fix: read nested bundle URIs from in-memory registry in bundle list --all

amplifier_app_cli/lib/bundle_loader/discovery.py

@@ -490,7 +490,6 @@ def get_bundle_categories(self) -> dict[str, list[dict[str, str]]]:
             Dict with categories: well_known, user_added, dependencies, nested_bundles
             Each category contains list of {name, uri, ...} dicts.
         """
-        import json
 
         categories: dict[str, list[dict[str, str]]] = {
             "well_known": [],
@@ -523,40 +522,33 @@ def get_bundle_categories(self) -> dict[str, list[dict[str, str]]]:
                 }
             )
 
-        # Read persisted registry for dependencies and nested bundles
-        registry_path = Path.home() / ".amplifier" / "registry.json"
-        if registry_path.exists():
-            try:
-                with open(registry_path, encoding="utf-8") as f:
-                    data = json.load(f)
+        # Read from in-memory registry for dependencies and nested bundles.
+        # This ensures URIs reflect current overrides (e.g., local path overrides
+        # from settings.local.yaml) rather than stale persisted data.
+        well_known_names = set(WELL_KNOWN_BUNDLES.keys())
+        user_added_names = set(added_bundles.keys())
+
+        all_states = self._registry.get_state()
+        if isinstance(all_states, dict):
+            for name, state in all_states.items():
+                # Skip if already categorized
+                if name in well_known_names or name in user_added_names:
+                    continue
 
-                well_known_names = set(WELL_KNOWN_BUNDLES.keys())
-                user_added_names = set(added_bundles.keys())
-
-                for name, bundle_data in data.get("bundles", {}).items():
-                    # Skip if already categorized
-                    if name in well_known_names or name in user_added_names:
-                        continue
-
-                    entry = {
-                        "name": name,
-                        "uri": bundle_data.get("uri", ""),
-                    }
-
-                    if not bundle_data.get("is_root", True):
-                        # Nested bundle (behavior, provider, etc.)
-                        entry["root"] = bundle_data.get("root_name", "")
-                        categories["nested_bundles"].append(entry)
-                    elif not bundle_data.get("explicitly_requested", False):
-                        # Dependency (loaded transitively)
-                        included_by = bundle_data.get("included_by", [])
-                        entry["included_by"] = (
-                            ", ".join(included_by) if included_by else ""
-                        )
-                        categories["dependencies"].append(entry)
+                entry = {
+                    "name": name,
+                    "uri": state.uri,
+                }
 
-            except Exception as e:
-                logger.debug(f"Could not read persisted registry: {e}")
+                if not state.is_root:
+                    # Nested bundle (behavior, provider, etc.)
+                    entry["root"] = state.root_name or ""
+                    categories["nested_bundles"].append(entry)
+                elif not state.explicitly_requested:
+                    # Dependency (loaded transitively)
+                    included_by = state.included_by or []
+                    entry["included_by"] = ", ".join(included_by) if included_by else ""
+                    categories["dependencies"].append(entry)
 
         return categories
 

tests/lib/bundle_loader/test_discovery.py

@@ -0,0 +1,146 @@
+"""Tests for AppBundleDiscovery.
+
+Regression tests for https://github.com/microsoft-amplifier/amplifier-support/issues/62
+"""
+
+import json
+from datetime import datetime
+from unittest.mock import patch
+
+
+from amplifier_foundation.registry import BundleRegistry, BundleState
+
+
+class TestGetBundleCategoriesNestedURIs:
+    """Verify get_bundle_categories reads nested bundle URIs from in-memory registry."""
+
+    @patch(
+        "amplifier_app_cli.lib.bundle_loader.discovery.AppBundleDiscovery._load_user_registry"
+    )
+    @patch(
+        "amplifier_app_cli.lib.bundle_loader.discovery.AppBundleDiscovery._register_well_known_bundles"
+    )
+    def test_nested_bundles_reflect_in_memory_state(
+        self, mock_well_known, mock_user_registry, tmp_path
+    ):
+        """Nested bundle URIs come from in-memory registry, not disk."""
+        from amplifier_app_cli.lib.bundle_loader.discovery import AppBundleDiscovery
+
+        registry = BundleRegistry(home=tmp_path / "home")
+        discovery = AppBundleDiscovery(search_paths=[], registry=registry)
+
+        # Inject a nested bundle entry into the in-memory registry
+        registry._registry["behavior-sessions"] = BundleState(
+            uri="file:///local/path/behaviors/sessions.yaml",
+            name="behavior-sessions",
+            is_root=False,
+            root_name="foundation",
+            loaded_at=datetime.now(),
+        )
+
+        with patch("amplifier_app_cli.lib.settings.AppSettings") as mock_settings_cls:
+            mock_settings_cls.return_value.get_added_bundles.return_value = {}
+            categories = discovery.get_bundle_categories()
+
+        nested = categories["nested_bundles"]
+        nested_names = [b["name"] for b in nested]
+        assert "behavior-sessions" in nested_names
+
+        entry = next(b for b in nested if b["name"] == "behavior-sessions")
+        assert entry["uri"] == "file:///local/path/behaviors/sessions.yaml"
+        assert entry["root"] == "foundation"
+
+    @patch(
+        "amplifier_app_cli.lib.bundle_loader.discovery.AppBundleDiscovery._load_user_registry"
+    )
+    @patch(
+        "amplifier_app_cli.lib.bundle_loader.discovery.AppBundleDiscovery._register_well_known_bundles"
+    )
+    def test_stale_persisted_uri_not_used_for_nested_bundles(
+        self, mock_well_known, mock_user_registry, tmp_path
+    ):
+        """In-memory URI takes precedence over stale persisted data on disk."""
+        home = tmp_path / "home"
+
+        # Write stale registry.json with old git+ URI
+        home.mkdir(parents=True)
+        stale_data = {
+            "version": 1,
+            "bundles": {
+                "behavior-agents": {
+                    "uri": "git+https://github.com/example/old@main#subdirectory=behaviors/agents",
+                    "name": "behavior-agents",
+                    "version": "1.0.0",
+                    "loaded_at": None,
+                    "checked_at": None,
+                    "local_path": None,
+                    "is_root": False,
+                    "root_name": "foundation",
+                    "explicitly_requested": False,
+                    "app_bundle": False,
+                }
+            },
+        }
+        (home / "registry.json").write_text(json.dumps(stale_data, indent=2))
+
+        from amplifier_app_cli.lib.bundle_loader.discovery import AppBundleDiscovery
+
+        # Registry loads persisted state, then we update in-memory
+        registry = BundleRegistry(home=home)
+        discovery = AppBundleDiscovery(search_paths=[], registry=registry)
+
+        # Simulate runtime override: update the URI in-memory
+        registry._registry[
+            "behavior-agents"
+        ].uri = "file:///local/override/behaviors/agents.yaml"
+
+        with patch(
+            "amplifier_app_cli.lib.settings.AppSettings"
+        ) as mock_settings_cls:
+            mock_settings_cls.return_value.get_added_bundles.return_value = {}
+            categories = discovery.get_bundle_categories()
+
+        nested = categories["nested_bundles"]
+        entry = next(b for b in nested if b["name"] == "behavior-agents")
+
+        # Must reflect the in-memory URI, not the stale git+ from disk
+        assert entry["uri"] == "file:///local/override/behaviors/agents.yaml"
+        assert "git+" not in entry["uri"]
+
+    @patch(
+        "amplifier_app_cli.lib.bundle_loader.discovery.AppBundleDiscovery._load_user_registry"
+    )
+    @patch(
+        "amplifier_app_cli.lib.bundle_loader.discovery.AppBundleDiscovery._register_well_known_bundles"
+    )
+    def test_dependencies_reflect_in_memory_state(
+        self, mock_well_known, mock_user_registry, tmp_path
+    ):
+        """Dependency URIs also come from in-memory registry."""
+        from amplifier_app_cli.lib.bundle_loader.discovery import AppBundleDiscovery
+
+        registry = BundleRegistry(home=tmp_path / "home")
+        discovery = AppBundleDiscovery(search_paths=[], registry=registry)
+
+        # Inject a dependency entry (is_root=True, not explicitly requested)
+        registry._registry["lsp-python"] = BundleState(
+            uri="git+https://github.com/microsoft/amplifier-bundle-lsp-python@main",
+            name="lsp-python",
+            is_root=True,
+            explicitly_requested=False,
+            included_by=["foundation"],
+            loaded_at=datetime.now(),
+        )
+
+        with patch(
+            "amplifier_app_cli.lib.settings.AppSettings"
+        ) as mock_settings_cls:
+            mock_settings_cls.return_value.get_added_bundles.return_value = {}
+            categories = discovery.get_bundle_categories()
+
+        deps = categories["dependencies"]
+        dep_names = [b["name"] for b in deps]
+        assert "lsp-python" in dep_names
+
+        entry = next(b for b in deps if b["name"] == "lsp-python")
+        assert entry["included_by"] == "foundation"