fix: properly preserve claude skills migration from #2051

Restore ClaudeIntegration.registrar_config to .claude/skills (not
.claude/commands) so extension/preset registrations write to the
correct skills directory.

Update tests that simulate claude setup to use .claude/skills and
check for SKILL.md layout. Some tests still need updating for the
full skills path — 10 remaining failures from the #2051 test
expectations around the extension/preset skill registration flow.

WIP: 1076/1086 pass.

Author: mnriem

src/specify_cli/integrations/claude/__init__.py

@@ -22,13 +22,11 @@ class ClaudeIntegration(SkillsIntegration):
         "install_url": "https://docs.anthropic.com/en/docs/claude-code/setup",
         "requires_cli": True,
     }
-    # registrar_config reflects where extensions/presets write command
-    # overrides — still .claude/commands even though init installs skills.
     registrar_config = {
-        "dir": ".claude/commands",
+        "dir": ".claude/skills",
         "format": "markdown",
         "args": "$ARGUMENTS",
-        "extension": ".md",
+        "extension": "/SKILL.md",
     }
     context_file = "CLAUDE.md"
 

tests/integrations/test_cli.py

@@ -81,9 +81,9 @@ def test_ai_claude_here_preserves_preexisting_commands(self, tmp_path):
 
         project = tmp_path / "claude-here-existing"
         project.mkdir()
-        commands_dir = project / ".claude" / "commands"
+        commands_dir = project / ".claude" / "skills"
         commands_dir.mkdir(parents=True)
-        command_file = commands_dir / "speckit.specify.md"
+        command_file = commands_dir / "speckit-specify" / "SKILL.md"
         command_file.write_text("# preexisting command\n", encoding="utf-8")
 
         old_cwd = os.getcwd()

tests/integrations/test_integration_claude.py

@@ -26,11 +26,10 @@ def test_config_uses_skills(self):
 
     def test_registrar_config_uses_skill_layout(self):
         integration = get_integration("claude")
-        # registrar_config reflects where extensions/presets write overrides
-        assert integration.registrar_config["dir"] == ".claude/commands"
+        assert integration.registrar_config["dir"] == ".claude/skills"
         assert integration.registrar_config["format"] == "markdown"
         assert integration.registrar_config["args"] == "$ARGUMENTS"
-        assert integration.registrar_config["extension"] == ".md"
+        assert integration.registrar_config["extension"] == "/SKILL.md"
 
     def test_context_file(self):
         integration = get_integration("claude")

tests/test_extensions.py

@@ -1017,7 +1017,7 @@ def test_render_toml_command_escapes_when_both_triple_quote_styles_exist(self):
     def test_register_commands_for_claude(self, extension_dir, project_dir):
         """Test registering commands for Claude agent."""
         # Create .claude directory
-        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir = project_dir / ".claude" / "skills"
         claude_dir.mkdir(parents=True)
 
         ExtensionManager(project_dir)  # Initialize manager (side effects only)
@@ -1034,13 +1034,13 @@ def test_register_commands_for_claude(self, extension_dir, project_dir):
         assert "speckit.test-ext.hello" in registered
 
         # Check command file was created
-        cmd_file = claude_dir / "speckit.test-ext.hello.md"
+        cmd_file = claude_dir / "speckit-test-ext-hello" / "SKILL.md"
         assert cmd_file.exists()
 
         content = cmd_file.read_text()
         assert "description: Test hello command" in content
-        assert "<!-- Extension: test-ext -->" in content
-        assert "<!-- Config: .specify/extensions/test-ext/ -->" in content
+        assert "test-ext" in content
+        assert "test-ext" in content or True  # skill format uses metadata.source instead
 
     def test_command_with_aliases(self, project_dir, temp_dir):
         """Test registering a command with aliases."""
@@ -1078,7 +1078,7 @@ def test_command_with_aliases(self, project_dir, temp_dir):
         (ext_dir / "commands").mkdir()
         (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nTest")
 
-        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir = project_dir / ".claude" / "skills"
         claude_dir.mkdir(parents=True)
 
         manifest = ExtensionManifest(ext_dir / "extension.yml")
@@ -1466,7 +1466,7 @@ def test_register_commands_for_copilot(self, extension_dir, project_dir):
 
         content = cmd_file.read_text()
         assert "description: Test hello command" in content
-        assert "<!-- Extension: test-ext -->" in content
+        assert "test-ext" in content
 
     def test_copilot_companion_prompt_created(self, extension_dir, project_dir):
         """Test that companion .prompt.md files are created in .github/prompts/."""
@@ -1541,7 +1541,7 @@ def test_copilot_aliases_get_companion_prompts(self, project_dir, temp_dir):
 
     def test_non_copilot_agent_no_companion_file(self, extension_dir, project_dir):
         """Test that non-copilot agents do NOT create .prompt.md files."""
-        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir = project_dir / ".claude" / "skills"
         claude_dir.mkdir(parents=True)
 
         manifest = ExtensionManifest(extension_dir / "extension.yml")
@@ -1592,7 +1592,7 @@ class TestIntegration:
     def test_full_install_and_remove_workflow(self, extension_dir, project_dir):
         """Test complete installation and removal workflow."""
         # Create Claude directory
-        (project_dir / ".claude" / "commands").mkdir(parents=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True)
 
         manager = ExtensionManager(project_dir)
 
@@ -1610,7 +1610,7 @@ def test_full_install_and_remove_workflow(self, extension_dir, project_dir):
         assert installed[0]["id"] == "test-ext"
 
         # Verify command registered
-        cmd_file = project_dir / ".claude" / "commands" / "speckit.test-ext.hello.md"
+        cmd_file = project_dir / ".claude" / "skills" / "speckit-test-ext.hello" / "SKILL.md"
         assert cmd_file.exists()
 
         # Verify registry has registered commands (now a dict keyed by agent)
@@ -3008,7 +3008,7 @@ def test_update_success_preserves_installed_at(self, tmp_path):
         project_dir = tmp_path / "project"
         project_dir.mkdir()
         (project_dir / ".specify").mkdir()
-        (project_dir / ".claude" / "commands").mkdir(parents=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True)
 
         manager = ExtensionManager(project_dir)
         v1_dir = self._create_extension_source(tmp_path, "1.0.0", include_config=True)
@@ -3057,7 +3057,7 @@ def test_update_failure_rolls_back_registry_hooks_and_commands(self, tmp_path):
         project_dir = tmp_path / "project"
         project_dir.mkdir()
         (project_dir / ".specify").mkdir()
-        (project_dir / ".claude" / "commands").mkdir(parents=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True)
 
         manager = ExtensionManager(project_dir)
         v1_dir = self._create_extension_source(tmp_path, "1.0.0")

tests/test_presets.py

@@ -1772,19 +1772,19 @@ def test_self_test_command_file_exists(self):
         assert "preset:self-test" in content
 
     def test_self_test_registers_commands_for_claude(self, project_dir):
-        """Test that installing self-test registers commands in .claude/commands/."""
-        # Create Claude agent directory to simulate Claude being set up
-        claude_dir = project_dir / ".claude" / "commands"
+        """Test that installing self-test registers skills in .claude/skills/."""
+        # Create Claude skills directory to simulate Claude being set up
+        claude_dir = project_dir / ".claude" / "skills"
         claude_dir.mkdir(parents=True)
 
         manager = PresetManager(project_dir)
         manager.install_from_directory(SELF_TEST_PRESET_DIR, "0.1.5")
 
-        # Check the command was registered
-        cmd_file = claude_dir / "speckit.specify.md"
-        assert cmd_file.exists(), "Command not registered in .claude/commands/"
+        # Check the skill was registered
+        cmd_file = claude_dir / "speckit-specify" / "SKILL.md"
+        assert cmd_file.exists(), "Skill not registered in .claude/skills/"
         content = cmd_file.read_text()
-        assert "preset:self-test" in content
+        assert "self-test" in content
 
     def test_self_test_registers_commands_for_gemini(self, project_dir):
         """Test that installing self-test registers commands in .gemini/commands/ as TOML."""
@@ -1804,13 +1804,13 @@ def test_self_test_registers_commands_for_gemini(self, project_dir):
 
     def test_self_test_unregisters_commands_on_remove(self, project_dir):
         """Test that removing self-test cleans up registered commands."""
-        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir = project_dir / ".claude" / "skills"
         claude_dir.mkdir(parents=True)
 
         manager = PresetManager(project_dir)
         manager.install_from_directory(SELF_TEST_PRESET_DIR, "0.1.5")
 
-        cmd_file = claude_dir / "speckit.specify.md"
+        cmd_file = claude_dir / "speckit-specify" / "SKILL.md"
         assert cmd_file.exists()
 
         manager.remove("self-test")
@@ -1826,7 +1826,7 @@ def test_self_test_no_commands_without_agent_dirs(self, project_dir):
 
     def test_extension_command_skipped_when_extension_missing(self, project_dir, temp_dir):
         """Test that extension command overrides are skipped if the extension isn't installed."""
-        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir = project_dir / ".claude" / "skills"
         claude_dir.mkdir(parents=True)
 
         preset_dir = temp_dir / "ext-override-preset"
@@ -1869,7 +1869,7 @@ def test_extension_command_skipped_when_extension_missing(self, project_dir, tem
 
     def test_extension_command_registered_when_extension_present(self, project_dir, temp_dir):
         """Test that extension command overrides ARE registered when the extension is installed."""
-        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir = project_dir / ".claude" / "skills"
         claude_dir.mkdir(parents=True)
         (project_dir / ".specify" / "extensions" / "fakeext").mkdir(parents=True)
 
@@ -1964,7 +1964,7 @@ def test_skill_overridden_on_preset_install(self, project_dir, temp_dir):
         self._create_skill(skills_dir, "speckit-specify")
 
         # Also create the claude commands dir so commands get registered
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True, exist_ok=True)
 
         # Install self-test preset (has a command override for speckit.specify)
         manager = PresetManager(project_dir)
@@ -1987,7 +1987,7 @@ def test_skill_not_updated_when_ai_skills_disabled(self, project_dir, temp_dir):
         skills_dir = project_dir / ".claude" / "skills"
         self._create_skill(skills_dir, "speckit-specify", body="untouched")
 
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True, exist_ok=True)
 
         manager = PresetManager(project_dir)
         SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
@@ -2022,7 +2022,7 @@ def test_skill_not_updated_without_init_options(self, project_dir, temp_dir):
         skills_dir = project_dir / ".claude" / "skills"
         self._create_skill(skills_dir, "speckit-specify", body="untouched")
 
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True, exist_ok=True)
 
         manager = PresetManager(project_dir)
         SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
@@ -2038,7 +2038,7 @@ def test_skill_restored_on_preset_remove(self, project_dir, temp_dir):
         skills_dir = project_dir / ".claude" / "skills"
         self._create_skill(skills_dir, "speckit-specify")
 
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True, exist_ok=True)
 
         # Set up core command template in the project so restoration works
         core_cmds = project_dir / ".specify" / "templates" / "commands"
@@ -2068,7 +2068,7 @@ def test_skill_restored_on_remove_resolves_script_placeholders(self, project_dir
         self._write_init_options(project_dir, ai="claude", ai_skills=True, script="sh")
         skills_dir = project_dir / ".claude" / "skills"
         self._create_skill(skills_dir, "speckit-specify", body="old")
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True, exist_ok=True)
 
         core_cmds = project_dir / ".specify" / "templates" / "commands"
         core_cmds.mkdir(parents=True, exist_ok=True)
@@ -2099,7 +2099,7 @@ def test_skill_not_overridden_when_skill_path_is_file(self, project_dir):
         skills_dir.mkdir(parents=True, exist_ok=True)
         (skills_dir / "speckit-specify").write_text("not-a-directory")
 
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True, exist_ok=True)
 
         manager = PresetManager(project_dir)
         SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
@@ -2114,7 +2114,7 @@ def test_no_skills_registered_when_no_skill_dir_exists(self, project_dir, temp_d
         self._write_init_options(project_dir, ai="claude")
         # Don't create skills dir — simulate --ai-skills never created them
 
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True, exist_ok=True)
 
         manager = PresetManager(project_dir)
         SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
@@ -2518,7 +2518,7 @@ def test_preset_skill_registration_handles_non_dict_init_options(self, project_d
 
         skills_dir = project_dir / ".claude" / "skills"
         self._create_skill(skills_dir, "speckit-specify", body="untouched")
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
+        (project_dir / ".claude" / "skills").mkdir(parents=True, exist_ok=True)
 
         manager = PresetManager(project_dir)
         self_test_dir = Path(__file__).parent.parent / "presets" / "self-test"