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>

integrations/catalog.json

@@ -272,6 +272,15 @@
       "author": "spec-kit-core",
       "repository": "https://github.com/github/spec-kit",
       "tags": ["cli"]
+    },
+    "hermes": {
+      "id": "hermes",
+      "name": "Hermes Agent",
+      "version": "1.0.0",
+      "description": "Hermes Agent skills-based integration by Nous Research",
+      "author": "spec-kit-core",
+      "repository": "https://github.com/github/spec-kit",
+      "tags": ["cli", "skills"]
     }
   }
 }

src/specify_cli/__init__.py

@@ -1218,11 +1218,14 @@ def integration_uninstall(
         console.print(f"[dim]Details:[/dim] {exc}")
         raise typer.Exit(1)
 
-    removed, skipped = manifest.uninstall(project_root, force=force)
-
-    # Remove managed context section from the agent context file
-    if integration:
-        integration.remove_context_section(project_root)
+    if not integration:
+        console.print(
+            f"[yellow]Warning:[/yellow] Integration '{key}' not found "
+            "in registry. Falling back to manifest-based cleanup."
+        )
+        removed, skipped = manifest.uninstall(project_root, force=force)
+    else:
+        removed, skipped = integration.teardown(project_root, manifest, force=force)
 
     remaining = [installed for installed in installed_keys if installed != key]
     new_default = default_key if default_key != key else (remaining[0] if remaining else None)
@@ -1364,8 +1367,9 @@ def integration_switch(
                     f"run [cyan]specify integration uninstall {installed_key}[/cyan], then retry."
                 )
                 raise typer.Exit(1)
-            removed, skipped = old_manifest.uninstall(project_root, force=force)
-            current_integration.remove_context_section(project_root)
+            removed, skipped = current_integration.teardown(
+                project_root, old_manifest, force=force,
+            )
             if removed:
                 console.print(f"  Removed {len(removed)} file(s)")
             if skipped:
@@ -3601,7 +3605,9 @@ def extension_update(
                     if agent_name not in registrar.AGENT_CONFIGS:
                         continue
                     agent_config = registrar.AGENT_CONFIGS[agent_name]
-                    commands_dir = project_root / agent_config["dir"]
+                    commands_dir = _AgentReg._resolve_agent_dir(
+                        agent_name, agent_config, project_root
+                    )
 
                     for cmd_name in cmd_names:
                         output_name = _AgentReg._compute_output_name(agent_name, cmd_name, agent_config)
@@ -3762,7 +3768,9 @@ def extension_update(
                             if agent_name not in registrar.AGENT_CONFIGS:
                                 continue
                             agent_config = registrar.AGENT_CONFIGS[agent_name]
-                            commands_dir = project_root / agent_config["dir"]
+                            commands_dir = _AgentReg._resolve_agent_dir(
+                                agent_name, agent_config, project_root
+                            )
 
                             for cmd_name in cmd_names:
                                 output_name = _AgentReg._compute_output_name(agent_name, cmd_name, agent_config)

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,
             )

src/specify_cli/integrations/__init__.py

@@ -61,6 +61,7 @@ def _register_builtins() -> None:
     from .gemini import GeminiIntegration
     from .generic import GenericIntegration
     from .goose import GooseIntegration
+    from .hermes import HermesIntegration
     from .iflow import IflowIntegration
     from .junie import JunieIntegration
     from .kilocode import KilocodeIntegration
@@ -93,6 +94,7 @@ def _register_builtins() -> None:
     _register(GeminiIntegration())
     _register(GenericIntegration())
     _register(GooseIntegration())
+    _register(HermesIntegration())
     _register(IflowIntegration())
     _register(JunieIntegration())
     _register(KilocodeIntegration())

src/specify_cli/integrations/hermes/__init__.py

@@ -0,0 +1,278 @@
+"""Hermes Agent integration — skills-based agent.
+
+Hermes Agent (https://github.com/NousResearch/hermes-agent) is an open-source
+AI agent framework by Nous Research.  It stores skills in
+``~/.hermes/skills/`` (user-global) rather than a project-local directory.
+
+Usage::
+
+    specify init my-project --integration hermes
+    specify init --here --ai hermes
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from shutil import rmtree
+from typing import Any
+
+import yaml
+
+from ..base import IntegrationOption, SkillsIntegration
+from ..manifest import IntegrationManifest
+
+
+class HermesIntegration(SkillsIntegration):
+    """Integration for Hermes Agent skills.
+
+    Hermes loads skills from ``~/.hermes/skills/`` (user home directory)
+    rather than a project-local path.  Skills are installed directly to
+    the global directory — no project-local copies are created since
+    Hermes discovers them globally.  A project-local marker directory
+    (``.hermes/skills/`` empty) is created so extension commands (e.g.
+    git) can detect Hermes as an active integration.  Uninstall removes
+    both the marker and all global ``speckit-*`` skills, matching the
+    standard integration teardown behaviour.
+    """
+
+    key = "hermes"
+    config = {
+        "name": "Hermes Agent",
+        "folder": ".hermes/",
+        "commands_subdir": "skills",
+        "install_url": "https://github.com/NousResearch/hermes-agent",
+        "requires_cli": True,
+    }
+    registrar_config = {
+        "dir": "~/.hermes/skills",
+        "detect_dir": ".hermes/skills",
+        "format": "markdown",
+        "args": "$ARGUMENTS",
+        "extension": "/SKILL.md",
+    }
+    context_file = "AGENTS.md"
+
+    # -- Helpers -----------------------------------------------------------
+
+    @staticmethod
+    def _hermes_home_skills_dir() -> Path:
+        """Return ``~/.hermes/skills/`` — the global skills directory."""
+        return Path.home() / ".hermes" / "skills"
+
+    # -- Options -----------------------------------------------------------
+
+    @classmethod
+    def options(cls) -> list[IntegrationOption]:
+        return [
+            IntegrationOption(
+                "--skills",
+                is_flag=True,
+                default=True,
+                help="Install as agent skills (default for Hermes Agent)",
+            ),
+        ]
+
+    # -- Setup -------------------------------------------------------------
+
+    def setup(
+        self,
+        project_root: Path,
+        manifest: IntegrationManifest,
+        parsed_options: dict[str, Any] | None = None,
+        **opts: Any,
+    ) -> list[Path]:
+        """Install command templates as global Hermes skills.
+
+        Writes each skill directly to
+        ``~/.hermes/skills/speckit-<name>/SKILL.md`` where Hermes
+        discovers them at runtime.  No project-local SKILL.md copies are
+        created — the global directory is the single source of truth.
+        A project-local marker (``.hermes/skills/`` empty) is created
+        so extension commands (e.g. git) can detect Hermes as an active
+        integration.
+        """
+        templates = self.list_command_templates()
+        if not templates:
+            return []
+
+        # Safety check: verify manifest project_root matches (standard pattern)
+        project_root_resolved = project_root.resolve()
+        if manifest.project_root != project_root_resolved:
+            raise ValueError(
+                f"manifest.project_root ({manifest.project_root}) does not match "
+                f"project_root ({project_root_resolved})"
+            )
+
+        script_type = opts.get("script_type", "sh")
+        arg_placeholder = (
+            self.registrar_config.get("args", "$ARGUMENTS")
+            if self.registrar_config
+            else "$ARGUMENTS"
+        )
+
+        global_skills_dir = self._hermes_home_skills_dir()
+        global_skills_dir.mkdir(parents=True, exist_ok=True)
+
+        created: list[Path] = []
+
+        for src_file in templates:
+            raw = src_file.read_text(encoding="utf-8")
+
+            # Derive the skill name from the template stem
+            command_name = src_file.stem  # e.g. "plan"
+            skill_name = f"speckit-{command_name.replace('.', '-')}"
+
+            # Parse frontmatter for description
+            frontmatter: dict[str, Any] = {}
+            if raw.startswith("---"):
+                parts = raw.split("---", 2)
+                if len(parts) >= 3:
+                    try:
+                        fm = yaml.safe_load(parts[1])
+                        if isinstance(fm, dict):
+                            frontmatter = fm
+                    except yaml.YAMLError:
+                        pass
+
+            # Process body through the standard template pipeline
+            processed_body = self.process_template(
+                raw,
+                self.key,
+                script_type,
+                arg_placeholder,
+                context_file=self.context_file or "",
+                invoke_separator=self.invoke_separator,
+            )
+            # Strip the processed frontmatter — we rebuild it for skills.
+            if processed_body.startswith("---"):
+                parts = processed_body.split("---", 2)
+                if len(parts) >= 3:
+                    processed_body = parts[2]
+
+            # Select description
+            description = frontmatter.get("description", "")
+            if not description:
+                description = f"Spec Kit: {command_name} workflow"
+
+            # Build SKILL.md with manually formatted frontmatter
+            def _quote(v: str) -> str:
+                escaped = v.replace("\\", "\\\\").replace('"', '\\"')
+                return f'"{escaped}"'
+
+            skill_content = (
+                f"---\n"
+                f"name: {_quote(skill_name)}\n"
+                f"description: {_quote(description)}\n"
+                f"compatibility: "
+                f"{_quote('Requires spec-kit project structure with .specify/ directory')}\n"
+                f"metadata:\n"
+                f"  author: {_quote('github-spec-kit')}\n"
+                f"  source: {_quote('templates/commands/' + src_file.name)}\n"
+                f"---\n"
+                f"{processed_body}"
+            )
+
+            # Write directly to global ~/.hermes/skills/speckit-<name>/SKILL.md
+            skill_dir = global_skills_dir / skill_name
+            skill_dir.mkdir(parents=True, exist_ok=True)
+            skill_file = skill_dir / "SKILL.md"
+            normalized = skill_content.replace("\r\n", "\n")
+            skill_file.write_bytes(normalized.encode("utf-8"))
+            created.append(skill_file)
+
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
+        # Create project-local marker directory so extension commands
+        # (e.g. git) can detect Hermes as an active integration.
+        # Hermes itself ignores this directory — skills live globally.
+        (project_root / ".hermes" / "skills").mkdir(parents=True, exist_ok=True)
+
+        return created
+
+    # -- Uninstall ---------------------------------------------------------
+
+    def teardown(
+        self,
+        project_root: Path,
+        manifest: IntegrationManifest,
+        *,
+        force: bool = False,
+    ) -> tuple[list[Path], list[Path]]:
+        """Uninstall integration files including global Hermes skills.
+
+        Removes the managed context section from AGENTS.md, removes the
+        project-local marker directory (if empty), delegates to
+        ``manifest.uninstall()`` for project-local tracked files, and
+        removes all ``speckit-*`` skills under ``~/.hermes/skills/``.
+
+        Global skills are always removed on teardown — this matches the
+        standard integration behaviour where all files created by the
+        integration are removed on ``specify integration uninstall``.
+        """
+        # Remove managed context section from AGENTS.md
+        self.remove_context_section(project_root)
+
+        # Delegate to manifest for project-local tracked files (scripts,
+        # templates, context entries tracked in the manifest).
+        removed, skipped = manifest.uninstall(project_root, force=force)
+
+        # Remove project-local marker directory if empty
+        local_skills_dir = project_root / ".hermes" / "skills"
+        if local_skills_dir.is_dir() and not any(local_skills_dir.iterdir()):
+            local_skills_dir.rmdir()
+            hermes_dir = project_root / ".hermes"
+            if hermes_dir.is_dir() and not any(hermes_dir.iterdir()):
+                hermes_dir.rmdir()
+
+        # Remove all global Hermes skills for speckit — these are always
+        # removed on uninstall regardless of the force flag, matching the
+        # standard behaviour where all integration files are cleaned up.
+        global_skills_dir = self._hermes_home_skills_dir()
+        if global_skills_dir.is_dir():
+            for skill_dir in sorted(global_skills_dir.iterdir()):
+                if skill_dir.is_dir() and skill_dir.name.startswith("speckit-"):
+                    try:
+                        rmtree(skill_dir)
+                        removed.append(skill_dir)
+                    except OSError:
+                        skipped.append(skill_dir)
+
+        return removed, skipped
+
+    # -- CLI dispatch ------------------------------------------------------
+
+    def build_exec_args(
+        self,
+        prompt: str,
+        *,
+        model: str | None = None,
+        output_json: bool = True,
+    ) -> list[str] | None:
+        """Build Hermes CLI invocation for programmatic dispatch.
+
+        Uses ``hermes chat -Q -q`` for one-shot queries in quiet mode,
+        mapping slash-command invocations to the appropriate skill-based
+        dispatch.
+        """
+        args = [self.key, "chat", "-Q"]
+
+        if model:
+            args.extend(["-m", model])
+        if output_json:
+            args.append("--json")
+
+        # If prompt starts with a slash command, pass it directly
+        # so Hermes can dispatch to the appropriate skill.
+        if prompt.startswith("/"):
+            command, _, remainder = prompt[1:].partition(" ")
+            if command:
+                args.extend(["-s", command])
+                if remainder:
+                    args.extend(["-q", remainder])
+            else:
+                args.extend(["-q", prompt])
+        else:
+            args.extend(["-q", prompt])
+
+        return args

tests/integrations/test_integration_hermes.py

@@ -0,0 +1,329 @@
+"""Tests for HermesIntegration.
+
+Hermes is special among SkillsIntegration subclasses: it writes skills
+to ``~/.hermes/skills/`` (global) rather than the project-local
+``.hermes/skills/`` directory.  A project-local marker (empty directory)
+is created so extension commands (e.g. git) can detect Hermes.
+
+All tests that touch ``~/.hermes/`` use ``monkeypatch`` to isolate
+``Path.home()`` to a temp directory so the test suite is hermetic and
+non-destructive to a developer's real Hermes installation.
+"""
+
+from pathlib import Path
+
+from specify_cli.integrations import get_integration
+from specify_cli.integrations.manifest import IntegrationManifest
+
+from .test_integration_base_skills import SkillsIntegrationTests
+
+
+def _fake_home(tmp_path: Path) -> Path:
+    """Create and return an isolated home directory under *tmp_path*."""
+    home = tmp_path / "home"
+    home.mkdir(exist_ok=True)
+    return home
+
+
+class TestHermesIntegration(SkillsIntegrationTests):
+    KEY = "hermes"
+    FOLDER = ".hermes/"
+    COMMANDS_SUBDIR = "skills"
+    REGISTRAR_DIR = "~/.hermes/skills"
+    CONTEXT_FILE = "AGENTS.md"
+
+    # -- Hermes-specific setup: skills go to ~/.hermes/skills/ -------------
+
+    def test_setup_writes_to_global_skills_dir(self, tmp_path, monkeypatch):
+        """Skills are written to ~/.hermes/skills/, not project-local."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        created = i.setup(tmp_path, m)
+        skill_files = [f for f in created if "scripts" not in f.parts]
+
+        assert len(skill_files) > 0, "No skill files were created"
+        for f in skill_files:
+            # Every skill file should be under ~/.hermes/skills/speckit-*/
+            expected_prefix = str(home / ".hermes" / "skills")
+            assert str(f).startswith(expected_prefix), (
+                f"{f} is not under ~/.hermes/skills/"
+            )
+
+    def test_local_marker_dir_created(self, tmp_path, monkeypatch):
+        """Project-local .hermes/skills/ should exist but be empty."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        marker = tmp_path / ".hermes" / "skills"
+        assert marker.is_dir(), "Marker directory was not created"
+        # Should be empty (no SKILL.md files)
+        children = list(marker.iterdir())
+        assert children == [], f"Marker directory should be empty, got: {children}"
+
+    # -- Override shared tests that assume project-local skills ------------
+
+    def test_setup_writes_to_correct_directory(self, tmp_path, monkeypatch):
+        """Override: Hermes writes to global, not project-local."""
+        self.test_setup_writes_to_global_skills_dir(tmp_path, monkeypatch)
+
+    def test_plan_references_correct_context_file(self, tmp_path, monkeypatch):
+        """Plan skill goes to global dir, but we check it still references AGENTS.md."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        # Find the plan skill in global ~/.hermes/skills/
+        plan_file = home / ".hermes" / "skills" / "speckit-plan" / "SKILL.md"
+        assert plan_file.exists(), f"Plan skill {plan_file} not created globally"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan skill should reference {i.context_file!r} but it was not found"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            "Plan skill has unprocessed __CONTEXT_FILE__ placeholder"
+        )
+
+    def test_all_files_tracked_in_manifest(self, tmp_path, monkeypatch):
+        """Override: Hermes does not track skills in the project manifest
+        since they live globally.  Only project-local files (scripts,
+        templates, context) are tracked."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        created = i.setup(tmp_path, m)
+        for f in created:
+            # Global files (in ~/.hermes/) are not tracked in manifest
+            if str(f).startswith(str(home)):
+                continue
+            rel = f.resolve().relative_to(tmp_path.resolve()).as_posix()
+            assert rel in m.files, f"{rel} not tracked in manifest"
+
+    def test_install_uninstall_roundtrip(self, tmp_path, monkeypatch):
+        """Override: Hermes uninstall removes global skills + local marker."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        created = i.install(tmp_path, m)
+        assert len(created) > 0
+        m.save()
+        # All SKILL.md files should exist globally
+        for f in created:
+            if "SKILL.md" in str(f):
+                assert f.exists(), f"{f} does not exist"
+        # Global skills are removed on teardown without needing force
+        removed, skipped = i.teardown(tmp_path, m, force=False)
+        for f in created:
+            if "SKILL.md" in str(f):
+                assert not f.exists(), f"{f} should have been removed"
+        # Local marker should be gone
+        assert not (tmp_path / ".hermes" / "skills").exists()
+
+    def test_modified_file_survives_uninstall(self, tmp_path, monkeypatch):
+        """Override: Hermes global skills are ALWAYS removed on uninstall
+        (they live outside the project root and aren't hash-tracked in the
+        manifest), so a modified global skill is still removed — matching
+        the standard behaviour where all integration files are cleaned up."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        created = i.install(tmp_path, m)
+        m.save()
+        # Pick a global skill file
+        skill_files = [f for f in created if "SKILL.md" in str(f)]
+        assert len(skill_files) > 0
+        modified_file = skill_files[0]
+        modified_file.write_text("user modified this", encoding="utf-8")
+        removed, skipped = i.uninstall(tmp_path, m)
+        assert not modified_file.exists(), (
+            "Modified global skill should be removed on teardown (standard behaviour)"
+        )
+
+    def test_modified_global_skill_removed_on_teardown(self, tmp_path, monkeypatch):
+        """Override: Hermes global skills are removed on uninstall regardless
+        of the force flag, matching standard integration behaviour."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        created = i.install(tmp_path, m)
+        m.save()
+        # Pick a global skill file
+        skill_files = [f for f in created if "SKILL.md" in str(f)]
+        assert len(skill_files) > 0
+        modified_file = skill_files[0]
+        modified_file.write_text("user modified this", encoding="utf-8")
+        # Global skills are removed on teardown regardless of force flag
+        removed, skipped = i.teardown(tmp_path, m, force=False)
+        assert not modified_file.exists(), (
+            "Modified global skill should be removed on teardown (standard behaviour)"
+        )
+
+    def test_pre_existing_skills_not_removed(self, tmp_path, monkeypatch):
+        """Pre-existing non-speckit global skills should survive Hermes uninstall."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        # Create a foreign skill in the global dir first
+        global_skills_dir = i._hermes_home_skills_dir()
+        foreign_dir = global_skills_dir / "other-tool"
+        foreign_dir.mkdir(parents=True, exist_ok=True)
+        (foreign_dir / "SKILL.md").write_text("# Foreign skill\n")
+
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+
+        # Run teardown to verify foreign skill survives uninstall
+        i.teardown(tmp_path, m)
+
+        assert (foreign_dir / "SKILL.md").exists(), (
+            "Foreign skill was removed by teardown"
+        )
+
+    def test_complete_file_inventory_sh(self, tmp_path, monkeypatch):
+        """Override: Hermes init produces no local SKILL.md files,
+        only the empty .hermes/skills/ marker."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"inventory-sh-{self.KEY}"
+        project.mkdir()
+        old_cwd = Path.cwd()
+        import os
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY,
+                "--script", "sh", "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0, f"init failed: {result.output}"
+        actual = sorted(
+            p.relative_to(project).as_posix()
+            for p in project.rglob("*") if p.is_file()
+        )
+        # Ensure no .hermes/skills/speckit-*/SKILL.md in project dir
+        hermes_skill_files = [f for f in actual if f.startswith(".hermes/skills/speckit-")]
+        assert hermes_skill_files == [], (
+            f"Expected no local SKILL.md files, found: {hermes_skill_files}"
+        )
+        # Ensure the marker exists (empty dir won't appear in file listing)
+        assert (project / ".hermes" / "skills").is_dir()
+
+    def test_complete_file_inventory_ps(self, tmp_path, monkeypatch):
+        """Override: Same as sh variant but for PowerShell script type."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"inventory-ps-{self.KEY}"
+        project.mkdir()
+        old_cwd = Path.cwd()
+        import os
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY,
+                "--script", "ps", "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0, f"init failed: {result.output}"
+        actual = sorted(
+            p.relative_to(project).as_posix()
+            for p in project.rglob("*") if p.is_file()
+        )
+        hermes_skill_files = [f for f in actual if f.startswith(".hermes/skills/speckit-")]
+        assert hermes_skill_files == [], (
+            f"Expected no local SKILL.md files, found: {hermes_skill_files}"
+        )
+        assert (project / ".hermes" / "skills").is_dir()
+
+    def test_install_uninstall_cleanup(self, tmp_path, monkeypatch):
+        """Verify global skills are cleaned and local marker is removed."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        created = i.setup(tmp_path, m)
+
+        # Verify global skills exist
+        global_skills = [
+            f for f in created
+            if "SKILL.md" in str(f)
+            and str(f).startswith(str(home / ".hermes"))
+        ]
+        assert len(global_skills) > 0
+        for f in global_skills:
+            assert f.exists()
+
+        # Verify local marker exists
+        assert (tmp_path / ".hermes" / "skills").is_dir()
+
+        # Teardown — global skills removed without needing force=True
+        removed, skipped = i.teardown(tmp_path, m, force=False)
+
+        # Global skills removed
+        for f in global_skills:
+            assert not f.exists(), f"{f} should have been removed"
+
+        # Local marker removed
+        assert not (tmp_path / ".hermes" / "skills").exists(), (
+            "Local marker should be removed on teardown"
+        )
+
+
+class TestHermesAutoPromote:
+    """--ai hermes auto-promotes to integration path."""
+
+    def test_ai_hermes_without_ai_skills_auto_promotes(self, tmp_path, monkeypatch):
+        """--ai hermes should work the same as --integration hermes,
+        creating global skills and a local marker."""
+        home = _fake_home(tmp_path)
+        monkeypatch.setattr(Path, "home", lambda: home)
+
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        runner = CliRunner()
+        target = tmp_path / "test-proj"
+        result = runner.invoke(app, [
+            "init", str(target),
+            "--ai", "hermes",
+            "--no-git",
+            "--ignore-agent-tools",
+            "--script", "sh",
+        ])
+
+        assert result.exit_code == 0, f"init --ai hermes failed: {result.output}"
+        # Skills should be in global ~/.hermes/skills/
+        assert (home / ".hermes" / "skills" / "speckit-plan" / "SKILL.md").exists()
+        # Local marker should exist
+        assert (target / ".hermes" / "skills").is_dir()
+        # No SKILL.md files in project-local dir
+        local_skills = list((target / ".hermes" / "skills").iterdir())
+        assert local_skills == [], f"Local skills dir should be empty, got: {local_skills}"

tests/test_extensions.py

@@ -3744,13 +3744,20 @@ class TestExtensionUpdateCLI:
         ).read_text()
         assert restored_config_content == original_config_content
 
-    def test_update_failure_rolls_back_registry_hooks_and_commands(self, tmp_path):
+    def test_update_failure_rolls_back_registry_hooks_and_commands(self, tmp_path, monkeypatch):
         """Failed update should restore original registry, hooks, and command files."""
         from typer.testing import CliRunner
         from unittest.mock import patch
         from specify_cli import app
         import yaml
 
+        # Isolate home directory so Hermes' global ~/.hermes/skills/ doesn't
+        # interfere — without a real skills dir, Hermes is skipped during
+        # command registration, keeping the test focused on Claude/Codex/etc.
+        fake_home = tmp_path / "home"
+        fake_home.mkdir()
+        monkeypatch.setattr(Path, "home", lambda: fake_home)
+
         runner = CliRunner()
         project_dir = tmp_path / "project"
         project_dir.mkdir()
@@ -3772,7 +3779,9 @@ class TestExtensionUpdateCLI:
             if agent_name not in agent_registrar.AGENT_CONFIGS:
                 continue
             agent_cfg = agent_registrar.AGENT_CONFIGS[agent_name]
-            commands_dir = project_dir / agent_cfg["dir"]
+            commands_dir = AgentRegistrar._resolve_agent_dir(
+                agent_name, agent_cfg, project_dir
+            )
             for cmd_name in cmd_names:
                 output_name = AgentRegistrar._compute_output_name(agent_name, cmd_name, agent_cfg)
                 cmd_path = commands_dir / f"{output_name}{agent_cfg['extension']}"