feat: introduce skill management tool for agent-created skills and skills migration to ~/.hermes

- Added a new `skill_manager_tool` to enable agents to create, update, and delete their own skills, enhancing procedural memory capabilities.
- Updated the skills directory structure to support user-created skills in `~/.hermes/skills/`, allowing for better organization and management.
- Enhanced the CLI and documentation to reflect the new skill management functionalities, including detailed instructions on creating and modifying skills.
- Implemented a manifest-based syncing mechanism for bundled skills to ensure user modifications are preserved during updates.

hermes_cli/main.py

@@ -190,6 +190,19 @@ def cmd_update(args):
         print()
         print("✓ Code updated!")
         
+        # Sync any new bundled skills (manifest-based -- won't overwrite or re-add deleted skills)
+        try:
+            from tools.skills_sync import sync_skills
+            print()
+            print("→ Checking for new bundled skills...")
+            result = sync_skills(quiet=True)
+            if result["copied"]:
+                print(f"  + {len(result['copied'])} new skill(s): {', '.join(result['copied'])}")
+            else:
+                print("  ✓ Skills are up to date")
+        except Exception:
+            pass
+        
         # Check for config migrations
         print()
         print("→ Checking configuration for new options...")