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.

tools/skills_sync.py

@@ -0,0 +1,150 @@
+#!/usr/bin/env python3
+"""
+Skills Sync -- Manifest-based seeding of bundled skills into ~/.hermes/skills/.
+
+On fresh install: copies all bundled skills from the repo's skills/ directory
+into ~/.hermes/skills/ and records every skill name in a manifest file.
+
+On update: copies only NEW bundled skills (names not in the manifest) so that
+user deletions are permanent and user modifications are never overwritten.
+
+The manifest lives at ~/.hermes/skills/.bundled_manifest and is a simple
+newline-delimited list of skill names that have been offered to the user.
+"""
+
+import json
+import os
+import shutil
+from pathlib import Path
+from typing import List, Tuple
+
+
+HERMES_HOME = Path(os.getenv("HERMES_HOME", Path.home() / ".hermes"))
+SKILLS_DIR = HERMES_HOME / "skills"
+MANIFEST_FILE = SKILLS_DIR / ".bundled_manifest"
+
+
+def _get_bundled_dir() -> Path:
+    """Locate the bundled skills/ directory in the repo."""
+    return Path(__file__).parent.parent / "skills"
+
+
+def _read_manifest() -> set:
+    """Read the set of skill names already offered to the user."""
+    if not MANIFEST_FILE.exists():
+        return set()
+    try:
+        return set(
+            line.strip()
+            for line in MANIFEST_FILE.read_text(encoding="utf-8").splitlines()
+            if line.strip()
+        )
+    except (OSError, IOError):
+        return set()
+
+
+def _write_manifest(names: set):
+    """Write the manifest file."""
+    MANIFEST_FILE.parent.mkdir(parents=True, exist_ok=True)
+    MANIFEST_FILE.write_text(
+        "\n".join(sorted(names)) + "\n",
+        encoding="utf-8",
+    )
+
+
+def _discover_bundled_skills(bundled_dir: Path) -> List[Tuple[str, Path]]:
+    """
+    Find all SKILL.md files in the bundled directory.
+    Returns list of (skill_name, skill_directory_path) tuples.
+    """
+    skills = []
+    if not bundled_dir.exists():
+        return skills
+
+    for skill_md in bundled_dir.rglob("SKILL.md"):
+        path_str = str(skill_md)
+        if "/.git/" in path_str or "/.github/" in path_str or "/.hub/" in path_str:
+            continue
+        skill_dir = skill_md.parent
+        skill_name = skill_dir.name
+        skills.append((skill_name, skill_dir))
+
+    return skills
+
+
+def _compute_relative_dest(skill_dir: Path, bundled_dir: Path) -> Path:
+    """
+    Compute the destination path in SKILLS_DIR preserving the category structure.
+    e.g., bundled/skills/mlops/axolotl -> ~/.hermes/skills/mlops/axolotl
+    """
+    rel = skill_dir.relative_to(bundled_dir)
+    return SKILLS_DIR / rel
+
+
+def sync_skills(quiet: bool = False) -> dict:
+    """
+    Sync bundled skills into ~/.hermes/skills/ using the manifest.
+
+    - Skills whose names are already in the manifest are skipped (even if deleted by user).
+    - New skills (not in manifest) are copied to SKILLS_DIR and added to the manifest.
+
+    Returns:
+        dict with keys: copied (list of names), skipped (int), total_bundled (int)
+    """
+    bundled_dir = _get_bundled_dir()
+    if not bundled_dir.exists():
+        return {"copied": [], "skipped": 0, "total_bundled": 0}
+
+    SKILLS_DIR.mkdir(parents=True, exist_ok=True)
+    manifest = _read_manifest()
+    bundled_skills = _discover_bundled_skills(bundled_dir)
+    copied = []
+    skipped = 0
+
+    for skill_name, skill_src in bundled_skills:
+        if skill_name in manifest:
+            skipped += 1
+            continue
+
+        dest = _compute_relative_dest(skill_src, bundled_dir)
+        try:
+            if dest.exists():
+                # Skill dir exists (maybe user created one with same name) -- don't overwrite
+                skipped += 1
+            else:
+                dest.parent.mkdir(parents=True, exist_ok=True)
+                shutil.copytree(skill_src, dest)
+                copied.append(skill_name)
+                if not quiet:
+                    print(f"  + {skill_name}")
+        except (OSError, IOError) as e:
+            if not quiet:
+                print(f"  ! Failed to copy {skill_name}: {e}")
+
+        manifest.add(skill_name)
+
+    # Also copy DESCRIPTION.md files for categories (if not already present)
+    for desc_md in bundled_dir.rglob("DESCRIPTION.md"):
+        rel = desc_md.relative_to(bundled_dir)
+        dest_desc = SKILLS_DIR / rel
+        if not dest_desc.exists():
+            try:
+                dest_desc.parent.mkdir(parents=True, exist_ok=True)
+                shutil.copy2(desc_md, dest_desc)
+            except (OSError, IOError):
+                pass
+
+    _write_manifest(manifest)
+
+    return {
+        "copied": copied,
+        "skipped": skipped,
+        "total_bundled": len(bundled_skills),
+    }
+
+
+if __name__ == "__main__":
+    print("Syncing bundled skills into ~/.hermes/skills/ ...")
+    result = sync_skills(quiet=False)
+    print(f"\nDone: {len(result['copied'])} new, {result['skipped']} skipped, "
+          f"{result['total_bundled']} total bundled.")