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.

Author: majordave

src/specify_cli/__init__.py

@@ -4328,7 +4328,9 @@ 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)
@@ -4489,7 +4491,9 @@ 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 +654,25 @@ def _resolve_agent_dir(
     ) -> 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("~"):
+            agent_dir = Path(dir_str).expanduser()
+        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:

src/specify_cli/integrations/hermes/__init__.py

@@ -44,7 +44,7 @@ class HermesIntegration(SkillsIntegration):
         "requires_cli": True,
     }
     registrar_config = {
-        "dir": ".hermes/skills",
+        "dir": "~/.hermes/skills",
         "format": "markdown",
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",

tests/integrations/test_integration_hermes.py

@@ -29,7 +29,7 @@ class TestHermesIntegration(SkillsIntegrationTests):
     KEY = "hermes"
     FOLDER = ".hermes/"
     COMMANDS_SUBDIR = "skills"
-    REGISTRAR_DIR = ".hermes/skills"
+    REGISTRAR_DIR = "~/.hermes/skills"
     CONTEXT_FILE = "AGENTS.md"
 
     # -- Hermes-specific setup: skills go to ~/.hermes/skills/ -------------

tests/test_extensions.py

@@ -3744,13 +3744,20 @@ def fake_install_from_zip(self_obj, _zip_path, speckit_version):
         ).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 @@ def test_update_failure_rolls_back_registry_hooks_and_commands(self, tmp_path):
             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']}"