feat: add Hermes Agent integration (with review fixes)

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

@@ -1944,11 +1944,14 @@ 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)
@@ -2090,8 +2093,9 @@ 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:
@@ -4325,7 +4329,9 @@ 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)
@@ -4486,7 +4492,9 @@ 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 @@ 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("~"):
+            # 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 @@ def register_commands_for_all_agents(
 
         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 @@ def register_commands_for_non_skill_agents(
         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())