feat: legacy fallback tests and docs (PR 3)

- Add test_tool_instances_legacy.py with 8 unit tests:
  - dockerfile definition type builds from template
  - dockerfile build failure raises HTTP 500
  - compose definition type renders template
  - manifest compiler is NOT called for legacy types
  - start_instance legacy/compose/dockerfile types all skip manifest flow
  - start_instance manifest type correctly invokes compiler
- Mark T3.2 and T3.3 tasks complete in OpenSpec
- Add openspec/docs/tool-workshop-guide.md with user guide covering
  definition types, manifest creation workflow, base definitions,
  migration path, and permissions

apps/api/tests/unit/test_tool_instances_legacy.py

@@ -0,0 +1,804 @@
+"""Unit tests for legacy tool instance fallback paths.
+
+Verifies that tool types with definition_type "dockerfile", "compose",
+and "legacy" continue to use the original startup flow after the
+manifest-based flow was introduced.
+"""
+
+import os
+import uuid
+from datetime import datetime
+from unittest.mock import AsyncMock, MagicMock, patch
+
+import pytest
+
+from src.api.tool_instances import create_instance, start_instance
+from src.models.git_repository import GitRepository
+from src.models.tool_instance import ToolInstance
+from src.models.tool_type import ToolType
+from src.models.ssh_key import SSHKey
+from src.models.user import User
+
+
+@pytest.fixture
+def fake_user_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def fake_project_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def fake_repo_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def fake_tool_type_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def fake_instance_id() -> uuid.UUID:
+    return uuid.uuid4()
+
+
+@pytest.fixture
+def mock_session(fake_user_id, fake_project_id, fake_repo_id, fake_tool_type_id):
+    """Return an async SQLAlchemy session with basic mocks."""
+    session = AsyncMock()
+
+    user = User(id=fake_user_id, email="test@example.com")
+    project = MagicMock()
+    project.id = fake_project_id
+    repo = GitRepository(
+        id=fake_repo_id,
+        project_id=fake_project_id,
+        name="test-repo",
+        path="/data/repos/test-repo",
+        remote_url=None,
+        ssh_key_id=None,
+    )
+
+    async def _get(model, pk):
+        if model is User and pk == fake_user_id:
+            return user
+        if model is GitRepository and pk == fake_repo_id:
+            return repo
+        return None
+
+    def _add(instance):
+        if getattr(instance, "created_at", None) is None:
+            instance.created_at = datetime.now()
+        if getattr(instance, "updated_at", None) is None:
+            instance.updated_at = datetime.now()
+
+    session.get.side_effect = _get
+    session.add = MagicMock(side_effect=_add)
+    session.execute.return_value = MagicMock(scalars=MagicMock(return_value=MagicMock(all=MagicMock(return_value=[]))))
+    return session
+
+
+class TestCreateInstanceDockerfileLegacy:
+    """Legacy dockerfile definition type in create_instance."""
+
+    @patch("src.api.tool_instances.ensure_instance_directory")
+    @patch("src.api.tool_instances.find_free_port")
+    @patch("src.api.tool_instances.build_image")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_builds_from_dockerfile_template(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_write_compose,
+        mock_build_image,
+        mock_find_port,
+        mock_ensure_dir,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'dockerfile', build_image is called with the template."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_find_port.return_value = 12345
+        mock_ensure_dir.return_value = "/data/instances/test-instance"
+        mock_build_image.return_value = (0, "built", "")
+
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-df-tool",
+            display_name="Legacy DF Tool",
+            default_port=8080,
+            definition_type="dockerfile",
+            dockerfile_template="FROM python:3.11\nRUN echo hi",
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        data = MagicMock()
+        data.tool_type_id = str(fake_tool_type_id)
+        data.display_name = None
+        data.clone_mode = "mount"
+        data.branch = None
+        data.new_branch = None
+        data.config_profile_id = None
+
+        result = await create_instance(
+            project_id=fake_project_id,
+            repo_id=fake_repo_id,
+            data=data,
+            user_id=fake_user_id,
+            session=mock_session,
+        )
+
+        assert result["status"] == "pending"
+        mock_build_image.assert_called_once()
+        call_kwargs = mock_build_image.call_args.kwargs
+        assert call_kwargs["dockerfile"] == "FROM python:3.11\nRUN echo hi"
+        mock_write_compose.assert_called_once()
+
+    @patch("src.api.tool_instances.ensure_instance_directory")
+    @patch("src.api.tool_instances.find_free_port")
+    @patch("src.api.tool_instances.build_image")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_dockerfile_build_failure_raises_500(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_write_compose,
+        mock_build_image,
+        mock_find_port,
+        mock_ensure_dir,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_tool_type_id,
+    ) -> None:
+        """Failed dockerfile build should raise HTTP 500."""
+        from fastapi import HTTPException
+
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_find_port.return_value = 12345
+        mock_ensure_dir.return_value = "/data/instances/test-instance"
+        mock_build_image.return_value = (1, "", "build failed")
+
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-df-tool",
+            display_name="Legacy DF Tool",
+            default_port=8080,
+            definition_type="dockerfile",
+            dockerfile_template="FROM invalid",
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        data = MagicMock()
+        data.tool_type_id = str(fake_tool_type_id)
+        data.display_name = None
+        data.clone_mode = "mount"
+        data.branch = None
+        data.new_branch = None
+        data.config_profile_id = None
+
+        with pytest.raises(HTTPException) as exc_info:
+            await create_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                data=data,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert exc_info.value.status_code == 500
+        assert "Failed to build Docker image" in exc_info.value.detail
+
+
+class TestCreateInstanceComposeLegacy:
+    """Legacy compose definition type in create_instance."""
+
+    @patch("src.api.tool_instances.ensure_instance_directory")
+    @patch("src.api.tool_instances.find_free_port")
+    @patch("src.api.tool_instances.render_compose_template")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_renders_compose_template(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_write_compose,
+        mock_render_compose,
+        mock_find_port,
+        mock_ensure_dir,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'compose', render_compose_template is called."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_find_port.return_value = 12345
+        mock_ensure_dir.return_value = "/data/instances/test-instance"
+        mock_render_compose.return_value = "services:\n  app:\n    image: nginx"
+
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-compose-tool",
+            display_name="Legacy Compose Tool",
+            default_port=80,
+            definition_type="compose",
+            dockerfile_template=None,
+            compose_template="services:\n  app:\n    image: nginx\n    ports:\n      - ${TOOL_PORT}:80",
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        data = MagicMock()
+        data.tool_type_id = str(fake_tool_type_id)
+        data.display_name = None
+        data.clone_mode = "mount"
+        data.branch = None
+        data.new_branch = None
+        data.config_profile_id = None
+
+        result = await create_instance(
+            project_id=fake_project_id,
+            repo_id=fake_repo_id,
+            data=data,
+            user_id=fake_user_id,
+            session=mock_session,
+        )
+
+        assert result["status"] == "pending"
+        mock_render_compose.assert_called_once()
+        args = mock_render_compose.call_args[0]
+        assert "services:" in args[0]
+        mock_write_compose.assert_called_once()
+
+
+class TestCreateInstanceManifestNotCalledForLegacy:
+    """Ensure manifest compiler is never invoked for legacy types."""
+
+    @patch("src.api.tool_instances.ensure_instance_directory")
+    @patch("src.api.tool_instances.find_free_port")
+    @patch("src.api.tool_instances.build_image")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_dockerfile_does_not_call_manifest_compiler(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_prepare_manifest,
+        mock_write_compose,
+        mock_build_image,
+        mock_find_port,
+        mock_ensure_dir,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_tool_type_id,
+    ) -> None:
+        """Legacy dockerfile type must not trigger manifest compilation."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_find_port.return_value = 12345
+        mock_ensure_dir.return_value = "/data/instances/test-instance"
+        mock_build_image.return_value = (0, "built", "")
+
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-df",
+            display_name="Legacy",
+            default_port=8080,
+            definition_type="dockerfile",
+            dockerfile_template="FROM alpine",
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        data = MagicMock()
+        data.tool_type_id = str(fake_tool_type_id)
+        data.display_name = None
+        data.clone_mode = "mount"
+        data.branch = None
+        data.new_branch = None
+        data.config_profile_id = None
+
+        await create_instance(
+            project_id=fake_project_id,
+            repo_id=fake_repo_id,
+            data=data,
+            user_id=fake_user_id,
+            session=mock_session,
+        )
+
+        mock_prepare_manifest.assert_not_called()
+
+
+class TestStartInstanceLegacyFallback:
+    """Legacy paths in start_instance must NOT call manifest compiler."""
+
+    @patch("src.api.tool_instances.wait_for_container_running")
+    @patch("src.api.tool_instances.execute_compose_command")
+    @patch("src.api.tool_instances.get_container_id")
+    @patch("src.api.tool_instances.get_container_name")
+    @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._sanitize_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_legacy_type_skips_manifest_flow(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_prepare_manifest,
+        mock_sanitize,
+        mock_connect_network,
+        mock_get_container_name,
+        mock_get_container_id,
+        mock_execute_compose,
+        mock_wait_container,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_instance_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'legacy', start_instance uses old flow."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_execute_compose.return_value = (0, "started", "")
+        mock_get_container_id.return_value = "abc123"
+        mock_get_container_name.return_value = "test-container"
+        mock_connect_network.return_value = True
+        mock_wait_container.return_value = {"success": True, "status": "running", "waited_seconds": 0.5}
+
+        instance = ToolInstance(
+            id=fake_instance_id,
+            name="legacy-instance",
+            repository_id=fake_repo_id,
+            tool_type_id=fake_tool_type_id,
+            compose_path="/data/instances/legacy-instance/docker-compose.yml",
+            status="stopped",
+            clone_mode="mount",
+            created_at=datetime.now(),
+            updated_at=datetime.now(),
+        )
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="legacy-tool",
+            display_name="Legacy Tool",
+            default_port=8080,
+            definition_type="legacy",
+            manifest_id=None,
+            dockerfile_template=None,
+            compose_template="services:\n  app:\n    image: nginx",
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolInstance and pk == fake_instance_id:
+                return instance
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        # Ensure compose file exists so the check passes
+        with patch("os.path.exists", return_value=True):
+            result = await start_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                instance_id=fake_instance_id,
+                data=None,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert result["status"] == "running"
+        mock_prepare_manifest.assert_not_called()
+        mock_execute_compose.assert_called_once()
+
+    @patch("src.api.tool_instances.wait_for_container_running")
+    @patch("src.api.tool_instances.execute_compose_command")
+    @patch("src.api.tool_instances.get_container_id")
+    @patch("src.api.tool_instances.get_container_name")
+    @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._sanitize_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_compose_type_skips_manifest_flow(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_prepare_manifest,
+        mock_sanitize,
+        mock_connect_network,
+        mock_get_container_name,
+        mock_get_container_id,
+        mock_execute_compose,
+        mock_wait_container,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_instance_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'compose', start_instance uses old flow."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_execute_compose.return_value = (0, "started", "")
+        mock_get_container_id.return_value = "abc123"
+        mock_get_container_name.return_value = "test-container"
+        mock_connect_network.return_value = True
+        mock_wait_container.return_value = {"success": True, "status": "running", "waited_seconds": 0.5}
+
+        instance = ToolInstance(
+            id=fake_instance_id,
+            name="compose-instance",
+            repository_id=fake_repo_id,
+            tool_type_id=fake_tool_type_id,
+            compose_path="/data/instances/compose-instance/docker-compose.yml",
+            status="stopped",
+            clone_mode="mount",
+            created_at=datetime.now(),
+            updated_at=datetime.now(),
+        )
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="compose-tool",
+            display_name="Compose Tool",
+            default_port=8080,
+            definition_type="compose",
+            manifest_id=None,
+            dockerfile_template=None,
+            compose_template="services:\n  app:\n    image: nginx",
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolInstance and pk == fake_instance_id:
+                return instance
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        with patch("os.path.exists", return_value=True):
+            result = await start_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                instance_id=fake_instance_id,
+                data=None,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert result["status"] == "running"
+        mock_prepare_manifest.assert_not_called()
+        mock_execute_compose.assert_called_once()
+
+    @patch("src.api.tool_instances.wait_for_container_running")
+    @patch("src.api.tool_instances.execute_compose_command")
+    @patch("src.api.tool_instances.get_container_id")
+    @patch("src.api.tool_instances.get_container_name")
+    @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._sanitize_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_dockerfile_type_skips_manifest_flow(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_prepare_manifest,
+        mock_sanitize,
+        mock_connect_network,
+        mock_get_container_name,
+        mock_get_container_id,
+        mock_execute_compose,
+        mock_wait_container,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_instance_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'dockerfile', start_instance uses old flow."""
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_execute_compose.return_value = (0, "started", "")
+        mock_get_container_id.return_value = "abc123"
+        mock_get_container_name.return_value = "test-container"
+        mock_connect_network.return_value = True
+        mock_wait_container.return_value = {"success": True, "status": "running", "waited_seconds": 0.5}
+
+        instance = ToolInstance(
+            id=fake_instance_id,
+            name="df-instance",
+            repository_id=fake_repo_id,
+            tool_type_id=fake_tool_type_id,
+            compose_path="/data/instances/df-instance/docker-compose.yml",
+            status="stopped",
+            clone_mode="mount",
+            created_at=datetime.now(),
+            updated_at=datetime.now(),
+        )
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="df-tool",
+            display_name="Dockerfile Tool",
+            default_port=8080,
+            definition_type="dockerfile",
+            manifest_id=None,
+            dockerfile_template="FROM alpine",
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+
+        async def _get(model, pk):
+            if model is ToolInstance and pk == fake_instance_id:
+                return instance
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            return None
+
+        mock_session.get.side_effect = _get
+
+        with patch("os.path.exists", return_value=True):
+            result = await start_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                instance_id=fake_instance_id,
+                data=None,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert result["status"] == "running"
+        mock_prepare_manifest.assert_not_called()
+        mock_execute_compose.assert_called_once()
+
+
+class TestStartInstanceManifestBranch:
+    """Manifest branch is taken ONLY when definition_type == 'manifest'."""
+
+    @patch("src.api.tool_instances.wait_for_container_running")
+    @patch("src.api.tool_instances.execute_compose_command")
+    @patch("src.api.tool_instances.get_container_id")
+    @patch("src.api.tool_instances.get_container_name")
+    @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._sanitize_compose_file")
+    @patch("src.api.tool_instances._prepare_manifest_instance")
+    @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances._get_user")
+    @patch("src.api.tool_instances._get_owned_project")
+    async def test_manifest_type_calls_compiler(
+        self,
+        mock_get_project,
+        mock_get_user,
+        mock_write_compose,
+        mock_prepare_manifest,
+        mock_sanitize,
+        mock_connect_network,
+        mock_get_container_name,
+        mock_get_container_id,
+        mock_execute_compose,
+        mock_wait_container,
+        mock_session,
+        fake_user_id,
+        fake_project_id,
+        fake_repo_id,
+        fake_instance_id,
+        fake_tool_type_id,
+    ) -> None:
+        """When definition_type is 'manifest' and manifest_id is set, compiler runs."""
+        from src.models.tool_definition_manifest import ToolDefinitionManifest
+
+        manifest_id = uuid.uuid4()
+
+        mock_get_user.return_value = AsyncMock()
+        mock_get_project.return_value = AsyncMock()
+        mock_execute_compose.return_value = (0, "started", "")
+        mock_get_container_id.return_value = "abc123"
+        mock_get_container_name.return_value = "test-container"
+        mock_connect_network.return_value = True
+        mock_wait_container.return_value = {"success": True, "status": "running", "waited_seconds": 0.5}
+        mock_prepare_manifest.return_value = (
+            "headquarter/test:latest",
+            "services:\n  app:\n    image: test",
+            {"name": "test-manifest"},
+        )
+
+        instance = ToolInstance(
+            id=fake_instance_id,
+            name="manifest-instance",
+            repository_id=fake_repo_id,
+            tool_type_id=fake_tool_type_id,
+            compose_path="/data/instances/manifest-instance/docker-compose.yml",
+            status="stopped",
+            clone_mode="mount",
+            created_at=datetime.now(),
+            updated_at=datetime.now(),
+        )
+        tool_type = ToolType(
+            id=fake_tool_type_id,
+            name="manifest-tool",
+            display_name="Manifest Tool",
+            default_port=8080,
+            definition_type="manifest",
+            manifest_id=manifest_id,
+            dockerfile_template=None,
+            compose_template=None,
+        )
+        repo = GitRepository(
+            id=fake_repo_id,
+            project_id=fake_project_id,
+            name="test-repo",
+            path="/data/repos/test-repo",
+            remote_url=None,
+            ssh_key_id=None,
+        )
+        manifest_def = ToolDefinitionManifest(
+            id=manifest_id,
+            name="test-manifest",
+            display_name="Test Manifest",
+            interface_type="web",
+            manifest={"base_image": "alpine"},
+        )
+
+        async def _get(model, pk):
+            if model is ToolInstance and pk == fake_instance_id:
+                return instance
+            if model is ToolType and pk == fake_tool_type_id:
+                return tool_type
+            if model is GitRepository and pk == fake_repo_id:
+                return repo
+            if model is User and pk == fake_user_id:
+                return User(id=fake_user_id, email="test@example.com")
+            if model is ToolDefinitionManifest and pk == manifest_id:
+                return manifest_def
+            return None
+
+        mock_session.get.side_effect = _get
+
+        with patch("os.path.exists", return_value=True):
+            result = await start_instance(
+                project_id=fake_project_id,
+                repo_id=fake_repo_id,
+                instance_id=fake_instance_id,
+                data=None,
+                user_id=fake_user_id,
+                session=mock_session,
+            )
+
+        assert result["status"] == "running"
+        mock_prepare_manifest.assert_called_once()
+        mock_execute_compose.assert_called_once()

openspec/docs/tool-workshop-guide.md

@@ -0,0 +1,81 @@
+# Tool Workshop User Guide
+
+## Overview
+
+The Tool Workshop lets you define and manage tool types — the blueprints for
+containers that run inside Headquarter. Each tool type specifies how to build
+and start a container (Docker image, Compose file, or a declarative manifest).
+
+## Definition Types
+
+### 1. Compose (Legacy)
+Write a raw Docker Compose template. Variable substitution is supported:
+- `${REPO_PATH}` — path to the mounted repository
+- `${TOOL_PORT}` — dynamically assigned free port
+- `${INSTANCE_NAME}` — generated instance name
+- `${USER_ID}`, `${PROJECT_ID}` — IDs for reference
+
+Best for: simple web services, databases, or anything that already has a
+Docker image.
+
+### 2. Dockerfile (Legacy)
+Write a raw Dockerfile. Headquarter builds the image and generates a minimal
+Compose file automatically.
+
+Best for: custom environments where you need full control over the image build.
+
+### 3. Manifest (Declarative) — **Recommended**
+Define your tool with structured JSON instead of raw Docker files:
+- **Base image** — pick a base definition (e.g. `ubuntu-24.04-dev`)
+- **Packages** — declare apt, npm global, pip, and Node.js version
+- **Scripts** — build scripts (run at image build time) and startup scripts
+  (run when container starts)
+- **Mounts** — workspace, SSH keys, instance state, git-mounted dotfiles
+- **Runtime** — command, working directory, stdin/tty settings
+- **Live preview** — see generated Dockerfile and Compose as you edit
+
+Best for: reproducible, versioned, self-documenting tool definitions.
+
+## Creating a Manifest-Based Tool
+
+1. Go to **Settings → Tool Workshop**
+2. Click **New Tool Type**
+3. Select **Manifest (Declarative)** as the definition type
+4. Choose a **Base Image** (e.g. `ubuntu-24.04-dev v1`)
+5. Add packages:
+   - Apt: `neovim`, `tmux`, `git`
+   - NPM global: `@earendil-works/pi-coding-agent`
+   - Node.js version: `20`
+6. Add build scripts (e.g. configure git defaults)
+7. Add startup scripts (e.g. fix workspace permissions)
+8. Configure mounts:
+   - Workspace → `/workspace` (writable)
+   - SSH keys → `/home/user/.ssh` (readonly, mode 0700)
+9. Set runtime: command `/bin/bash`, working dir `/workspace`
+10. Click **Preview** to verify generated Dockerfile and Compose
+11. Save
+
+## Base Definitions
+
+Base definitions are versioned manifest templates that other tools extend.
+They are marked with the **Base** badge in the list.
+
+The default base `ubuntu-24.04-dev` provides:
+- Ubuntu 24.04 base image
+- Common build tools (curl, wget, git, build-essential)
+- A non-root `user` account (uid 1000)
+
+## Migration from Legacy
+
+Existing tool types using Compose or Dockerfile continue to work unchanged.
+You can migrate a tool type to Manifest by:
+1. Editing the tool type
+2. Switching definition type to **Manifest**
+3. Re-creating the configuration in the manifest editor
+4. Saving (the old template is cleared automatically)
+
+## Permissions
+
+For manifest-based tools, mount permissions are fixed automatically after the
+container starts. The system runs `chown` and `chmod` via `docker exec` as
+root, then drops back to the configured runtime user.

openspec/tasks/tool-definition-manifest.md

@@ -80,10 +80,10 @@
 - [ ] Update existing pi-agent tool_type row
 
 ### T3.2 Legacy Fallback
-- [ ] Ensure `definition_type == "legacy"` still uses old flow
+- [x] Ensure `definition_type == "legacy"` still uses old flow
-- [ ] Ensure `dockerfile_template` / `compose_template` still work
+- [x] Ensure `dockerfile_template` / `compose_template` still work
-- [ ] Tests for legacy path
+- [x] Tests for legacy path
 
 ### T3.3 Documentation
-- [ ] Update API docs
+- [x] Update API docs
-- [ ] Add Tool Workshop user guide
+- [x] Add Tool Workshop user guide