features/steps/plan_cli_spec_alignment_steps.py

@@ -337,7 +337,7 @@ def step_plan_list_no_filters(context: Context) -> None:
     """
     import cleveragents.cli.commands.plan as _plan_mod
 
-    wide_runner = CliRunner(mix_stderr=False)
+    wide_runner = CliRunner()
     original_width = _plan_mod.console._width
     _plan_mod.console._width = 200
     try:

features/steps/project_service_steps.py

@@ -18,9 +18,8 @@ from cleveragents.core.exceptions import FileSystemError, NotFoundError, Validat
 from cleveragents.domain.models.core import (
     Plan,
     PlanStatus,
-    Project,
-    ProjectSettings,
 )
+from cleveragents.domain.models.core.project import NamespacedProject
 from cleveragents.infrastructure.database.unit_of_work import UnitOfWork
 
 
@@ -189,35 +188,22 @@ def step_check_migrated_project_returned(context: Context) -> None:
 @then("no duplicate project should be created")
 def step_check_no_duplicate_project(context: Context) -> None:
     """Check that no duplicate project was created."""
-    with context.unit_of_work.transaction() as ctx:
-        projects = ctx.projects.get_by_name("legacy-project")
-        assert projects is not None  # Should exist
-        # Try to get all projects and check count
-        all_projects = ctx.projects.get_all()
-        project_names = [p.name for p in all_projects]
-        assert project_names.count("legacy-project") == 1
+    # Use the project repository to verify uniqueness
+    all_projects = context.project_service.list_projects()
+    project_names = [p.name for p in all_projects]
+    assert project_names.count("legacy-project") == 1
 
 
 @given('I have a project already in database with name "{name}"')
 def step_create_existing_project(context: Context, name: str) -> None:
-    """Create an existing project in the database."""
-    with context.unit_of_work.transaction() as ctx:
-        project = Project(
-            id=None,
-            name=name,
-            path=context.temp_dir / name,
-            created_at=datetime.now(),
-            updated_at=datetime.now(),
-            current_plan_id=None,
-            settings=ProjectSettings(
-                auto_build=False,
-                auto_apply=False,
-                confirm_apply=True,
-                max_context_size=50 * 1024 * 1024,
-                default_model="mock-gpt",
-            ),
-        )
-        context.existing_project = ctx.projects.create(project)
+    """Create an existing project in the database via ProjectService."""
+    project_path = context.temp_dir / name
+    project_path.mkdir(parents=True, exist_ok=True)
+    context.existing_project = context.project_service.initialize_project(
+        name=name,
+        path=project_path,
+        force=False,
+    )
 
 
 @given("I have legacy JSON project data for migration with same name")
@@ -383,32 +369,27 @@ def step_create_saved_project(context: Context, name: str) -> None:
 
 @when("I update the project's settings")
 def step_update_project_settings(context: Context) -> None:
-    """Update the project's settings."""
-    # Modify the project settings
-    context.saved_project.settings.auto_build = True
-    context.saved_project.settings.auto_apply = True
-    context.saved_project.settings.default_model = "updated-model"
-    context.saved_project.updated_at = datetime.now()
-
-    # Update the project
-    context.updated_project = context.project_service.update_project(
-        context.saved_project
+    """Update the project's description (spec-aligned NamespacedProject has no settings)."""
+    # NamespacedProject uses description instead of legacy settings fields
+    updated = context.saved_project.model_copy(
+        update={"description": "updated-description"}
     )
+    context.updated_project = context.project_service.update_project(updated)
 
 
 @then("the project should be updated successfully")
 def step_check_project_updated(context: Context) -> None:
     """Check that the project was updated successfully."""
     assert context.updated_project is not None
-    assert context.updated_project.settings.auto_build is True
-    assert context.updated_project.settings.auto_apply is True
-    assert context.updated_project.settings.default_model == "updated-model"
+    assert context.updated_project.description == "updated-description"
 
 
 @then("the updated project should be returned")
 def step_check_updated_project_returned(context: Context) -> None:
     """Check that the updated project was returned."""
-    assert context.updated_project.id == context.saved_project.id
+    assert (
+        context.updated_project.namespaced_name == context.saved_project.namespaced_name
+    )
     assert context.updated_project.name == context.saved_project.name
 
 
@@ -443,9 +424,10 @@ def step_create_multiple_projects_times(context: Context) -> None:
             name=f"project{i}", path=project_path, force=False
         )
         # Update created_at to simulate different creation times
-        with context.unit_of_work.transaction() as ctx:
-            project.created_at = base_time + timedelta(hours=i)
-            ctx.projects.update(project)
+        updated = project.model_copy(
+            update={"created_at": base_time + timedelta(hours=i)}
+        )
+        context.project_service.update_project(updated)
 
 
 @when("I list all projects ordered by created date")
@@ -544,20 +526,22 @@ def step_create_project_with_plans_contexts(context: Context) -> None:
         name="full-project", path=context.project_path, force=False
     )
 
-    # Add some plans
+    # Add some plans via the legacy UoW (look up the legacy project by bare name)
     with context.unit_of_work.transaction() as ctx:
-        for i in range(3):
-            plan = Plan(
-                id=None,
-                project_id=context.stats_project.id,
-                name=f"plan{i}",
-                prompt=f"Test plan {i}",
-                status=PlanStatus.PENDING,
-                current=i == 0,
-                created_at=datetime.now(),
-                updated_at=datetime.now(),
-            )
-            ctx.plans.create(plan)
+        legacy_project = ctx.projects.get_by_name(context.stats_project.name)
+        if legacy_project and legacy_project.id:
+            for i in range(3):
+                plan = Plan(
+                    id=None,
+                    project_id=legacy_project.id,
+                    name=f"plan{i}",
+                    prompt=f"Test plan {i}",
+                    status=PlanStatus.PENDING,
+                    current=i == 0,
+                    created_at=datetime.now(),
+                    updated_at=datetime.now(),
+                )
+                ctx.plans.create(plan)
 
 
 @then("the stats should show correct counts for plans and contexts")
@@ -629,10 +613,15 @@ def step_delete_project(context: Context) -> None:
 
 @then("the project should not exist in the database")
 def step_check_project_not_in_database(context: Context) -> None:
-    """Check that the project was deleted from the database."""
-    with context.unit_of_work.transaction() as ctx:
-        project = ctx.projects.get_by_name(context.saved_project.name)
-        assert project is None, "Project should not exist in database"
+    """Check that the project was deleted from the repository."""
+    try:
+        context.project_service.get_project_by_name(context.saved_project.name)
+        raise AssertionError("Project should not exist in repository after deletion")
+    except Exception as exc:
+        # NotFoundError or ProjectNotFoundError is expected
+        assert (
+            "not found" in str(exc).lower() or "NotFoundError" in type(exc).__name__
+        ), f"Unexpected exception type: {type(exc)}: {exc}"
 
 
 # Missing step definitions for scenario: "Create project with special characters in name"
@@ -734,21 +723,16 @@ def step_check_permission_error(context: Context) -> None:
 # Missing step definitions for scenario: "Update project that does not exist"
 @given("I have a project object that is not in database")
 def step_create_project_not_in_db(context: Context) -> None:
-    """Create a project object that is not in the database."""
-    context.non_existent_project = Project(
-        id=999999,  # Non-existent ID
+    """Create a NamespacedProject object that is not in the database."""
+    from datetime import UTC, datetime
+
+    context.non_existent_project = NamespacedProject(
         name="non-existent",
-        path=context.temp_dir / "non-existent",
-        created_at=datetime.now(),
-        updated_at=datetime.now(),
-        current_plan_id=None,
-        settings=ProjectSettings(
-            auto_build=False,
-            auto_apply=False,
-            confirm_apply=True,
-            max_context_size=50 * 1024 * 1024,
-            default_model="mock-gpt",
-        ),
+        namespace="local",
+        description=None,
+        linked_resources=[],
+        created_at=datetime.now(tz=UTC),
+        updated_at=datetime.now(tz=UTC),
     )
 
 
@@ -926,7 +910,11 @@ def step_existing_project_reused(context: Context) -> None:
     assert context.error is None, f"Unexpected error: {context.error}"
     assert context.project_result is not None, "No project was returned"
     assert hasattr(context, "initial_project"), "Initial project missing from context"
-    assert context.project_result.id == context.initial_project.id
+    # NamespacedProject is identified by namespaced_name, not integer id
+    assert (
+        context.project_result.namespaced_name
+        == context.initial_project.namespaced_name
+    )
 
 
 @given('I set up a standalone project directory named "{name}" with a name file')
@@ -998,7 +986,8 @@ def step_assert_temporary_project(context: Context, name: str) -> None:
     project = getattr(context, "current_project_result", None)
     assert project is not None, "Expected a temporary project to be returned"
     assert project.name == name
-    assert project.id is None
+    # NamespacedProject has no integer id; verify it is a NamespacedProject instance
+    assert isinstance(project, NamespacedProject)
 
 
 @then("no current project should be found")
@@ -1026,15 +1015,22 @@ def step_assert_alias_project_created(context: Context) -> None:
     project = getattr(context, "alias_project", None)
     assert project is not None, "Alias project was not created"
     assert project.name == context.prepared_project_name
-    assert project.path == context.prepared_project_path
+    # NamespacedProject has no path attribute; verify the .cleveragents dir was created
+    assert (context.prepared_project_path / ".cleveragents").exists()
 
 
 @when("I look up the project by its saved path")
 def step_lookup_project_by_path(context: Context) -> None:
-    """Retrieve the project using its stored filesystem path."""
+    """Retrieve the project using its stored filesystem path.
+
+    Since ``NamespacedProject`` has no ``path`` attribute, we use the
+    ``test_dir`` (the path passed to ``initialize_project``) directly.
+    """
     assert hasattr(context, "project"), "A project must exist before lookup"
+    # Use the test_dir as the project path (where .cleveragents was created)
+    project_path = Path(context.test_dir)
     context.found_project_by_path = context.project_service.get_project_by_path(
-        context.project.path
+        project_path
     )
 
 

features/steps/service_steps.py

@@ -43,6 +43,7 @@ def step_have_project_service(context: Context) -> None:
 
     unit_of_work = UnitOfWork(db_url)
 
+    context.unit_of_work = unit_of_work
     context.project_service = ProjectService(settings, unit_of_work)
     context.project_service.search_root = Path(context.test_dir)
 
@@ -121,12 +122,17 @@ def step_project_name_should_be(context: Context, name: str) -> None:
 
 @then('the project path should be "{path}"')
 def step_project_path_should_be(context: Context, path: str) -> None:
-    """Verify project path."""
+    """Verify project path via the .cleveragents directory on the filesystem.
+
+    ``NamespacedProject`` does not carry a ``path`` attribute; instead we
+    verify that the ``.cleveragents`` directory was created at the expected
+    location, which is the observable side-effect of project initialisation.
+    """
     if path == "/tmp/test":
         path = context.test_dir
-    expected_path = Path(path)
-    assert context.project.path == expected_path, (
-        f"Expected path {expected_path}, got {context.project.path}"
+    expected_cleveragents = Path(path) / ".cleveragents"
+    assert expected_cleveragents.exists(), (
+        f"Expected .cleveragents directory at {expected_cleveragents}"
     )
 
 
@@ -1387,16 +1393,38 @@ def step_project_should_have_name(context: Context) -> None:
 
 @then("the project should have a path")
 def step_project_should_have_path(context: Context) -> None:
-    """Verify project has a path."""
-    assert context.current_project.path is not None, "Project has no path"
+    """Verify project has a namespaced_name (spec-aligned identity).
+
+    ``NamespacedProject`` is identified by its ``namespaced_name`` rather
+    than a filesystem path.  We verify that the namespaced_name is set.
+    """
+    assert context.current_project.namespaced_name is not None, (
+        "Project has no namespaced_name"
+    )
 
 
 @given("I have a current project")
 def step_have_current_project(context: Context) -> None:
     """Ensure we have a current project."""
     if not hasattr(context, "project_service"):
+        import uuid
+
         settings = Settings()
-        context.project_service = ProjectService(settings, "sqlite:///test.db")
+        context.test_dir = tempfile.mkdtemp(prefix="test_project_")
+        db_file = Path(context.test_dir) / f"test_{uuid.uuid4().hex}.db"
+        db_url = f"sqlite:///{db_file}"
+
+        from cleveragents.infrastructure.database.unit_of_work import UnitOfWork
+
+        unit_of_work = UnitOfWork(db_url)
+        context.project_service = ProjectService(settings, unit_of_work)
+        context.project_service.search_root = Path(context.test_dir)
+
+        def cleanup():
+            if hasattr(context, "test_dir") and Path(context.test_dir).exists():
+                shutil.rmtree(context.test_dir)
+
+        add_cleanup(context, cleanup)
 
     if not hasattr(context, "test_dir"):
         context.test_dir = tempfile.mkdtemp(prefix="test_project_")

src/cleveragents/application/container.py

@@ -697,11 +697,22 @@ class Container(containers.DeclarativeContainer):
         event_bus=event_bus,
     )
 
+    # Namespaced Project Repository — defined early so ProjectService can
+    # receive it as a constructor argument (spec-aligned NamespacedProject
+    # persistence, ADR-007).
+    namespaced_project_repo = providers.Factory(
+        _build_namespaced_project_repo,
+        database_url=database_url,
+    )
+
     # Services - Factory (new instance per request with injected dependencies)
+    # ProjectService receives the spec-aligned NamespacedProjectRepository so
+    # that all project CRUD operations use NamespacedProject (ADR-007).
     project_service = providers.Factory(
         ProjectService,
         settings=settings,
         unit_of_work=unit_of_work,
+        project_repository=namespaced_project_repo,
         event_bus=event_bus,
     )
 
@@ -814,12 +825,6 @@ class Container(containers.DeclarativeContainer):
         database_url=database_url,
     )
 
-    # Namespaced Project Repository
-    namespaced_project_repo = providers.Factory(
-        _build_namespaced_project_repo,
-        database_url=database_url,
-    )
-
     # Project Resource Link Repository
     project_resource_link_repo = providers.Factory(
         _build_project_resource_link_repo,

src/cleveragents/application/services/context_service.py

@@ -21,7 +21,7 @@ import structlog
 
 from cleveragents.config.settings import Settings
 from cleveragents.core.exceptions import ConfigurationError, FileSystemError, PlanError
-from cleveragents.domain.models.core import Context, ContextType, Plan, Project
+from cleveragents.domain.models.core import Context, ContextType, Plan
 from cleveragents.infrastructure.database.unit_of_work import (
     UnitOfWork,
     UnitOfWorkContext,
@@ -115,8 +115,79 @@ class ContextService:
         self.extra_ignore_patterns: list[str] = []
         self._agentsignore_cache: dict[Path, list[str]] = {}
 
+    # ------------------------------------------------------------------
+    # Compatibility helpers — bridge NamespacedProject ↔ legacy Project
+    # ------------------------------------------------------------------
+
+    def _resolve_legacy_project_id(self, project: Any) -> int | None:
+        """Return the legacy integer project ID for *project*.
+
+        Handles both the legacy ``Project`` model (which has a numeric ``.id``)
+        and the spec-aligned ``NamespacedProject`` model (which uses
+        ``namespaced_name`` as its identifier).  For ``NamespacedProject``
+        instances the legacy record is looked up by bare name via the
+        ``UnitOfWork``.
+
+        Returns ``None`` if no matching legacy record is found.
+        """
+        # Legacy Project — has a numeric .id attribute
+        legacy_id = getattr(project, "id", None)
+        if legacy_id is not None:
+            return int(legacy_id)
+
+        # NamespacedProject — look up by bare name
+        bare_name = getattr(project, "name", None)
+        if bare_name is None:
+            return None
+        try:
+            with self.unit_of_work.transaction() as ctx:
+                legacy = ctx.projects.get_by_name(bare_name)
+                return legacy.id if legacy is not None else None
+        except Exception:
+            return None
+
+    def _resolve_project_path(self, project: Any) -> Path | None:
+        """Return the filesystem path for *project*, or ``None`` if unavailable.
+
+        ``NamespacedProject`` is path-agnostic by design; this helper returns
+        ``None`` for such instances so callers can skip path-relative operations.
+        """
+        return getattr(project, "path", None)
+
+    def _get_exclude_patterns(self, project: Any) -> list[str]:
+        """Return the exclude/ignore glob patterns for *project*.
+
+        Handles both the legacy ``Project.settings.exclude_paths`` and the
+        spec-aligned ``NamespacedProject.context_config.ignore_patterns``.
+        """
+        # NamespacedProject — use context_config
+        context_config = getattr(project, "context_config", None)
+        if context_config is not None:
+            return list(getattr(context_config, "ignore_patterns", []))
+        # Legacy Project — use settings.exclude_paths
+        settings = getattr(project, "settings", None)
+        if settings is not None:
+            return list(getattr(settings, "exclude_paths", []))
+        return []
+
+    def _get_include_patterns(self, project: Any) -> list[str]:
+        """Return the include glob patterns for *project*.
+
+        Handles both the legacy ``Project.settings.include_paths`` and the
+        spec-aligned ``NamespacedProject.context_config.include_patterns``.
+        """
+        # NamespacedProject — use context_config
+        context_config = getattr(project, "context_config", None)
+        if context_config is not None:
+            return list(getattr(context_config, "include_patterns", []))
+        # Legacy Project — use settings.include_paths
+        settings = getattr(project, "settings", None)
+        if settings is not None:
+            return list(getattr(settings, "include_paths", []))
+        return []
+
     def add_to_context(
-        self, project: Project, path: Path, recursive: bool = True
+        self, project: Any, path: Path, recursive: bool = True
     ) -> tuple[list[Path], list[Path]]:
         """Add files to the current plan's context.
 
@@ -140,9 +211,10 @@ class ContextService:
 
         plan_id: int | None = None
         with self.unit_of_work.transaction() as ctx:
-            # Get current plan
+            # Get current plan — resolve legacy project ID for NamespacedProject
+            _legacy_id = self._resolve_legacy_project_id(project)
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(_legacy_id) if _legacy_id else None
             )
 
             if not current_plan:
@@ -335,37 +407,51 @@ class ContextService:
             return True
         return rel_str.startswith(f"{cleaned}/")
 
-    def _project_path_matches(self, project: Project, path: Path, pattern: str) -> bool:
-        """Match a path against a project-level include/exclude glob."""
+    def _project_path_matches(self, project: Any, path: Path, pattern: str) -> bool:
+        """Match a path against a project-level include/exclude glob.
 
-        try:
-            rel = path.relative_to(project.path)
-        except ValueError:
-            return False
-        rel_str = rel.as_posix()
-        name = path.name
-        return fnmatch(rel_str, pattern) or fnmatch(name, pattern)
+        Handles both legacy ``Project`` (which has a ``.path`` attribute) and
+        spec-aligned ``NamespacedProject`` (which is path-agnostic).  When the
+        project has no ``.path``, falls back to matching against the filename
+        only.
+        """
+        project_path = self._resolve_project_path(project)
+        if project_path is not None:
+            try:
+                rel = path.relative_to(project_path)
+                rel_str = rel.as_posix()
+                name = path.name
+                return fnmatch(rel_str, pattern) or fnmatch(name, pattern)
+            except ValueError:
+                return False
+        # NamespacedProject — no filesystem path; match against filename only
+        return fnmatch(path.name, pattern)
 
-    def _should_ignore(self, project: Project, path: Path) -> bool:
-        """Check whether to ignore a path via settings and .agentsignore."""
+    def _should_ignore(self, project: Any, path: Path) -> bool:
+        """Check whether to ignore a path via settings and .agentsignore.
+
+        Handles both legacy ``Project.settings`` and spec-aligned
+        ``NamespacedProject.context_config`` via the compatibility helpers.
+        """
 
         if self._matches_default_ignore(path):
             return True
 
-        for pattern in project.settings.exclude_paths:
+        for pattern in self._get_exclude_patterns(project):
             if self._project_path_matches(project, path, pattern):
                 return True
 
-        if project.settings.include_paths and not any(
+        include_patterns = self._get_include_patterns(project)
+        if include_patterns and not any(
             self._project_path_matches(project, path, pattern)
-            for pattern in project.settings.include_paths
+            for pattern in include_patterns
         ):
             return True
 
         rules = self._collect_ignore_rules(path)
         return any(self._matches_ignore(base, pattern, path) for base, pattern in rules)
 
-    def remove_from_context(self, project: Project, path: Path) -> int:
+    def remove_from_context(self, project: Any, path: Path) -> int:
         """Remove files from the context.
 
         Args:
@@ -377,8 +463,9 @@ class ContextService:
         """
         plan_id: int | None = None
         with self.unit_of_work.transaction() as ctx:
+            _legacy_id = self._resolve_legacy_project_id(project)
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(_legacy_id) if _legacy_id else None
             )
 
             if not current_plan or not current_plan.id:
@@ -402,7 +489,7 @@ class ContextService:
 
         return removed_count
 
-    def clear_context(self, project: Project) -> int:
+    def clear_context(self, project: Any) -> int:
         """Clear all context for the current plan.
 
         Args:
@@ -413,8 +500,9 @@ class ContextService:
         """
         plan_id: int | None = None
         with self.unit_of_work.transaction() as ctx:
+            _legacy_id = self._resolve_legacy_project_id(project)
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(_legacy_id) if _legacy_id else None
             )
 
             if not current_plan or not current_plan.id:
@@ -431,7 +519,7 @@ class ContextService:
 
         return count
 
-    def list_context(self, project: Project) -> list[Context]:
+    def list_context(self, project: Any) -> list[Context]:
         """List all files in the current plan's context.
 
         Args:
@@ -440,18 +528,19 @@ class ContextService:
         Returns:
             List of context entries
         """
-        if not project.id:
+        _legacy_id = self._resolve_legacy_project_id(project)
+        if not _legacy_id:
             return []
 
         with self.unit_of_work.transaction() as ctx:
-            current_plan = ctx.plans.get_current_for_project(project.id)
+            current_plan = ctx.plans.get_current_for_project(_legacy_id)
 
             if not current_plan or not current_plan.id:
                 return []
 
             return ctx.contexts.get_for_plan(current_plan.id)
 
-    def get_context_size(self, project: Project) -> int:
+    def get_context_size(self, project: Any) -> int:
         """Get the total size of all context files.
 
         Args:
@@ -463,7 +552,7 @@ class ContextService:
         contexts = self.list_context(project)
         return sum(c.size for c in contexts)
 
-    def show_context_content(self, project: Project) -> dict[str, str]:
+    def show_context_content(self, project: Any) -> dict[str, str]:
         """Get the content of all context files.
 
         Args:
@@ -475,7 +564,7 @@ class ContextService:
         contexts = self.list_context(project)
         return {c.path: c.content or "" for c in contexts}
 
-    def get_context_content(self, project: Project, path: Path) -> str | None:
+    def get_context_content(self, project: Any, path: Path) -> str | None:
         """Get the content of a specific context file.
 
         Args:
@@ -493,7 +582,7 @@ class ContextService:
                 return context.content
         return None
 
-    def list_files(self, project: Project | None = None) -> list[str]:
+    def list_files(self, project: Any | None = None) -> list[str]:
         """List all file paths in the current plan's context.
 
         This is a convenience method that returns just the file paths
@@ -526,17 +615,18 @@ class ContextService:
         contexts = self.list_context(project)
         return [context.path for context in contexts]
 
-    def _get_current_plan(self, project: Project) -> Plan | None:
+    def _get_current_plan(self, project: Any) -> Plan | None:
         """Fetch the current plan for metadata enrichment."""
 
-        if not project.id:
+        _legacy_id = self._resolve_legacy_project_id(project)
+        if not _legacy_id:
             return None
         with self.unit_of_work.transaction() as ctx:
-            return ctx.plans.get_current_for_project(project.id)
+            return ctx.plans.get_current_for_project(_legacy_id)
 
     def _build_langsmith_config(
         self,
-        project: Project,
+        project: Any,
         *,
         run_name: str,
         file_paths: list[str],
@@ -548,8 +638,9 @@ class ContextService:
             return {}
 
         plan = self._get_current_plan(project)
+        _legacy_id = self._resolve_legacy_project_id(project)
         metadata = {
-            "project_id": project.id,
+            "project_id": _legacy_id,
             "project_name": project.name,
             "plan_id": getattr(plan, "id", None),
             "plan_name": getattr(plan, "name", None),
@@ -562,8 +653,8 @@ class ContextService:
             "service:context",
             f"mode:{mode}",
         ]
-        if project.id is not None:
-            tags.append(f"project:{project.id}")
+        if _legacy_id is not None:
+            tags.append(f"project:{_legacy_id}")
         return (
             self.settings.build_langsmith_config(
                 tags=tags,
@@ -575,7 +666,7 @@ class ContextService:
 
     def _prepare_analysis_config(
         self,
-        project: Project,
+        project: Any,
         *,
         run_name: str,
         file_paths: list[str],
@@ -634,7 +725,7 @@ class ContextService:
 
     def analyze_context(
         self,
-        project: Project,
+        project: Any,
         llm: BaseLanguageModel | None = None,
     ) -> ContextAnalysisState:
         """Analyze the current plan's context using LangGraph workflow.
@@ -699,7 +790,7 @@ class ContextService:
 
     async def analyze_context_async(
         self,
-        project: Project,
+        project: Any,
         llm: BaseLanguageModel | None = None,
     ) -> ContextAnalysisState:
         """Asynchronously analyze the current plan's context.
@@ -750,7 +841,7 @@ class ContextService:
 
     def analyze_context_streaming(
         self,
-        project: Project,
+        project: Any,
         llm: BaseLanguageModel | None = None,
     ) -> Iterator[dict[str, Any]]:
         """Stream the context analysis workflow execution.
@@ -795,7 +886,7 @@ class ContextService:
 
     async def analyze_context_streaming_async(
         self,
-        project: Project,
+        project: Any,
         llm: BaseLanguageModel | None = None,
     ) -> AsyncIterator[dict[str, Any]]:
         """Asynchronously stream the context analysis workflow execution.
@@ -840,7 +931,7 @@ class ContextService:
 
     def get_context_summary(
         self,
-        project: Project,
+        project: Any,
         llm: BaseLanguageModel | None = None,
     ) -> str:
         """Get a high-level summary of the current context.
@@ -860,7 +951,7 @@ class ContextService:
 
     def get_context_dependencies(
         self,
-        project: Project,
+        project: Any,
         llm: BaseLanguageModel | None = None,
     ) -> dict[str, list[str]]:
         """Get extracted dependencies for all context files.
@@ -880,7 +971,7 @@ class ContextService:
 
     def get_relevant_files(
         self,
-        project: Project,
+        project: Any,
         threshold: float = 0.5,
         llm: BaseLanguageModel | None = None,
     ) -> list[tuple[str, float]]:
@@ -906,7 +997,7 @@ class ContextService:
 
     def search_context(
         self,
-        project: Project,
+        project: Any,
         query: str,
         *,
         limit: int = 5,

src/cleveragents/application/services/plan_service.py

@@ -45,7 +45,6 @@ from cleveragents.domain.models.core import (
     PlanBuild,
     PlanResult,
     PlanStatus,
-    Project,
 )
 from cleveragents.domain.providers.ai_provider import (
     ActorInvocationContext,
@@ -100,6 +99,45 @@ class PlanService:
         self._llm = llm
         self._logger = structlog.get_logger(__name__).bind(service="plan")
 
+    # ------------------------------------------------------------------
+    # Compatibility helpers — bridge NamespacedProject ↔ legacy Project
+    # ------------------------------------------------------------------
+
+    def _resolve_legacy_project_id(self, project: Any) -> int | None:
+        """Return the legacy integer project ID for *project*.
+
+        Handles both the legacy ``Project`` model (which has a numeric ``.id``)
+        and the spec-aligned ``NamespacedProject`` model (which uses
+        ``namespaced_name`` as its identifier).  For ``NamespacedProject``
+        instances the legacy record is looked up by bare name via the
+        ``UnitOfWork``.
+
+        Returns ``None`` if no matching legacy record is found.
+        """
+        # Legacy Project — has a numeric .id attribute
+        legacy_id = getattr(project, "id", None)
+        if legacy_id is not None:
+            return int(legacy_id)
+
+        # NamespacedProject — look up by bare name
+        bare_name = getattr(project, "name", None)
+        if bare_name is None:
+            return None
+        try:
+            with self.unit_of_work.transaction() as ctx:
+                legacy = ctx.projects.get_by_name(bare_name)
+                return legacy.id if legacy is not None else None
+        except Exception:
+            return None
+
+    def _resolve_project_path(self, project: Any) -> Path | None:
+        """Return the filesystem path for *project*, or ``None`` if unavailable.
+
+        ``NamespacedProject`` is path-agnostic by design; this helper returns
+        ``None`` for such instances so callers can skip path-relative operations.
+        """
+        return getattr(project, "path", None)
+
     def _use_mock_provider(self) -> bool:
         """Return True when the runtime is configured to force the mock provider."""
 
@@ -510,7 +548,7 @@ class PlanService:
 
     def _build_langsmith_config(
         self,
-        project: Project,
+        project: Any,
         plan: Plan | None,
         *,
         run_name: str,
@@ -522,8 +560,9 @@ class PlanService:
         if not getattr(self.settings, "is_langsmith_enabled", False):
             return {}
 
+        _legacy_id = self._resolve_legacy_project_id(project)
         base_metadata: dict[str, Any] = {
-            "project_id": project.id,
+            "project_id": _legacy_id,
             "project_name": project.name,
         }
         if plan and plan.id:
@@ -539,8 +578,8 @@ class PlanService:
         global_tags = list(self.settings.langsmith_tags)
         if global_tags:
             base_tags.extend(global_tags)
-        if project.id is not None:
-            base_tags.append(f"project:{project.id}")
+        if _legacy_id is not None:
+            base_tags.append(f"project:{_legacy_id}")
         if plan and plan.id is not None:
             base_tags.append(f"plan:{plan.id}")
         if tags:
@@ -557,7 +596,7 @@ class PlanService:
 
     def _prepare_langsmith_config(
         self,
-        project: Project,
+        project: Any,
         plan: Plan | None,
         *,
         run_name: str,
@@ -578,9 +617,7 @@ class PlanService:
         config["configurable"]["thread_id"] = f"{thread_prefix}-{uuid.uuid4()}"
         return config
 
-    def create_plan(
-        self, project: Project, prompt: str, name: str | None = None
-    ) -> Plan:
+    def create_plan(self, project: Any, prompt: str, name: str | None = None) -> Plan:
         """Create a new plan with instructions for AI.
 
         Args:
@@ -599,8 +636,9 @@ class PlanService:
             words = prompt.split()[:3] if prompt else ["new", "plan"]
             name = "_".join(words).lower()
 
-        # Ensure project has a valid ID
-        if not project.id:
+        # Ensure project has a valid legacy ID
+        _legacy_id = self._resolve_legacy_project_id(project)
+        if not _legacy_id:
             raise ValidationError(
                 message=(
                     "Cannot create plan: this directory is not linked to a saved "
@@ -623,7 +661,7 @@ class PlanService:
 
         plan = Plan(
             id=None,
-            project_id=project.id,
+            project_id=_legacy_id,
             name=name,
             prompt=prompt,
             status=PlanStatus.PENDING,
@@ -647,13 +685,13 @@ class PlanService:
             created_plan = ctx.plans.create(plan)
 
             # Set as current plan for the project
-            if project.id and created_plan.id:
-                ctx.plans.set_current(project.id, created_plan.id)
+            if _legacy_id and created_plan.id:
+                ctx.plans.set_current(_legacy_id, created_plan.id)
                 created_plan.current = True
 
         return created_plan
 
-    def new_plan(self, project: Project, name: str | None = None) -> Plan:
+    def new_plan(self, project: Any, name: str | None = None) -> Plan:
         """Create a new empty plan.
 
         Args:
@@ -668,7 +706,7 @@ class PlanService:
 
     def build_plan(
         self,
-        project: Project,
+        project: Any,
         progress_callback: Callable[[int], None] | None = None,
         actor: str | None = None,
     ) -> list[Change]:
@@ -685,9 +723,10 @@ class PlanService:
         Raises:
             PlanError: If no current plan or build fails
         """
+        _legacy_id = self._resolve_legacy_project_id(project)
         with self.unit_of_work.transaction() as ctx:
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(_legacy_id) if _legacy_id else None
             )
 
             if not current_plan or not current_plan.id:
@@ -784,7 +823,7 @@ class PlanService:
 
     def auto_debug_build(
         self,
-        project: Project,
+        project: Any,
         max_attempts: int = 3,
         progress_callback: Callable[[int], None] | None = None,
     ) -> tuple[bool, list[Change], str | None]:
@@ -807,9 +846,10 @@ class PlanService:
         from cleveragents.agents import AutoDebugAgent, AutoDebugState
         from cleveragents.domain.models.core import DebugAttempt
 
+        _legacy_id = self._resolve_legacy_project_id(project)
         with self.unit_of_work.transaction() as ctx:
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(_legacy_id) if _legacy_id else None
             )
 
             if not current_plan or not current_plan.id:
@@ -942,7 +982,7 @@ class PlanService:
         # If we exhausted all attempts, return failure
         return (False, changes, last_error)
 
-    def get_pending_changes(self, project: Project) -> list[Change]:
+    def get_pending_changes(self, project: Any) -> list[Change]:
         """Get pending (not applied) changes for the current plan.
 
         Args:
@@ -951,9 +991,10 @@ class PlanService:
         Returns:
             List of pending changes
         """
+        _legacy_id = self._resolve_legacy_project_id(project)
         with self.unit_of_work.transaction() as ctx:
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(_legacy_id) if _legacy_id else None
             )
 
             if not current_plan or not current_plan.id:
@@ -962,7 +1003,7 @@ class PlanService:
             all_changes = ctx.changes.get_for_plan(current_plan.id)
             return [c for c in all_changes if not c.applied]
 
-    def apply_changes(self, project: Project) -> int:
+    def apply_changes(self, project: Any) -> int:
         """Apply pending changes to the filesystem.
 
         Args:
@@ -974,9 +1015,11 @@ class PlanService:
         Raises:
             PlanError: If apply fails
         """
+        _legacy_id = self._resolve_legacy_project_id(project)
+        _project_path = self._resolve_project_path(project)
         with self.unit_of_work.transaction() as ctx:
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(_legacy_id) if _legacy_id else None
             )
 
             if not current_plan or not current_plan.id:
@@ -988,14 +1031,14 @@ class PlanService:
             changes = ctx.changes.get_for_plan(current_plan.id)
             pending_changes = [c for c in changes if not c.applied]
 
-            project_root = project.path.resolve()
+            project_root = _project_path.resolve() if _project_path else Path.cwd()
 
             def _safe_resolve(raw_path: str) -> Path:
                 """Resolve *raw_path* and reject it if it escapes *project_root*."""
                 if Path(raw_path).is_absolute():
                     resolved = Path(raw_path).resolve()
                 else:
-                    resolved = (project.path / raw_path).resolve()
+                    resolved = ((_project_path or Path.cwd()) / raw_path).resolve()
                 if not resolved.is_relative_to(project_root):
                     raise PlanError(
                         message=(
@@ -1068,7 +1111,7 @@ class PlanService:
 
         return applied_count
 
-    def get_current_plan(self, project: Project) -> Plan | None:
+    def get_current_plan(self, project: Any) -> Plan | None:
         """Get the current active plan for a project.
 
         Args:
@@ -1077,13 +1120,14 @@ class PlanService:
         Returns:
             Current plan or None
         """
-        if not project.id:
+        _legacy_id = self._resolve_legacy_project_id(project)
+        if not _legacy_id:
             return None
 
         with self.unit_of_work.transaction() as ctx:
-            return ctx.plans.get_current_for_project(project.id)
+            return ctx.plans.get_current_for_project(_legacy_id)
 
-    def list_plans(self, project: Project) -> list[Plan]:
+    def list_plans(self, project: Any) -> list[Plan]:
         """List all plans in the project.
 
         Args:
@@ -1092,13 +1136,14 @@ class PlanService:
         Returns:
             List of plans
         """
-        if not project.id:
+        _legacy_id = self._resolve_legacy_project_id(project)
+        if not _legacy_id:
             return []
 
         with self.unit_of_work.transaction() as ctx:
-            return ctx.plans.get_all_for_project(project.id)
+            return ctx.plans.get_all_for_project(_legacy_id)
 
-    def switch_to_plan(self, project: Project, name: str) -> Plan:
+    def switch_to_plan(self, project: Any, name: str) -> Plan:
         """Switch to a different plan.
 
         Args:
@@ -1111,19 +1156,20 @@ class PlanService:
         Raises:
             ValidationError: If plan not found
         """
-        if not project.id:
+        _legacy_id = self._resolve_legacy_project_id(project)
+        if not _legacy_id:
             raise ValidationError(
                 message="Project not initialized",
                 details={"hint": "Initialize project first with 'agents init'"},
             )
 
         with self.unit_of_work.transaction() as ctx:
-            plans = ctx.plans.get_all_for_project(project.id)
+            plans = ctx.plans.get_all_for_project(_legacy_id)
 
             for plan in plans:
                 if plan.name == name:
                     if plan.id:
-                        ctx.plans.set_current(project.id, plan.id)
+                        ctx.plans.set_current(_legacy_id, plan.id)
                     return plan
 
             raise ValidationError(
@@ -1131,7 +1177,7 @@ class PlanService:
                 details={"available_plans": [p.name for p in plans]},
             )
 
-    def add_to_plan(self, project: Project, prompt: str) -> None:
+    def add_to_plan(self, project: Any, prompt: str) -> None:
         """Add additional instructions to the current plan.
 
         Args:
@@ -1141,9 +1187,10 @@ class PlanService:
         Raises:
             PlanError: If no current plan
         """
+        _legacy_id = self._resolve_legacy_project_id(project)
         with self.unit_of_work.transaction() as ctx:
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(_legacy_id) if _legacy_id else None
             )
 
             if not current_plan or not current_plan.id:
@@ -1161,7 +1208,7 @@ class PlanService:
             current_plan.status = PlanStatus.PENDING
             ctx.plans.update(current_plan)
 
-    def continue_plan(self, project: Project, prompt: str) -> None:
+    def continue_plan(self, project: Any, prompt: str) -> None:
         """Alias for add_to_plan for compatibility.
 
         Args:
@@ -1172,7 +1219,7 @@ class PlanService:
 
     async def generate_plan_streaming(
         self,
-        project: Project,
+        project: Any,
         description: str,
         name: str | None = None,
         actor: str | None = None,

src/cleveragents/application/services/project_service.py

@@ -1,17 +1,26 @@
 """Project service for managing CleverAgents projects.
 
 This service handles project initialization, configuration, and management.
-Uses repository pattern and Unit of Work for persistence (ADR-007).
+Uses the spec-aligned ``NamespacedProject`` model and ``ProjectRepositoryProtocol``
+for all persistence operations (ADR-007).
+
+The service accepts a ``ProjectRepositoryProtocol`` implementation (e.g.
+``NamespacedProjectRepository``) as its primary repository dependency, wired
+via the DI container.  A ``UnitOfWork`` is retained for legacy migration
+support and plan/context statistics queries that still rely on the legacy
+schema.
 """
 
 from __future__ import annotations
 
 import os
-from datetime import datetime
+from datetime import UTC, datetime
 from pathlib import Path
 from typing import TYPE_CHECKING, Any
 
 import structlog
+from sqlalchemy import create_engine
+from sqlalchemy.orm import sessionmaker
 
 from cleveragents.application.services.context_service import DEFAULT_IGNORE_PATTERNS
 from cleveragents.config.settings import Settings
@@ -21,6 +30,20 @@ from cleveragents.core.exceptions import (
     ValidationError,
 )
 from cleveragents.domain.models.core import Plan, PlanStatus, Project, ProjectSettings
+from cleveragents.domain.models.core.project import (
+    ContextConfig,
+    NamespacedProject,
+    parse_namespaced_name,
+)
+from cleveragents.domain.repositories.project_repository import (
+    ProjectRepositoryProtocol,
+)
+from cleveragents.infrastructure.database.legacy_migrator import (
+    check_and_migrate_legacy_data,
+)
+from cleveragents.infrastructure.database.repositories import (
+    NamespacedProjectRepository,
+)
 from cleveragents.infrastructure.database.unit_of_work import UnitOfWork
 from cleveragents.infrastructure.events.models import DomainEvent
 from cleveragents.infrastructure.events.types import EventType
@@ -35,20 +58,28 @@ class ProjectService:
     """Service for managing CleverAgents projects.
 
     This service provides methods for initializing, configuring, and
-    managing projects throughout their lifecycle.
+    managing projects throughout their lifecycle.  All persistence
+    operations use the spec-aligned ``NamespacedProject`` model via
+    ``ProjectRepositoryProtocol``.
     """
 
     def __init__(
         self,
         settings: Settings,
         unit_of_work: UnitOfWork,
+        project_repository: ProjectRepositoryProtocol | None = None,
         event_bus: EventBus | None = None,
     ):
         """Initialize the project service.
 
         Args:
-            settings: Application settings
-            unit_of_work: Unit of Work for database transactions
+            settings: Application settings.
+            unit_of_work: Unit of Work for legacy migration and plan/context
+                statistics queries.
+            project_repository: Spec-aligned repository for ``NamespacedProject``
+                persistence.  When ``None`` a ``NamespacedProjectRepository``
+                backed by the same database URL as *unit_of_work* is built
+                automatically.
             event_bus: Optional EventBus for domain event emission.
         """
         self.settings = settings
@@ -57,6 +88,45 @@ class ProjectService:
         # Optional search root to limit filesystem discovery (used in tests)
         self.search_root: Path | None = None
 
+        if project_repository is not None:
+            self._project_repo: ProjectRepositoryProtocol = project_repository
+        else:
+            # Build a NamespacedProjectRepository from the UnitOfWork database URL
+            self._project_repo = self._build_default_repo(unit_of_work)
+
+    # ------------------------------------------------------------------
+    # Internal helpers
+    # ------------------------------------------------------------------
+
+    @staticmethod
+    def _build_default_repo(unit_of_work: UnitOfWork) -> ProjectRepositoryProtocol:
+        """Build a ``NamespacedProjectRepository`` from the UoW database URL."""
+        engine = create_engine(unit_of_work.database_url, echo=False)
+        factory = sessionmaker(bind=engine, expire_on_commit=False)
+        return NamespacedProjectRepository(session_factory=factory)
+
+    @staticmethod
+    def _parse_name_to_parts(name: str) -> tuple[str, str]:
+        """Parse a project name into (namespace, bare_name).
+
+        Accepts bare names (defaulting to ``local/``) or fully qualified
+        ``[[server:]namespace/]name`` strings.
+
+        Returns:
+            Tuple of (namespace, bare_name).
+        """
+        parsed = parse_namespaced_name(name)
+        return parsed.namespace, parsed.name
+
+    def _namespaced_name_for(self, name: str) -> str:
+        """Return the ``namespace/name`` string for a given project name."""
+        namespace, bare = self._parse_name_to_parts(name)
+        return f"{namespace}/{bare}"
+
+    # ------------------------------------------------------------------
+    # Core CRUD — spec-aligned NamespacedProject
+    # ------------------------------------------------------------------
+
     def initialize_project(
         self,
         name: str,
@@ -64,39 +134,44 @@ class ProjectService:
         force: bool = False,
         create_ignore_file: bool = False,
         apply_default_filters: bool = False,
-    ) -> Project:
+    ) -> NamespacedProject:
         """Initialize a new CleverAgents project.
 
+        Creates the ``.cleveragents`` directory structure on the filesystem
+        and persists a ``NamespacedProject`` record via the repository.
+
         Args:
-            name: Project name
-            path: Project path
-            force: Force reinitialization if project exists
-            create_ignore_file: Whether to write a default .agentsignore
-                in the project root
+            name: Project name (bare or ``[[server:]namespace/]name``).
+            path: Project filesystem path.
+            force: Force reinitialization if project exists.
+            create_ignore_file: Whether to write a default ``.agentsignore``
+                in the project root.
+            apply_default_filters: Whether to populate ``context_config``
+                with the default ignore patterns.
 
         Returns:
-            Project: The initialized project
+            The initialized ``NamespacedProject``.
 
         Raises:
-            ValidationError: If project already exists and force is False
-            FileSystemError: If unable to create project directories
+            ValidationError: If project already exists and *force* is False.
+            FileSystemError: If unable to create project directories.
         """
         project_dir = path / ".cleveragents"
 
-        # Check if already initialized
+        # Check if already initialized on the filesystem
         if project_dir.exists() and not force:
             raise ValidationError(
                 message=f"Project already initialized at {path}",
                 details={"path": str(path), "use_force": "Add --force to reinitialize"},
             )
 
-        # Create project structure
+        # Create project structure on filesystem
         try:
             project_dir.mkdir(parents=True, exist_ok=True)
             (project_dir / "db.sqlite").touch()
             (project_dir / "config.yaml").touch()
             (project_dir / "current").write_text("main")
-            # Store the project name
+            # Store the project name for later discovery
             (project_dir / "project.name").write_text(name)
 
             if create_ignore_file:
@@ -110,97 +185,133 @@ class ProjectService:
                 path=path,
             ) from e
 
-        # Create project in database
-        project = Project(
-            id=None,
-            name=name,
-            path=path,
-            created_at=datetime.now(),
-            updated_at=datetime.now(),
-            current_plan_id=None,
-            settings=ProjectSettings(
-                auto_build=False,
-                auto_apply=False,
-                confirm_apply=True,
-                max_context_size=50 * 1024 * 1024,  # 50MB
-                default_model="mock-gpt",
-                include_paths=[],
-                exclude_paths=list(DEFAULT_IGNORE_PATTERNS)
-                if apply_default_filters
-                else [],
-            ),
-        )
-
-        # Initialize database and save project
+        # Ensure the database schema exists
         self.unit_of_work.init_database()
 
         # Check for and migrate legacy JSON data if it exists
-        from cleveragents.infrastructure.database.legacy_migrator import (
-            check_and_migrate_legacy_data,
-        )
-
         migrated = check_and_migrate_legacy_data(path, self.unit_of_work)
 
-        with self.unit_of_work.transaction() as ctx:
-            # Check if project with this name already exists FIRST
-            existing = ctx.projects.get_by_name(name)
-            if existing and not force:
-                # If we just migrated, return the existing project
-                if migrated:
-                    return existing
-                raise ValidationError(
-                    message=f"Project with name '{name}' already exists",
-                    details={"name": name},
-                )
+        # Parse the namespaced name
+        namespace, bare_name = self._parse_name_to_parts(name)
+        namespaced_name = f"{namespace}/{bare_name}"
 
-            # If project was created during migration, just return it
-            if migrated and existing:
+        # Check if project already exists in the repository
+        try:
+            existing = self._project_repo.get(namespaced_name)
+        except NotFoundError:
+            existing = None
+
+        if existing is not None and not force:
+            if migrated:
                 return existing
+            raise ValidationError(
+                message=f"Project with name '{name}' already exists",
+                details={"name": name},
+            )
 
-            # If force=True and project exists, delete it first
-            if existing and force and existing.id:
-                ctx.projects.delete(existing.id)
-                # Flush to ensure delete is committed before creating new project
-                ctx.flush()
+        if migrated and existing is not None:
+            return existing
 
-            # Now create the project
-            created_project = ctx.projects.create(project)
+        # If force=True and project exists, delete it first
+        if existing is not None and force:
+            self._project_repo.delete(namespaced_name)
 
-            # Create default "main" plan for the project
-            if created_project.id:
-                main_plan = Plan(
-                    id=None,
-                    project_id=created_project.id,
-                    name="main",
-                    prompt="Main development plan",
-                    status=PlanStatus.PENDING,
-                    current=True,
-                    created_at=datetime.now(),
-                    updated_at=datetime.now(),
-                    build=None,
-                    build_started_at=None,
-                    build_completed_at=None,
-                    model_used=None,
-                    token_count=None,
-                    result=None,
-                    applied_at=None,
-                    files_created=None,
-                    files_modified=None,
-                    files_deleted=None,
-                )
-                created_plan = ctx.plans.create(main_plan)
-                if created_plan.id:
-                    ctx.plans.set_current(created_project.id, created_plan.id)
-                    created_project.current_plan_id = created_plan.id
-                    ctx.projects.update(created_project)
+        # Build context_config
+        ignore_patterns = list(DEFAULT_IGNORE_PATTERNS) if apply_default_filters else []
+        context_config = ContextConfig(
+            ignore_patterns=ignore_patterns,
+            include_patterns=[],
+        )
+
+        # Create the NamespacedProject
+        now = datetime.now(tz=UTC)
+        project = NamespacedProject(
+            name=bare_name,
+            namespace=namespace,
+            description=None,
+            linked_resources=[],
+            context_config=context_config,
+            created_at=now,
+            updated_at=now,
+        )
+
+        created_project = self._project_repo.create(project)
+
+        # Create a default "main" plan in the legacy schema so that
+        # plan-based operations continue to work during the transition.
+        self._create_default_plan_for_project(bare_name)
 
         return created_project
 
-    def get_current_project(self) -> Project | None:
+    def _create_default_plan_for_project(self, bare_name: str) -> None:
+        """Create a default 'main' plan for a newly created project.
+
+        This uses the legacy UnitOfWork/Plan schema so that plan-based
+        operations continue to work during the transition period.
+        """
+        # Look up the legacy project record (created by migration or existing)
+        with self.unit_of_work.transaction() as ctx:
+            legacy_project = ctx.projects.get_by_name(bare_name)
+            if legacy_project is None:
+                # Create a minimal legacy record so plans can be attached
+                legacy_project = Project(
+                    id=None,
+                    name=bare_name,
+                    path=Path("."),
+                    created_at=datetime.now(),
+                    updated_at=datetime.now(),
+                    current_plan_id=None,
+                    settings=ProjectSettings(
+                        auto_build=False,
+                        auto_apply=False,
+                        confirm_apply=True,
+                        max_context_size=50 * 1024 * 1024,
+                    ),
+                )
+                legacy_project = ctx.projects.create(legacy_project)
+
+            if legacy_project.id is None:
+                return
+
+            # Check if a "main" plan already exists
+            existing_plans = ctx.plans.get_all_for_project(legacy_project.id)
+            if existing_plans:
+                return
+
+            main_plan = Plan(
+                id=None,
+                project_id=legacy_project.id,
+                name="main",
+                prompt="Main development plan",
+                status=PlanStatus.PENDING,
+                current=True,
+                created_at=datetime.now(),
+                updated_at=datetime.now(),
+                build=None,
+                build_started_at=None,
+                build_completed_at=None,
+                model_used=None,
+                token_count=None,
+                result=None,
+                applied_at=None,
+                files_created=None,
+                files_modified=None,
+                files_deleted=None,
+            )
+            created_plan = ctx.plans.create(main_plan)
+            if created_plan.id:
+                ctx.plans.set_current(legacy_project.id, created_plan.id)
+
+    def get_current_project(self) -> NamespacedProject | None:
         """Get the current project from the working directory.
 
+        Walks up the directory tree looking for a ``.cleveragents`` directory.
+        If found, looks up the project in the repository by its namespaced name.
+        Falls back to a synthesized ``NamespacedProject`` if the record is not
+        in the repository (e.g. for projects not yet migrated).
+
         Returns:
-            Project or None if no project found
+            ``NamespacedProject`` or ``None`` if no project found.
         """
         path = Path.cwd().resolve()
         env_root = os.getenv("CLEVERAGENTS_PROJECT_SEARCH_ROOT")
@@ -209,117 +320,98 @@ class ProjectService:
         )
         limit = search_root.resolve() if isinstance(search_root, Path) else None
 
-        # Look for .cleveragents directory
         while path != path.parent:
             if limit and not path.is_relative_to(limit):
                 break
 
             if (path / ".cleveragents").exists():
-                # Try to read the project name from file
                 name_file = path / ".cleveragents" / "project.name"
                 if name_file.exists():
-                    project_name = name_file.read_text().strip()
-
-                    # Look up in database
-                    with self.unit_of_work.transaction() as ctx:
-                        project = ctx.projects.get_by_name(project_name)
-                        if project:
-                            return project
-
-                    # If not in database, return a temporary project object
-                    # This handles projects that exist but haven't been
-                    # migrated to DB yet
-                    try:
-                        return Project(
-                            id=None,
-                            name=project_name,
-                            path=path,
-                            created_at=datetime.now(),
-                            updated_at=datetime.now(),
-                            current_plan_id=None,
-                            settings=ProjectSettings(
-                                auto_build=False,
-                                auto_apply=False,
-                                confirm_apply=True,
-                                max_context_size=50 * 1024 * 1024,
-                                default_model="mock-gpt",
-                            ),
-                        )
-                    except Exception:
-                        return None
+                    raw_name = name_file.read_text().strip()
                 else:
-                    # Legacy project without name file
-                    project_name = path.name
+                    # Legacy project without name file — use directory name
+                    raw_name = path.name
+
+                # Try to look up in the repository
+                try:
+                    namespace, bare_name = self._parse_name_to_parts(raw_name)
+                    namespaced_name = f"{namespace}/{bare_name}"
+                    return self._project_repo.get(namespaced_name)
+                except NotFoundError:
+                    pass
+
+                # Fall back to a synthesized NamespacedProject
+                try:
+                    namespace, bare_name = self._parse_name_to_parts(raw_name)
+                    return NamespacedProject(
+                        name=bare_name,
+                        namespace=namespace,
+                        description=None,
+                        linked_resources=[],
+                        context_config=ContextConfig(),
+                        created_at=datetime.now(tz=UTC),
+                        updated_at=datetime.now(tz=UTC),
+                    )
+                except (ValueError, ValidationError):
+                    _logger.warning(
+                        "Could not synthesize project from name file",
+                        raw_name=raw_name,
+                    )
+                    return None
 
-                    try:
-                        return Project(
-                            id=None,
-                            name=project_name,
-                            path=path,
-                            created_at=datetime.now(),
-                            updated_at=datetime.now(),
-                            current_plan_id=None,
-                            settings=ProjectSettings(
-                                auto_build=False,
-                                auto_apply=False,
-                                confirm_apply=True,
-                                max_context_size=50 * 1024 * 1024,
-                                default_model="mock-gpt",
-                            ),
-                        )
-                    except Exception:
-                        return None
             path = path.parent
 
         return None
 
-    def get_project_by_name(self, name: str) -> Project:
+    def get_project_by_name(self, name: str) -> NamespacedProject:
         """Get a project by name.
 
         Args:
-            name: Project name
+            name: Project name (bare or ``[[server:]namespace/]name``).
 
         Returns:
-            Project
+            ``NamespacedProject``.
 
         Raises:
-            NotFoundError: If project not found
+            NotFoundError: If project not found.
         """
-        with self.unit_of_work.transaction() as ctx:
-            project = ctx.projects.get_by_name(name)
-            if not project:
-                raise NotFoundError(
-                    resource_type="project",
-                    resource_id=name,
-                )
-            return project
+        namespaced_name = self._namespaced_name_for(name)
+        try:
+            return self._project_repo.get(namespaced_name)
+        except Exception as exc:
+            raise NotFoundError(
+                resource_type="project",
+                resource_id=name,
+            ) from exc
 
-    def update_project(self, project: Project) -> Project:
+    def update_project(self, project: NamespacedProject) -> NamespacedProject:
         """Update a project.
 
         Args:
-            project: Project to update
+            project: ``NamespacedProject`` to update.
 
         Returns:
-            Updated project
+            Updated ``NamespacedProject``.
         """
-        with self.unit_of_work.transaction() as ctx:
-            return ctx.projects.update(project)
+        return self._project_repo.update(project)
 
-    def get_project_stats(self, project: Project) -> dict[str, Any]:
+    def get_project_stats(self, project: NamespacedProject) -> dict[str, Any]:
         """Get statistics for a project.
 
         Args:
-            project: The project to get stats for
+            project: The ``NamespacedProject`` to get stats for.
 
         Returns:
-            Dict with project statistics
+            Dict with project statistics.
         """
         with self.unit_of_work.transaction() as ctx:
-            # Get actual stats from database
-            plans = ctx.plans.get_all_for_project(project.id) if project.id else []
+            # Look up the legacy project record by bare name
+            legacy_project = ctx.projects.get_by_name(project.name)
+            legacy_id = legacy_project.id if legacy_project else None
+
+            plans = ctx.plans.get_all_for_project(legacy_id) if legacy_id else []
             current_plan = (
-                ctx.plans.get_current_for_project(project.id) if project.id else None
+                ctx.plans.get_current_for_project(legacy_id) if legacy_id else None
             )
 
             context_count = 0
@@ -346,22 +438,18 @@ class ProjectService:
         force: bool = False,
         create_ignore_file: bool = False,
         apply_default_filters: bool = False,
-    ) -> Project:
+    ) -> NamespacedProject:
         """Create a new CleverAgents project (alias for initialize_project).
 
-        This method is an alias for initialize_project to maintain API compatibility.
-
         Args:
-            name: Project name
-            path: Project path
-            force: Force reinitialization if project exists
+            name: Project name.
+            path: Project path.
+            force: Force reinitialization if project exists.
+            create_ignore_file: Whether to write a default ``.agentsignore``.
+            apply_default_filters: Whether to populate default ignore patterns.
 
         Returns:
-            Project: The created project
-
-        Raises:
-            ValidationError: If project already exists and force is False
-            FileSystemError: If unable to create project directories
+            The created ``NamespacedProject``.
         """
         return self.initialize_project(
             name,
@@ -371,46 +459,53 @@ class ProjectService:
             apply_default_filters=apply_default_filters,
         )
 
-    def get_project_by_path(self, path: Path) -> Project | None:
+    def get_project_by_path(self, path: Path) -> NamespacedProject | None:
         """Get a project by its filesystem path.
 
+        Walks the ``.cleveragents/project.name`` file at the given path and
+        looks up the project in the repository.
+
         Args:
-            path: Project path
+            path: Project filesystem path.
 
         Returns:
-            Project or None if not found
+            ``NamespacedProject`` or ``None`` if not found.
         """
-        with self.unit_of_work.transaction() as ctx:
-            all_projects = ctx.projects.get_all()
-            for project in all_projects:
-                if project.path == path:
-                    return project
+        name_file = path / ".cleveragents" / "project.name"
+        if not name_file.exists():
+            return None
+        raw_name = name_file.read_text().strip()
+        try:
+            namespaced_name = self._namespaced_name_for(raw_name)
+            return self._project_repo.get(namespaced_name)
+        except (NotFoundError, ValueError):
             return None
 
-    def list_projects(self, order_by: str = "created_at") -> list[Project]:
+    def list_projects(
+        self,
+        order_by: str = "created_at",
+        namespace: str | None = None,
+    ) -> list[NamespacedProject]:
         """List all projects with optional ordering.
 
         Args:
-            order_by: Field to order by (e.g., "created_at", "name")
+            order_by: Field to order by (``"created_at"`` or ``"name"``).
+            namespace: Optional namespace filter.
 
         Returns:
-            List of projects
+            List of ``NamespacedProject`` instances.
         """
-        with self.unit_of_work.transaction() as ctx:
-            projects = ctx.projects.get_all()
+        projects = self._project_repo.list_projects(namespace=namespace)
 
-            # Sort projects based on order_by parameter
-            if order_by == "name":
-                return sorted(projects, key=lambda p: p.name)
-            elif order_by == "created_at":
-                return sorted(projects, key=lambda p: p.created_at)
-            else:
-                # Default to created_at ordering
-                return sorted(projects, key=lambda p: p.created_at)
+        if order_by == "name":
+            return sorted(projects, key=lambda p: p.name)
+        else:
+            # Default to created_at ordering
+            return sorted(projects, key=lambda p: p.created_at)
 
     def update_file_filters(
         self,
-        project: Project,
+        project: NamespacedProject,
         *,
         include_add: list[str] | None = None,
         exclude_add: list[str] | None = None,
@@ -418,8 +513,24 @@ class ProjectService:
         exclude_remove: list[str] | None = None,
         clear_include: bool = False,
         clear_exclude: bool = False,
-    ) -> Project:
-        """Update project include/exclude globs and persist."""
+    ) -> NamespacedProject:
+        """Update project include/exclude globs and persist.
+
+        Maps to ``NamespacedProject.context_config.include_patterns`` and
+        ``context_config.ignore_patterns`` respectively.
+
+        Args:
+            project: The project to update.
+            include_add: Include patterns to add.
+            exclude_add: Exclude/ignore patterns to add.
+            include_remove: Include patterns to remove.
+            exclude_remove: Exclude/ignore patterns to remove.
+            clear_include: Clear all include patterns.
+            clear_exclude: Clear all exclude/ignore patterns.
+
+        Returns:
+            Updated ``NamespacedProject``.
+        """
 
         def _dedup(seq: list[str]) -> list[str]:
             seen: set[str] = set()
@@ -430,63 +541,93 @@ class ProjectService:
                     ordered.append(item)
             return ordered
 
-        with self.unit_of_work.transaction() as ctx:
-            refreshed = ctx.projects.get_by_name(project.name)
-            if not refreshed:
-                raise NotFoundError(
-                    message="Project not found", details={"name": project.name}
-                )
+        namespaced_name = project.namespaced_name
+        try:
+            refreshed = self._project_repo.get(namespaced_name)
+        except Exception as exc:
+            raise NotFoundError(
+                message="Project not found", details={"name": namespaced_name}
+            ) from exc
 
-            settings = refreshed.settings
-            includes = [] if clear_include else list(settings.include_paths)
-            excludes = [] if clear_exclude else list(settings.exclude_paths)
+        config = refreshed.context_config
 
-            if include_add:
-                includes.extend(include_add)
-            if exclude_add:
-                excludes.extend(exclude_add)
-            if include_remove:
-                includes = [p for p in includes if p not in include_remove]
-            if exclude_remove:
-                excludes = [p for p in excludes if p not in exclude_remove]
+        includes = [] if clear_include else list(config.include_patterns)
+        excludes = [] if clear_exclude else list(config.ignore_patterns)
 
-            settings.include_paths = _dedup(includes)
-            settings.exclude_paths = _dedup(excludes)
-            refreshed.settings = settings
-            ctx.projects.update(refreshed)
-            return refreshed
+        if include_add:
+            includes.extend(include_add)
+        if exclude_add:
+            excludes.extend(exclude_add)
+        if include_remove:
+            includes = [p for p in includes if p not in include_remove]
+        if exclude_remove:
+            excludes = [p for p in excludes if p not in exclude_remove]
 
-    def get_project_filters(self, project: Project) -> tuple[list[str], list[str]]:
-        """Return include and exclude globs for a project."""
+        new_config = ContextConfig(
+            ignore_patterns=_dedup(excludes),
+            include_patterns=_dedup(includes),
+            max_file_size=config.max_file_size,
+            max_total_size=config.max_total_size,
+            indexing_strategy=config.indexing_strategy,
+            chunking_policy=config.chunking_policy,
+            chunk_size=config.chunk_size,
+            hot_max_tokens=config.hot_max_tokens,
+            warm_max_decisions=config.warm_max_decisions,
+            cold_max_decisions=config.cold_max_decisions,
+            summarize=config.summarize,
+            summary_max_tokens=config.summary_max_tokens,
+            temporal_scope=config.temporal_scope,
+            auto_refresh=config.auto_refresh,
+            retention_policy=config.retention_policy,
+            execution_environment=config.execution_environment,
+            execution_env_priority=config.execution_env_priority,
+        )
 
-        with self.unit_of_work.transaction() as ctx:
-            refreshed = ctx.projects.get_by_name(project.name)
-            if not refreshed:
-                raise NotFoundError(
-                    message="Project not found", details={"name": project.name}
-                )
-            return (
-                list(refreshed.settings.include_paths),
-                list(refreshed.settings.exclude_paths),
-            )
+        updated = refreshed.model_copy(
+            update={
+                "context_config": new_config,
+                "updated_at": datetime.now(tz=UTC),
+            }
+        )
+        return self._project_repo.update(updated)
 
-    def delete_project(self, project: Project) -> None:
-        """Delete a project from the database.
+    def get_project_filters(
+        self, project: NamespacedProject
+    ) -> tuple[list[str], list[str]]:
+        """Return include and exclude globs for a project.
+
+        Returns:
+            Tuple of (include_patterns, ignore_patterns).
+        """
+        namespaced_name = project.namespaced_name
+        try:
+            refreshed = self._project_repo.get(namespaced_name)
+        except Exception as exc:
+            raise NotFoundError(
+                message="Project not found", details={"name": namespaced_name}
+            ) from exc
+        return (
+            list(refreshed.context_config.include_patterns),
+            list(refreshed.context_config.ignore_patterns),
+        )
+
+    def delete_project(self, project: NamespacedProject) -> None:
+        """Delete a project from the repository.
 
         Args:
-            project: The project to delete
+            project: The ``NamespacedProject`` to delete.
         """
-        with self.unit_of_work.transaction() as ctx:
-            if project.id:
-                ctx.projects.delete(project.id)
-        if project.id and self._event_bus is not None:
+        namespaced_name = project.namespaced_name
+        self._project_repo.delete(namespaced_name)
+
+        if self._event_bus is not None:
             try:
                 self._event_bus.emit(
                     DomainEvent(
                         event_type=EventType.ENTITY_DELETED,
                         details={
                             "entity_type": "project",
-                            "entity_name": project.name,
+                            "entity_name": namespaced_name,
                         },
                     )
                 )

src/cleveragents/cli/commands/auto_debug.py

@@ -5,7 +5,7 @@ automatic debugging of build failures.
 """
 
 from contextlib import suppress
-from typing import Annotated
+from typing import Annotated, Any
 
 import typer
 from rich.live import Live
@@ -14,7 +14,6 @@ from rich.text import Text
 
 from cleveragents.cli.renderers import _get_console
 from cleveragents.core.exceptions import CleverAgentsError, PlanError
-from cleveragents.domain.models.core import Project
 
 # Create sub-app for auto-debug commands
 app = typer.Typer(help="Auto-debug commands")
@@ -53,11 +52,11 @@ def auto_debug_command(max_attempts: int = 3) -> tuple[bool, int]:
     return (success, attempts_made)
 
 
-def _get_current_project() -> Project:
+def _get_current_project() -> Any:
     """Get the current project or exit with error.
 
     Returns:
-        Project: The current project
+        The current project (``NamespacedProject`` or legacy ``Project``).
 
     Raises:
         typer.Abort: If no project found

src/cleveragents/cli/commands/plan.py

@@ -209,8 +209,8 @@ if TYPE_CHECKING:
     from cleveragents.application.services.plan_lifecycle_service import (
         PlanLifecycleService,
     )
-    from cleveragents.domain.models.core import Project
     from cleveragents.domain.models.core.decision import Decision
+    from cleveragents.domain.models.core.project import NamespacedProject
 
 # Create sub-app for plan commands
 app = typer.Typer(
@@ -477,7 +477,7 @@ def _execute_output_dict(
     }
 
 
-def _get_current_project() -> Project:
+def _get_current_project() -> NamespacedProject:
     """Get the current project or exit with error.
 
     Returns:

src/cleveragents/cli/commands/project.py

@@ -260,11 +260,18 @@ def init_command(
         )
         console.print("[green]✓ OK[/green] Initialized (non-interactive)")
     else:
+        # NamespacedProject has no path attribute; display namespaced_name instead
+        project_location = getattr(project, "path", None)
+        location_str = (
+            str(project_location / ".cleveragents")
+            if project_location is not None
+            else project.namespaced_name
+        )
         console.print(
             Panel(
                 f"[green]✓[/green] Project '{project.name}' "
                 f"initialized successfully!\n\n"
-                f"Location: {project.path / '.cleveragents'}\n"
+                f"Location: {location_str}\n"
                 f"Database: SQLite\n"
                 f"Status: Ready",
                 title="Project Initialized",
@@ -513,9 +520,11 @@ def status() -> None:
         stats = project_service.get_project_stats(project)
 
         # Display project information
+        # NamespacedProject has no path attribute; display namespaced_name instead
+        project_path_str = getattr(project, "path", project.namespaced_name)
         info_text = f"""
 [bold]Project:[/bold] {project.name}
-[bold]Path:[/bold] {project.path}
+[bold]Path:[/bold] {project_path_str}
 [bold]Created:[/bold] {project.created_at}
 
 [bold]Statistics:[/bold]