fix: address PR review - disabled extension resolution and corrupted entries

- Fix _get_all_extensions_by_priority to use include_disabled=True for tracking
  registered IDs, preventing disabled extensions from being picked up as
  unregistered directories
- Add corrupted entry handling to get() - returns None for non-dict entries
- Add integration tests for disabled extension template resolution
- Add tests for get() corrupted entry handling in both registries

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: iamaeroplane

src/specify_cli/extensions.py

@@ -325,10 +325,13 @@ def get(self, extension_id: str) -> Optional[dict]:
             extension_id: Extension ID
 
         Returns:
-            Deep copy of extension metadata, or None if not found
+            Deep copy of extension metadata, or None if not found or corrupted
         """
         entry = self.data["extensions"].get(extension_id)
-        return copy.deepcopy(entry) if entry is not None else None
+        # Return None for missing or corrupted (non-dict) entries
+        if entry is None or not isinstance(entry, dict):
+            return None
+        return copy.deepcopy(entry)
 
     def list(self) -> Dict[str, dict]:
         """Get all installed extensions.

src/specify_cli/presets.py

@@ -335,10 +335,13 @@ def get(self, pack_id: str) -> Optional[dict]:
             pack_id: Preset ID
 
         Returns:
-            Deep copy of preset metadata, or None if not found
+            Deep copy of preset metadata, or None if not found or corrupted
         """
         entry = self.data["presets"].get(pack_id)
-        return copy.deepcopy(entry) if entry is not None else None
+        # Return None for missing or corrupted (non-dict) entries
+        if entry is None or not isinstance(entry, dict):
+            return None
+        return copy.deepcopy(entry)
 
     def list(self) -> Dict[str, dict]:
         """Get all installed presets.
@@ -1498,12 +1501,17 @@ def _get_all_extensions_by_priority(self) -> list[tuple[int, str, dict | None]]:
             return []
 
         registry = ExtensionRegistry(self.extensions_dir)
-        registered_extensions = registry.list_by_priority()
-        registered_extension_ids = {ext_id for ext_id, _ in registered_extensions}
+        # Get ALL registered extensions (including disabled) to know which dirs are tracked
+        all_registered = registry.list_by_priority(include_disabled=True)
+        registered_extension_ids = {ext_id for ext_id, _ in all_registered}
 
         all_extensions: list[tuple[int, str, dict | None]] = []
 
-        for ext_id, metadata in registered_extensions:
+        # Only include enabled extensions in the result
+        for ext_id, metadata in all_registered:
+            # Skip disabled extensions
+            if not metadata.get("enabled", True):
+                continue
             priority = normalize_priority(metadata.get("priority") if metadata else None)
             all_extensions.append((priority, ext_id, metadata))
 

tests/test_extensions.py

@@ -481,6 +481,26 @@ def test_get_returns_deep_copy(self, temp_dir):
         internal = registry.data["extensions"]["test-ext"]
         assert internal["registered_commands"] == {"claude": ["cmd1"]}
 
+    def test_get_returns_none_for_corrupted_entry(self, temp_dir):
+        """Test that get() returns None for corrupted (non-dict) entries."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+
+        # Directly corrupt the registry with non-dict entries
+        registry.data["extensions"]["corrupted-string"] = "not a dict"
+        registry.data["extensions"]["corrupted-list"] = ["not", "a", "dict"]
+        registry.data["extensions"]["corrupted-int"] = 42
+        registry._save()
+
+        # All corrupted entries should return None
+        assert registry.get("corrupted-string") is None
+        assert registry.get("corrupted-list") is None
+        assert registry.get("corrupted-int") is None
+        # Non-existent should also return None
+        assert registry.get("nonexistent") is None
+
     def test_list_returns_deep_copy(self, temp_dir):
         """Test that list() returns deep copies for nested structures."""
         extensions_dir = temp_dir / "extensions"

tests/test_presets.py

@@ -450,6 +450,25 @@ def test_get_returns_deep_copy(self, temp_dir):
         assert fresh["version"] == "1.0.0"
         assert fresh["nested"]["key"] == "original"
 
+    def test_get_returns_none_for_corrupted_entry(self, temp_dir):
+        """Test that get() returns None for corrupted (non-dict) entries."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        # Directly corrupt the registry with non-dict entries
+        registry.data["presets"]["corrupted-string"] = "not a dict"
+        registry.data["presets"]["corrupted-list"] = ["not", "a", "dict"]
+        registry.data["presets"]["corrupted-int"] = 42
+        registry._save()
+
+        # All corrupted entries should return None
+        assert registry.get("corrupted-string") is None
+        assert registry.get("corrupted-list") is None
+        assert registry.get("corrupted-int") is None
+        # Non-existent should also return None
+        assert registry.get("nonexistent") is None
+
     def test_list_returns_deep_copy(self, temp_dir):
         """Test that list() returns deep copies to prevent mutation."""
         packs_dir = temp_dir / "packs"
@@ -840,6 +859,44 @@ def test_resolve_extension_provided_templates(self, project_dir):
         assert result is not None
         assert "Extension Custom Template" in result.read_text()
 
+    def test_resolve_disabled_extension_templates_skipped(self, project_dir):
+        """Test that disabled extension templates are not resolved."""
+        # Create extension with templates
+        ext_dir = project_dir / ".specify" / "extensions" / "disabled-ext"
+        ext_templates_dir = ext_dir / "templates"
+        ext_templates_dir.mkdir(parents=True)
+        ext_template = ext_templates_dir / "disabled-template.md"
+        ext_template.write_text("# Disabled Extension Template\n")
+
+        # Register extension as disabled
+        extensions_dir = project_dir / ".specify" / "extensions"
+        ext_registry = ExtensionRegistry(extensions_dir)
+        ext_registry.add("disabled-ext", {"version": "1.0.0", "priority": 1, "enabled": False})
+
+        # Template should NOT be resolved because extension is disabled
+        resolver = PresetResolver(project_dir)
+        result = resolver.resolve("disabled-template")
+        assert result is None, "Disabled extension template should not be resolved"
+
+    def test_resolve_disabled_extension_not_picked_up_as_unregistered(self, project_dir):
+        """Test that disabled extensions are not picked up via unregistered dir scan."""
+        # Create extension directory with templates
+        ext_dir = project_dir / ".specify" / "extensions" / "test-disabled-ext"
+        ext_templates_dir = ext_dir / "templates"
+        ext_templates_dir.mkdir(parents=True)
+        ext_template = ext_templates_dir / "unique-disabled-template.md"
+        ext_template.write_text("# Should Not Resolve\n")
+
+        # Register the extension but disable it
+        extensions_dir = project_dir / ".specify" / "extensions"
+        ext_registry = ExtensionRegistry(extensions_dir)
+        ext_registry.add("test-disabled-ext", {"version": "1.0.0", "enabled": False})
+
+        # Verify the template is NOT resolved (even though the directory exists)
+        resolver = PresetResolver(project_dir)
+        result = resolver.resolve("unique-disabled-template")
+        assert result is None, "Disabled extension should not be picked up as unregistered"
+
     def test_resolve_pack_over_extension(self, project_dir, pack_dir, temp_dir, valid_pack_data):
         """Test that pack templates take priority over extension templates."""
         # Create extension with templates