fix(integrations): only treat real renames as a Kiro filename migration

_command_file_names_changed() now needs a removed command file and an added one with the same name up to "."/"-" separators, so a release that adds one command and drops another no longer unregisters extension commands. When the rename does happen on the active integration, preset commands are unregistered before re-registration too, so dotted preset prompts such as speckit.fakeext.cmd.md don't survive the upgrade. Assisted-by: Claude Code (model: claude-opus-5-5, autonomous)
kartsan03 · Sep 30, 2026 · Sep 30, 2026 · Sep 30, 2026 · Sep 30, 2026 · Sep 30, 2026
commit 569a1bdb7fec874d4890027cddf08cc4751145d2
@@ -66,16 +66,20 @@ def _command_file_names_changed(integration, old_manifest, new_manifest) -> bool
     """Return True when core command files were renamed inside the command dir.
 
     Kiro CLI moved from ``speckit.<cmd>.md`` to ``speckit-<cmd>.md`` in the
-    same ``.kiro/prompts`` directory (#4797). Enabled extension commands are
-    tracked in the extension registry rather than the manifest, so
-    re-registering them alone would leave their old names beside the new ones.
+    same ``.kiro/prompts`` directory (#4797). Only a removed file that matches
+    an added one up to ``.``/``-`` separators counts, so a release that just
+    adds and drops commands is not a rename. Enabled extension and preset
+    commands are tracked outside the manifest, so re-registering them alone
+    would leave their old names beside the new ones.
     """
     commands_dir = (integration.registrar_config or {}).get("dir")
     if not isinstance(commands_dir, str) or not commands_dir.strip():
         return False
     old = {rel for rel in old_manifest.files if _manifest_path_under(rel, commands_dir)}
     new = {rel for rel in new_manifest.files if _manifest_path_under(rel, commands_dir)}
-    return bool(old - new) and bool(new - old)
+    removed = {PurePath(rel).name.replace(".", "-") for rel in old - new}
+    added = {PurePath(rel).name.replace(".", "-") for rel in new - old}
+    return bool(removed & added)
 
 
 def _legacy_command_root_upgrade_pending(integration, old_manifest) -> bool:

@@ -23,7 +23,7 @@
     _manifest_tracks_skill_layout,
 )
 from ._commands import integration_app
-from ._helpers import _MANIFEST_READ_ERRORS, _SharedTemplateRefreshError, _cli_error_detail, _cli_phase_label, _get_speckit_version, _read_integration_json, _refresh_init_options_speckit_version, _register_extensions_for_agent, _register_presets_for_agent, _resolve_integration_options, _resolve_integration_script_type, _resync_manifest_after_registration, _unregister_enabled_extension_commands_for_agent, _update_init_options_for_integration, _write_integration_json
+from ._helpers import _MANIFEST_READ_ERRORS, _SharedTemplateRefreshError, _cli_error_detail, _cli_phase_label, _get_speckit_version, _read_integration_json, _refresh_init_options_speckit_version, _register_extensions_for_agent, _register_presets_for_agent, _resolve_integration_options, _resolve_integration_script_type, _resync_manifest_after_registration, _unregister_enabled_extension_commands_for_agent, _unregister_presets_for_agent, _update_init_options_for_integration, _write_integration_json
 
 
 @integration_app.command("upgrade")
@@ -318,9 +318,10 @@ def integration_upgrade(
         old_manifest,
         new_manifest,
     )
-    if legacy_command_root_changed or _command_file_names_changed(
+    command_file_names_changed = _command_file_names_changed(
         integration, old_manifest, new_manifest
-    ):
+    )
+    if legacy_command_root_changed or command_file_names_changed:
         _unregister_enabled_extension_commands_for_agent(
             project_root,
             key,
@@ -341,6 +342,17 @@ def integration_upgrade(
             force=True,
             continuing="The integration was upgraded, but installed extensions may need re-registration.",
         )
+        if command_file_names_changed:
+            # Preset commands aren't in the manifest either, so drop them
+            # under their old file names before re-registering.
+            _unregister_presets_for_agent(
+                project_root,
+                key,
+                continuing=(
+                    "The integration command file names changed, but old "
+                    "preset command files may need manual cleanup."
+                ),
+            )
         _register_presets_for_agent(
             project_root,
             key,

@@ -300,12 +300,43 @@ def test_upgrade_migrates_kilocode_legacy_dir(self, tmp_path):
     def test_upgrade_replaces_dotted_kiro_prompts(self, tmp_path, monkeypatch):
         """Kiro installs used to write ``.kiro/prompts/speckit.<cmd>.md``,
         which Kiro CLI cannot invoke (#4797). Upgrade replaces them, including
-        enabled extension prompts, with ``speckit-<cmd>.md``, but a
+        enabled extension and preset prompts, with ``speckit-<cmd>.md``, but a
         user-modified one blocks it."""
+        import yaml
+
         from specify_cli.agents import CommandRegistrar
         from specify_cli.integrations.base import MarkdownIntegration
         from specify_cli.integrations.kiro_cli import KiroCliIntegration
 
+        preset_src = tmp_path / "custom-preset"
+        (preset_src / "commands").mkdir(parents=True)
+        (preset_src / "commands" / "speckit.fakeext.cmd.md").write_text(
+            "---\ndescription: Custom command\n---\nCustom preset content\n",
+            encoding="utf-8",
+        )
+        (preset_src / "preset.yml").write_text(
+            yaml.dump({
+                "schema_version": "1.0",
+                "preset": {
+                    "id": "custom-preset",
+                    "name": "Custom Preset",
+                    "version": "1.0.0",
+                    "description": "Test preset with a custom command",
+                },
+                "requires": {"speckit_version": ">=0.1.0"},
+                "provides": {
+                    "templates": [
+                        {
+                            "type": "command",
+                            "name": "speckit.fakeext.cmd",
+                            "file": "commands/speckit.fakeext.cmd.md",
+                        }
+                    ]
+                },
+            }),
+            encoding="utf-8",
+        )
+
         CommandRegistrar._ensure_configs()
         with monkeypatch.context() as m:
             m.setattr(
@@ -316,8 +347,13 @@ def test_upgrade_replaces_dotted_kiro_prompts(self, tmp_path, monkeypatch):
             project = _init_project(tmp_path, "kiro-cli")
             added = _run_in_project(project, ["extension", "add", "git"])
             assert added.exit_code == 0, added.output
+            added = _run_in_project(
+                project, ["preset", "add", "--dev", str(preset_src)]
+            )
+            assert added.exit_code == 0, added.output
         prompts = project / ".kiro" / "prompts"
         assert (prompts / "speckit.git.commit.md").is_file()
+        assert (prompts / "speckit.fakeext.cmd.md").is_file()
         dotted_plan = prompts / "speckit.plan.md"
         # Bytes, not text: write_text() would turn "\n" into "\r\n" on
         # Windows, so the restored file would no longer match the manifest.
@@ -335,6 +371,41 @@ def test_upgrade_replaces_dotted_kiro_prompts(self, tmp_path, monkeypatch):
         assert sorted(prompts.glob("speckit.*.md")) == []
         assert (prompts / "speckit-plan.md").is_file()
         assert (prompts / "speckit-git-commit.md").is_file()
+        assert "Custom preset content" in (
+            prompts / "speckit-fakeext-cmd.md"
+        ).read_text(encoding="utf-8")
+
+    @pytest.mark.parametrize(
+        ("old_files", "new_files", "expected"),
+        [
+            (["speckit.plan.md", "speckit.tasks.md"],
+             ["speckit-plan.md", "speckit-tasks.md"], True),
+            (["speckit.plan.md", "speckit.old.md"],
+             ["speckit.plan.md", "speckit.new.md"], False),
+            (["speckit.plan.md"], ["speckit.plan.md", "speckit.new.md"], False),
+        ],
+    )
+    def test_command_file_names_changed_needs_a_rename(
+        self, old_files, new_files, expected
+    ):
+        """Commands added and dropped in the same release are not a rename,
+        so upgrade must not unregister extension commands for them."""
+        from types import SimpleNamespace
+
+        from specify_cli.integrations._command_upgrade_layout import (
+            _command_file_names_changed,
+        )
+
+        integration = SimpleNamespace(registrar_config={"dir": ".kiro/prompts"})
+
+        def manifest(names):
+            return SimpleNamespace(
+                files={f".kiro/prompts/{name}": "hash" for name in names}
+            )
+
+        assert _command_file_names_changed(
+            integration, manifest(old_files), manifest(new_files)
+        ) is expected
 
     def test_upgrade_migrates_qodercli_extension_commands_to_skills(self, tmp_path):
         """Qoder upgrade retires old extension commands after skills exist."""