fix(extensions): let a disabled extension's manifest claim its files

A disabled extension claimed only the names its registry entry lists for
the agent, because its manifest's commands aren't registered. When that
entry can't be read (registered_commands or its per-agent value isn't a
list of names), it claimed nothing, so integration use, switch or upgrade
registered another extension's command over its prompt, e.g.
speckit.foo.bar-baz over a disabled speckit.foo-bar.baz. It now claims
its manifest's names in that case, and registration skips the pair.

Refs #4797

Assisted-by: Claude Code (model: claude-opus-5-5, autonomous)

Author: kartsan03

src/specify_cli/extensions/__init__.py

@@ -4175,7 +4175,8 @@ def _shared_command_files(
         Every extension claims the names already registered for the agent,
         because their files stay on disk, including names its manifest no
         longer declares. An enabled extension with a readable manifest also
-        claims every name it declares. A command, its own aliases, and a
+        claims every name it declares, and so does a disabled one whose
+        registered names can't be read. A command, its own aliases, and a
         registered name that writes the same file are one owner.
 
         Removal checks core files separately using the integration manifest
@@ -4202,10 +4203,16 @@ def _shared_command_files(
                 for name in [command["name"], *(command.get("aliases") or [])]:
                     primary_of[name] = command["name"]
             recorded = metadata.get("registered_commands")
-            names = self._valid_name_list(
-                recorded.get(agent_name) if isinstance(recorded, dict) else None
+            entry = recorded.get(agent_name) if isinstance(recorded, dict) else None
+            unreadable = (recorded is not None and not isinstance(recorded, dict)) or (
+                entry is not None
+                and (
+                    not isinstance(entry, list)
+                    or not all(isinstance(name, str) for name in entry)
+                )
             )
-            if manifest is not None and metadata.get("enabled", True):
+            names = self._valid_name_list(entry)
+            if manifest is not None and (metadata.get("enabled", True) or unreadable):
                 names = list(primary_of) + [n for n in names if n not in primary_of]
             primary_of_stem = {
                 os.path.normcase(

tests/specify_cli/integrations/test_command_upgrade.py

@@ -848,6 +848,40 @@ def test_inactive_extension_keeps_its_claim_on_a_shared_kiro_prompt(
         )
         assert not (prompts / "speckit.foo.bar-baz.md").exists()
 
+    @pytest.mark.parametrize(
+        "damage",
+        [[], "speckit.foo-bar.baz", {"kiro-cli": "speckit.foo-bar.baz"}, {"kiro-cli": [1]}],
+    )
+    def test_disabled_extension_with_unreadable_registration_keeps_its_prompt(
+        self, tmp_path, damage
+    ):
+        """A disabled extension's prompt stays on disk. When its registry
+        entry can't be read, its manifest still names the command, so another
+        extension that writes the same file is not registered over it
+        (#4797)."""
+        project = _init_project(tmp_path, "kiro-cli")
+        self._plant_extension(project, "foo-bar", [
+            {"name": "speckit.foo-bar.baz", "body": "BAR-BODY\n"},
+        ], enabled=False)
+        shared = project / ".kiro" / "prompts" / "speckit-foo-bar-baz.md"
+        body = b"---\ndescription: Bar\n---\n\n<!-- Extension: foo-bar -->\nBAR-BODY\n"
+        shared.write_bytes(body)
+        registry = project / ".specify" / "extensions" / ".registry"
+        data = json.loads(registry.read_text(encoding="utf-8"))
+        data["extensions"]["foo-bar"]["registered_commands"] = damage
+        registry.write_text(json.dumps(data), encoding="utf-8")
+        self._plant_extension(project, "foo", [
+            {"name": "speckit.foo.bar-baz", "body": "FOO-BODY\n"},
+        ])
+
+        result = _run_in_project(project, ["integration", "upgrade", "kiro-cli"])
+        assert result.exit_code == 0, result.output
+        assert (
+            "speckit.foo.bar-baz (speckit-foo-bar-baz, also written by "
+            "extension 'foo-bar')"
+        ) in " ".join(result.output.split())
+        assert shared.read_bytes() == body
+
     def test_enabling_a_colliding_extension_keeps_the_migrated_prompt(
         self, tmp_path, monkeypatch
     ):