}",
+            }
         return {
-            "healthy": 200 <= status_code < 400,
+            "tunnel_status": "error_response",
             "status_code": status_code,
-        }
-    except (ValueError, subprocess.TimeoutExpired, Exception) as e:
-        return {
             "healthy": False,
-            "status_code": None,
-            "error": str(e),
+            "error": f"HTTP {status_code}",
+        }
+    except subprocess.TimeoutExpired:
+        return {
+            "tunnel_status": "unreachable",
+            "status_code": None,
+            "healthy": False,
+            "error": "Tunnel request timed out",
+        }
+    except (ValueError, Exception) as exc:
+        error_str = str(exc).lower()
+        if any(
+            err in error_str
+            for err in [
+                "connection refused",
+                "econnrefused",
+                "could not resolve",
+                "nodename",
+            ]
+        ):
+            return {
+                "tunnel_status": "unreachable",
+                "status_code": None,
+                "healthy": False,
+                "error": f"Tunnel unreachable: {exc}",
+            }
+        return {
+            "tunnel_status": "unreachable",
+            "status_code": None,
+            "healthy": False,
+            "error": str(exc),
         }

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

@@ -1 +1,19 @@
-"""Git services package."""
+"""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/control.py

@@ -1,196 +0,0 @@
-"""Git control operations with repo validation."""
-
-import logging
-import os
-import uuid
-
-from fastapi import HTTPException, status
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.git_repository import GitRepository
-from src.models.user import User
-from src.schemas.git_repository import (
-    BranchCreateRequest,
-    CheckoutRequest,
-    CommitRequest,
-    FetchResponse,
-    MergeRequest,
-    MergeResponse,
-    PullResponse,
-    PushResponse,
-    StatusResponse,
-)
-from src.services.git.repository import ensure_repo_on_disk, get_repo_and_validate
-from src.utils.git_control import (
-    checkout_branch,
-    commit_changes,
-    create_branch,
-    delete_branch,
-    fetch,
-    get_status,
-    merge,
-    pull,
-    push,
-)
-
-logger = logging.getLogger(__name__)
-
-
-async def get_status_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-) -> StatusResponse:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        result = get_status(repo.path)
-        return StatusResponse(
-            branch=result.branch,
-            modified=result.modified,
-            added=result.added,
-            deleted=result.deleted,
-            untracked=result.untracked,
-            renamed=result.renamed,
-            ahead=result.ahead,
-            behind=result.behind,
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def create_branch_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: BranchCreateRequest,
-) -> dict:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        create_branch(repo.path, data.name, data.base_branch)
-        return {"message": f"Branch '{data.name}' created", "branch": data.name}
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def delete_branch_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch_name: str,
-    force: bool = False,
-) -> dict:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        delete_branch(repo.path, branch_name, force)
-        return {"message": f"Branch '{branch_name}' deleted"}
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def checkout_branch_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CheckoutRequest,
-) -> dict:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        checkout_branch(repo.path, data.branch)
-        return {"message": f"Checked out branch '{data.branch}'", "branch": data.branch}
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def commit_changes_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CommitRequest,
-    user: User,
-) -> dict:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    author_name = user.name or "Unknown"
-    author_email = user.email or "unknown@example.com"
-    try:
-        commit_hash = commit_changes(
-            repo_path=repo.path,
-            message=data.message,
-            author_name=author_name,
-            author_email=author_email,
-            files=data.files,
-        )
-        return {"commit_hash": commit_hash, "message": data.message}
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def fetch_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-) -> FetchResponse:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        fetch(repo.path)
-        return FetchResponse(message="Fetched from remote")
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def pull_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str | None = None,
-) -> PullResponse:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        pull(repo.path, branch)
-        return PullResponse(message="Pulled from remote")
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def push_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str | None = None,
-) -> PushResponse:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        push(repo.path, branch)
-        return PushResponse(message="Pushed to remote")
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def merge_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: MergeRequest,
-) -> MergeResponse:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        commit_hash = merge(
-            repo_path=repo.path,
-            source_branch=data.source_branch,
-            target_branch=data.target_branch,
-            message=data.message,
-        )
-        return MergeResponse(
-            commit_hash=commit_hash,
-            message=data.message or f"Merge {data.source_branch}",
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))

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

@@ -1,150 +0,0 @@
-"""Git file operations with repo validation."""
-
-import logging
-import uuid
-
-from fastapi import HTTPException, status
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.git_repository import GitRepository
-from src.models.user import User
-from src.schemas.git_repository import (
-    FileContentResponse,
-    FileListResponse,
-    FileUpdateRequest,
-    FileUpdateResponse,
-)
-from src.services.git.repository import ensure_repo_on_disk, get_repo_and_validate
-from src.utils.git_files import (
-    commit_file,
-    get_file_content,
-    list_branches,
-    list_tree,
-)
-
-logger = logging.getLogger(__name__)
-
-
-async def list_files(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str = "main",
-    path: str = "",
-) -> FileListResponse:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        entries = list_tree(repo.path, branch=branch, path=path)
-        return FileListResponse(
-            path=path,
-            branch=branch,
-            entries=[
-                {
-                    "name": e.name,
-                    "type": e.type,
-                    "path": e.path,
-                    "size": e.size,
-                    "mode": e.mode,
-                    "last_commit": e.last_commit,
-                }
-                for e in entries
-            ],
-        )
-    except RuntimeError as e:
-        logger.error(
-            "Failed to list files for repo %s (path=%s, branch=%s): %s",
-            repo_id,
-            path,
-            branch,
-            str(e),
-            exc_info=True,
-        )
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def get_file(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str,
-    path: str,
-) -> FileContentResponse:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        file_content = get_file_content(repo.path, branch=branch, path=path)
-        return FileContentResponse(
-            path=file_content.path,
-            branch=file_content.branch,
-            content=file_content.content,
-            size=file_content.size,
-            encoding=file_content.encoding,
-            language=file_content.language,
-            is_binary=file_content.is_binary,
-            last_commit=file_content.last_commit,
-        )
-    except FileNotFoundError:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="file not found")
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def update_file(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: FileUpdateRequest,
-    user: User,
-) -> FileUpdateResponse:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    author_name = user.name or "Unknown"
-    author_email = user.email or "unknown@example.com"
-    try:
-        commit_hash = commit_file(
-            repo_path=repo.path,
-            branch=data.branch,
-            path=data.path,
-            content=data.content,
-            commit_message=data.commit_message,
-            author_name=author_name,
-            author_email=author_email,
-        )
-        return FileUpdateResponse(
-            commit_hash=commit_hash,
-            message=data.commit_message,
-            branch=data.branch,
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-async def list_branches_with_validation(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-) -> dict:
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        branches, default_branch = list_branches(repo.path)
-        return {
-            "branches": [
-                {
-                    "name": b.name,
-                    "is_default": b.is_default,
-                    "last_commit": b.last_commit,
-                }
-                for b in branches
-            ],
-            "default_branch": default_branch,
-        }
-    except RuntimeError as e:
-        logger.error(
-            "Failed to list branches for repo %s: %s",
-            repo_id,
-            str(e),
-            exc_info=True,
-        )
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))

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/git/repository.py

@@ -1,211 +0,0 @@
-"""Repository lifecycle and path helpers."""
-
-import logging
-import os
-import shutil
-import subprocess
-import uuid
-
-from fastapi import HTTPException, status
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.config import Settings
-from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.user import User
-from src.schemas.git_repository import GitRepositoryCreate
-from src.utils.git_url_parser import parse_git_url
-
-logger = logging.getLogger(__name__)
-
-
-def _get_repo_path(user_id: uuid.UUID, project_id: uuid.UUID, name: str) -> str:
-    """Generate the filesystem path for a repository."""
-    base = Settings().repo_base_path or "/data/repos"
-    return os.path.join(base, str(user_id), str(project_id), f"{name}.git")
-
-
-def _build_provider_clone_url(owner: str, repo: str) -> str:
-    """Build the SSH clone URL for the fixed git provider."""
-    return f"git@git.commumedia.org:{owner}/{repo}.git"
-
-
-def _preflight_remote_repository(remote_url: str) -> None:
-    """Verify a remote repository is reachable before cloning."""
-    try:
-        result = subprocess.run(
-            ["git", "ls-remote", remote_url],
-            capture_output=True,
-            text=True,
-            timeout=60,
-        )
-    except subprocess.TimeoutExpired:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="remote repository check timed out")
-    except FileNotFoundError:
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
-
-    if result.returncode != 0:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="repository not found or inaccessible",
-        )
-
-
-def _clone_working_repository(remote_url: str, repo_path: str) -> None:
-    try:
-        result = subprocess.run(
-            ["git", "clone", remote_url, repo_path],
-            capture_output=True,
-            text=True,
-            timeout=300,
-        )
-    except subprocess.TimeoutExpired:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="clone operation timed out")
-    except FileNotFoundError:
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
-
-    if result.returncode != 0:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"failed to clone repository: {result.stderr}",
-        )
-
-
-def _init_working_repository(repo_path: str) -> None:
-    try:
-        result = subprocess.run(
-            ["git", "init", "-b", "main", repo_path],
-            capture_output=True,
-            text=True,
-        )
-    except FileNotFoundError:
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
-
-    if result.returncode == 0:
-        return
-
-    fallback = subprocess.run(
-        ["git", "init", repo_path],
-        capture_output=True,
-        text=True,
-    )
-    if fallback.returncode != 0:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"failed to initialize repository: {fallback.stderr}",
-        )
-
-    ref_result = subprocess.run(
-        ["git", "-C", repo_path, "symbolic-ref", "HEAD", "refs/heads/main"],
-        capture_output=True,
-        text=True,
-    )
-    if ref_result.returncode != 0:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"failed to set initial branch: {ref_result.stderr}",
-        )
-
-
-async def get_repo_and_validate(
-    session: AsyncSession,
-    repo_id: uuid.UUID,
-    project_id: uuid.UUID,
-) -> GitRepository:
-    """Fetch a repository and validate ownership + disk presence."""
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-    return repo
-
-
-def ensure_repo_on_disk(repo: GitRepository) -> None:
-    """Raise 404 if the repository is not present on disk."""
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-
-async def create_repository(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-    data: GitRepositoryCreate,
-    user: User,
-) -> GitRepository:
-    """Create a new git repository (clone or init)."""
-    # Check for duplicate name
-    existing = await session.execute(
-        select(GitRepository).where(
-            GitRepository.project_id == project_id,
-            GitRepository.name == data.name,
-        )
-    )
-    if existing.scalar_one_or_none():
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="repository name already exists")
-
-    # Validate and potentially correct the URL
-    remote_url = data.remote_url
-    if remote_url and not data.force_original_url:
-        parse_result = parse_git_url(remote_url)
-        if parse_result["needs_parsing"] and parse_result["base_url"]:
-            raise HTTPException(
-                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                detail={
-                    "message": "The provided URL appears to be a browser URL, not a git clone URL",
-                    "suggested_url": parse_result["base_url"],
-                    "original_url": remote_url,
-                    "error_code": "URL_NEEDS_PARSING",
-                },
-            )
-        if parse_result["base_url"]:
-            remote_url = parse_result["base_url"]
-
-    if remote_url:
-        _preflight_remote_repository(remote_url)
-
-    repo_path = _get_repo_path(user.id, project_id, data.name)
-    os.makedirs(os.path.dirname(repo_path), exist_ok=True)
-
-    if remote_url:
-        _clone_working_repository(remote_url, repo_path)
-    else:
-        _init_working_repository(repo_path)
-
-    repo = GitRepository(
-        name=data.name,
-        path=repo_path,
-        project_id=project_id,
-        owner_id=user.id,
-        is_mirror=False,
-        remote_url=remote_url,
-    )
-    session.add(repo)
-    await session.commit()
-    await session.refresh(repo)
-    return repo
-
-
-async def delete_repository(
-    session: AsyncSession,
-    repo_id: uuid.UUID,
-    project_id: uuid.UUID,
-) -> None:
-    """Delete a repository from DB and disk."""
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-
-    if os.path.exists(repo.path):
-        shutil.rmtree(repo.path)
-
-    await session.delete(repo)
-    await session.commit()
-
-
-async def list_repositories(
-    session: AsyncSession,
-    project_id: uuid.UUID,
-) -> list[GitRepository]:
-    """List all repositories in a project."""
-    result = await session.execute(
-        select(GitRepository).where(GitRepository.project_id == project_id)
-    )
-    return list(result.scalars().all())