fix(sync): skip DESCRIPTION.md copy for ghost category dirs

sync_skills() unconditionally copied DESCRIPTION.md into user skills
dir, recreating empty category directories that the user had removed.
The SKILL.md deletion logic already respected user choices (skip if
in manifest but not on disk), but DESCRIPTION.md copy bypassed this
by creating directories with mkdir(parents=True) before any check.

Fix: only copy DESCRIPTION.md when the category directory already
exists AND contains at least one SKILL.md. This aligns DESCRIPTION.md
behavior with the existing 'respect user deletion' principle.

Adds two regression tests:
- test_description_md_not_copied_to_ghost_dirs
- test_description_md_not_recreated_after_user_deletion

tests/tools/test_skills_sync.py

@@ -502,6 +502,58 @@ class TestSyncSkills:
         assert manifest["old-skill"] != old_hash
 
 
+    def test_description_md_not_copied_to_ghost_dirs(self, tmp_path):
+        """DESCRIPTION.md should not be copied into empty category dirs with no SKILL.md."""
+        bundled = tmp_path / "bundled_skills"
+        # Bundled: a category with both SKILL.md and DESCRIPTION.md
+        (bundled / "apple" / "findmy").mkdir(parents=True)
+        (bundled / "apple" / "findmy" / "SKILL.md").write_text("# FindMy")
+        (bundled / "apple" / "DESCRIPTION.md").write_text("Apple stuff")
+        # Bundled: a stub-only category (only DESCRIPTION.md, no SKILL.md anywhere)
+        (bundled / "empty-cat").mkdir(parents=True)
+        (bundled / "empty-cat" / "DESCRIPTION.md").write_text("Empty")
+
+        skills_dir = tmp_path / "user_skills"
+        manifest_file = skills_dir / ".bundled_manifest"
+        # User deleted all skills from apple — only the DESCRIPTION.md ghost remains
+        # (or was never installed). The category dir does NOT exist on disk.
+        # empty-cat also doesn't exist.
+
+        with self._patches(bundled, skills_dir, manifest_file):
+            sync_skills(quiet=True)
+
+        # findmy was synced (new install) → apple/ now has SKILL.md → DESCRIPTION.md should be copied
+        assert (skills_dir / "apple" / "findmy" / "SKILL.md").exists()
+        assert (skills_dir / "apple" / "DESCRIPTION.md").exists()
+
+        # empty-cat has no SKILL.md anywhere → DESCRIPTION.md should NOT be copied
+        # and the directory should NOT be created
+        assert not (skills_dir / "empty-cat").exists()
+
+    def test_description_md_not_recreated_after_user_deletion(self, tmp_path):
+        """After user deletes all skills from a category, DESCRIPTION.md should not come back."""
+        bundled = tmp_path / "bundled_skills"
+        (bundled / "apple" / "findmy").mkdir(parents=True)
+        (bundled / "apple" / "findmy" / "SKILL.md").write_text("# FindMy")
+        (bundled / "apple" / "DESCRIPTION.md").write_text("Apple stuff")
+
+        skills_dir = tmp_path / "user_skills"
+        manifest_file = skills_dir / ".bundled_manifest"
+        skills_dir.mkdir(parents=True)
+
+        # Simulate: user previously had findmy installed, then deleted it.
+        # Manifest still has findmy (origin hash from last sync).
+        old_hash = _dir_hash(bundled / "apple" / "findmy")
+        manifest_file.write_text(f"findmy:{old_hash}\n")
+        # No apple/ dir on disk — user deleted everything.
+
+        with self._patches(bundled, skills_dir, manifest_file):
+            sync_skills(quiet=True)
+
+        # findmy should NOT be re-added (user deleted it)
+        assert not (skills_dir / "apple").exists()
+
+
 class TestGetBundledDir:
     def test_env_var_override(self, tmp_path, monkeypatch):
         """HERMES_BUNDLED_SKILLS env var overrides the default path resolution."""

tools/skills_sync.py

@@ -278,16 +278,21 @@ def sync_skills(quiet: bool = False) -> dict:
     for name in cleaned:
         del manifest[name]
 
-    # Also copy DESCRIPTION.md files for categories (if not already present)
+    # Also copy DESCRIPTION.md files for categories (if not already present).
+    # Only copy when the category already has at least one SKILL.md on disk —
+    # this prevents recreating empty "ghost" directories that the user removed.
     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) as e:
-                logger.debug("Could not copy %s: %s", desc_md, e)
+        if dest_desc.exists():
+            continue
+        cat_dir = dest_desc.parent
+        if not cat_dir.exists() or not list(cat_dir.rglob("SKILL.md")):
+            continue
+        try:
+            shutil.copy2(desc_md, dest_desc)
+        except (OSError, IOError) as e:
+            logger.debug("Could not copy %s: %s", desc_md, e)
 
     _write_manifest(manifest)