feat: add Hermes Agent integration (with review fixes) (#2651)

* feat: add Hermes Agent integration

* feat: add Hermes Agent integration

* feat: add Hermes Agent integration

* feat: add Hermes Agent integration (with review fixes)

- Full SkillsIntegration subclass with dual install strategy
  (project-local .hermes/skills/ + global ~/.hermes/skills/)
- CLI fix: integration_uninstall now calls integration.teardown()
  instead of manifest.uninstall() directly, allowing custom cleanup
- Fix Copilot review issues:
  - Docstring now reflects both -Q (quiet) and -q (query) flags
  - Empty command guard prevents passing empty skill names
- Add catalog entry for hermes in integrations/catalog.json

Co-authored-by: Zhaoxiaoguang001 <3357983213@qq.com>

* feat: write Hermes skills directly to global ~/.hermes/skills/

Hermes loads skills from the global ~/.hermes/skills/ directory,
not from project-local paths.  The old dual-install strategy copied
SKILL.md files to both locations — project-local (for manifest
tracking) and global (for Hermes discovery).

This change removes the project-local copies entirely:
- setup() writes directly to ~/.hermes/skills/speckit-*/SKILL.md
- An empty .hermes/skills/ marker directory is created in the
  project so extension commands (e.g. git) can detect Hermes
  as an active integration via register_commands_for_all_agents()
- teardown() cleans both the global speckit-* dirs and the local
  marker
- import yaml moved to local import inside setup()

Tests updated: Hermes-specific tests now assert global skill
location, and shared SkillsIntegrationTests that assumed
project-local files are overridden with Hermes-appropriate
assertions.

Co-authored-by: Zhaoxiaoguang001 <3357983213@qq.com>

* fix: address Copilot review feedback on Hermes integration

Addresses all 6 review comments from copilot-pull-request-reviewer:

1. Hard-fail on missing integration key → fall back to
   manifest.uninstall() with a warning instead of raising an error.
   Allows users to always remove stale integration files even when
   the integration class is missing from the registry.

2. HOME isolation in tests → every test that calls setup() or
   CliRunner now monkeypatches Path.home() to a temp directory,
   keeping the test suite hermetic and non-destructive.

3. HermesIntegration.teardown() now delegates to
   manifest.uninstall() for project-local tracked files
   (scripts, manifest), merging results with global cleanup.

4. Global skills cleanup gated behind force=True to avoid destroying
   speckit-* skills shared across multiple Spec Kit projects when
   running 'specify integration uninstall hermes' without --force.

5. Line 160 isolation (CLI test test_complete_file_inventory_sh).

6. Line 258 isolation (Path.home assertion in
   test_ai_hermes_without_ai_skills_auto_promotes).

* fix: address second Copilot review round — 6 remaining observations

- Move  to module scope (was inside per-template loop)
- Add  safety checks in setup() matching standard
- Fix docstrings: global skills always removed on uninstall (standard)
- Fix removal tracking: only report after successful rmtree
- Override shared test_modified_file_survives_uninstall with Hermes-appropriate
  behaviour (global skills always removed, no hash tracking)
- Update PR description to match implementation (global-only skills + marker)

* fix: add first-class global/home-based agent dir support in CommandRegistrar

Resolves Copilot HIGH concern (discussion_r3312194525):
HermesIntegration.registrar_config.dir was '.hermes/skills' (project-
relative), but skills live in ~/.hermes/skills/ (global). Extensions
and presets registering commands for the 'hermes' agent via
CommandRegistrar would write to the project-local marker directory
instead of the real global skills directory, making those commands
invisible to Hermes.

Fix consists of three parts:

1. CommandRegistrar._resolve_agent_dir now supports '~/'-prefixed and
   absolute paths in agent_config['dir']. Relative paths still resolve
   against project_root as before — zero change for existing agents
   (Claude, Codex, Gemini, etc.).

2. HermesIntegration.registrar_config.dir changed from '.hermes/skills'
   to '~/.hermes/skills', so extensions/presets write directly to the
   global directory Hermes searches at runtime.

3. Two inline project_root / agent_config['dir'] calls in the extension
   update backup/restore paths (src/specify_cli/__init__.py) now delegate
   to _resolve_agent_dir, giving them the same global-dir support plus
   the legacy_dir fallback they were missing (improvement for all agents).

Test side-effect: test_update_failure_rolls_back_registry_hooks_and_commands
was constructing verification paths with project_dir / '~/.hermes/skills'
(literal tilde) — fixed to use _resolve_agent_dir and monkeypatch
Path.home() so Hermes' global dir doesn't leak into the real filesystem.

* fix: address remaining 3 Copilot review observations (round 3)

- teardown docstring: clarify marker removal is conditional (if empty)
- test_pre_existing_skills_not_removed: now actually calls teardown()
  to verify foreign skills survive uninstall (was only running setup)
- integration_switch Phase 1: replaced old_manifest.uninstall() +
  remove_context_section() with current_integration.teardown(),
  matching the pattern already used in integration_uninstall.
  This ensures custom teardown logic (e.g. Hermes global skills
  cleanup) runs during switches.

* fix: address Copilot round 4 — home-relative dir resolution + project-local detection

1. _resolve_agent_dir(): expand ~/... via Path.home() + slice instead of
   expanduser(), so tests that monkeypatch Path.home() properly isolate
   the home directory (Copilot r3312731595, r3312731729)

2. Add detect_dir field to registrar_config: Hermes declares
   detect_dir='.hermes/skills' (project-local marker). CommandRegistrar
   checks detect_dir before resolving the output dir, preventing global
   dirs like ~/.hermes/skills from causing false detection in every
   project (Copilot r3312731682)

3. test_update_failure_rolls_back: no additional changes needed — the
   _resolve_agent_dir fix makes the existing Path.home() monkeypatch
   effective, so ~/.hermes/skills is not found in the fake home and
   Hermes is properly skipped.

Tests: 2236 passed (2009 integration + 195 extension + 32 hermes)

---------

Co-authored-by: Zhaoxiaoguang001 <3357983213@qq.com>
Co-authored-by: majordave <majordave@users.noreply.github.com>

src/specify_cli/agents.py

@@ -654,15 +654,28 @@ class CommandRegistrar:
     ) -> Path:
         """Return the agent command directory, falling back to legacy_dir.
 
-        When the canonical directory (``agent_config["dir"]``) does not
-        exist but a ``legacy_dir`` is configured and present on disk,
-        returns the legacy path and emits a deprecation warning advising
-        the user to upgrade.
+        Supports project-relative paths (e.g. ``.claude/skills/``),
+        home-relative paths (e.g. ``~/.hermes/skills``), and absolute
+        paths — the ``agent_config["dir"]`` value is resolved verbatim
+        when absolute or starting with ``~/``, or joined with
+        ``project_root`` when relative.
+
+        When the canonical directory does not exist but a ``legacy_dir``
+        is configured and present on disk, returns the legacy path and
+        emits a deprecation warning advising the user to upgrade.
 
         Integrations that do not declare ``legacy_dir`` get the canonical
         path unconditionally — no fallback, no warning.
         """
-        agent_dir = project_root / agent_config["dir"]
+        dir_str = agent_config["dir"]
+        if dir_str.startswith("~"):
+            # Use Path.home() + remainder instead of expanduser() so tests
+            # that monkeypatch Path.home() can properly isolate the home dir.
+            # expanduser() uses OS env/user lookup and ignores monkeypatches.
+            agent_dir = Path.home() / dir_str[1:].lstrip("/")
+        else:
+            p = Path(dir_str)
+            agent_dir = p if p.is_absolute() else project_root / p
         if not agent_dir.exists():
             legacy = agent_config.get("legacy_dir")
             if legacy:
@@ -704,6 +717,15 @@ class CommandRegistrar:
 
         self._ensure_configs()
         for agent_name, agent_config in self.AGENT_CONFIGS.items():
+            # Check detect_dir first (project-local marker) if configured,
+            # falling back to the resolved dir for output.  This prevents
+            # global dirs (e.g. ~/.hermes/skills) from causing false
+            # detection in every project.
+            detect_dir_str = agent_config.get("detect_dir")
+            if detect_dir_str:
+                detect_path = project_root / detect_dir_str
+                if not detect_path.exists():
+                    continue
             agent_dir = self._resolve_agent_dir(
                 agent_name, agent_config, project_root,
             )
@@ -755,6 +777,11 @@ class CommandRegistrar:
         for agent_name, agent_config in self.AGENT_CONFIGS.items():
             if agent_config.get("extension") == "/SKILL.md":
                 continue
+            detect_dir_str = agent_config.get("detect_dir")
+            if detect_dir_str:
+                detect_path = project_root / detect_dir_str
+                if not detect_path.exists():
+                    continue
             agent_dir = self._resolve_agent_dir(
                 agent_name, agent_config, project_root,
             )