feat: wire skills.external_dirs into all remaining discovery paths

The config key skills.external_dirs and core resolution (get_all_skills_dirs,
get_external_skills_dirs in agent/skill_utils.py) already existed but several
code paths still only scanned SKILLS_DIR. Now external dirs are respected
everywhere:

- skills_categories(): scan all dirs for category discovery
- _get_category_from_path(): resolve categories against any skills root
- skill_manager_tool._find_skill(): search all dirs for edit/patch/delete
- credential_files.get_skills_directory_mount(): mount all dirs into
  Docker/Singularity containers (external dirs at external_skills/<idx>)
- credential_files.iter_skills_files(): list files from all dirs for
  Modal/Daytona upload
- tools/environments/ssh.py: rsync all skill dirs to remote hosts
- gateway _check_unavailable_skill(): check disabled skills across all dirs

Usage in config.yaml:
  skills:
    external_dirs:
      - ~/repos/agent-skills/hermes
      - /shared/team-skills

tools/skills_tool.py

@@ -427,15 +427,25 @@ def _get_category_from_path(skill_path: Path) -> Optional[str]:
     Extract category from skill path based on directory structure.
 
     For paths like: ~/.hermes/skills/mlops/axolotl/SKILL.md -> "mlops"
+    Also works for external skill dirs configured via skills.external_dirs.
     """
+    # Try the module-level SKILLS_DIR first (respects monkeypatching in tests),
+    # then fall back to external dirs from config.
+    dirs_to_check = [SKILLS_DIR]
     try:
-        rel_path = skill_path.relative_to(SKILLS_DIR)
-        parts = rel_path.parts
-        if len(parts) >= 3:
-            return parts[0]
-        return None
-    except ValueError:
-        return None
+        from agent.skill_utils import get_external_skills_dirs
+        dirs_to_check.extend(get_external_skills_dirs())
+    except Exception:
+        pass
+    for skills_dir in dirs_to_check:
+        try:
+            rel_path = skill_path.relative_to(skills_dir)
+            parts = rel_path.parts
+            if len(parts) >= 3:
+                return parts[0]
+        except ValueError:
+            continue
+    return None
 
 
 def _estimate_tokens(content: str) -> int:
@@ -645,7 +655,14 @@ def skills_categories(verbose: bool = False, task_id: str = None) -> str:
         JSON string with list of categories and their descriptions
     """
     try:
-        if not SKILLS_DIR.exists():
+        # Use module-level SKILLS_DIR (respects monkeypatching) + external dirs
+        all_dirs = [SKILLS_DIR] if SKILLS_DIR.exists() else []
+        try:
+            from agent.skill_utils import get_external_skills_dirs
+            all_dirs.extend(d for d in get_external_skills_dirs() if d.exists())
+        except Exception:
+            pass
+        if not all_dirs:
             return json.dumps(
                 {
                     "success": True,
@@ -657,25 +674,26 @@ def skills_categories(verbose: bool = False, task_id: str = None) -> str:
 
         category_dirs = {}
         category_counts: Dict[str, int] = {}
-        for skill_md in SKILLS_DIR.rglob("SKILL.md"):
-            if any(part in _EXCLUDED_SKILL_DIRS for part in skill_md.parts):
-                continue
+        for scan_dir in all_dirs:
+            for skill_md in scan_dir.rglob("SKILL.md"):
+                if any(part in _EXCLUDED_SKILL_DIRS for part in skill_md.parts):
+                    continue
 
-            try:
-                frontmatter, _ = _parse_frontmatter(
-                    skill_md.read_text(encoding="utf-8")[:4000]
-                )
-            except Exception:
-                frontmatter = {}
+                try:
+                    frontmatter, _ = _parse_frontmatter(
+                        skill_md.read_text(encoding="utf-8")[:4000]
+                    )
+                except Exception:
+                    frontmatter = {}
 
-            if not skill_matches_platform(frontmatter):
-                continue
+                if not skill_matches_platform(frontmatter):
+                    continue
 
-            category = _get_category_from_path(skill_md)
-            if category:
-                category_counts[category] = category_counts.get(category, 0) + 1
-                if category not in category_dirs:
-                    category_dirs[category] = SKILLS_DIR / category
+                category = _get_category_from_path(skill_md)
+                if category:
+                    category_counts[category] = category_counts.get(category, 0) + 1
+                    if category not in category_dirs:
+                        category_dirs[category] = skill_md.parent.parent
 
         categories = []
         for name in sorted(category_dirs.keys()):