Merge: skill reorganization + sub-category support

- Sub-category support in prompt_builder.py (backwards-compatible)
- Split mlops (40 skills) into 7 logical sub-categories
- Merged 8 singleton categories into logical parents
- Fixed 2 misplaced skills (code-review, ml-paper-writing)

agent/prompt_builder.py

@@ -195,6 +195,8 @@ def build_skills_system_prompt() -> str:
 
     # Collect skills with descriptions, grouped by category
     # Each entry: (skill_name, description)
+    # Supports sub-categories: skills/mlops/training/axolotl/SKILL.md
+    # → category "mlops/training", skill "axolotl"
     skills_by_category: dict[str, list[tuple[str, str]]] = {}
     for skill_file in skills_dir.rglob("SKILL.md"):
         # Skip skills incompatible with the current OS platform
@@ -203,8 +205,13 @@ def build_skills_system_prompt() -> str:
         rel_path = skill_file.relative_to(skills_dir)
         parts = rel_path.parts
         if len(parts) >= 2:
-            category = parts[0]
+            # Category is everything between skills_dir and the skill folder
+            # e.g. parts = ("mlops", "training", "axolotl", "SKILL.md")
+            #   → category = "mlops/training", skill_name = "axolotl"
+            # e.g. parts = ("github", "github-auth", "SKILL.md")
+            #   → category = "github", skill_name = "github-auth"
             skill_name = parts[-2]
+            category = "/".join(parts[:-2]) if len(parts) > 2 else parts[0]
         else:
             category = "general"
             skill_name = skill_file.parent.name
@@ -215,9 +222,11 @@ def build_skills_system_prompt() -> str:
         return ""
 
     # Read category-level descriptions from DESCRIPTION.md
+    # Checks both the exact category path and parent directories
     category_descriptions = {}
     for category in skills_by_category:
-        desc_file = skills_dir / category / "DESCRIPTION.md"
+        cat_path = Path(category)
+        desc_file = skills_dir / cat_path / "DESCRIPTION.md"
         if desc_file.exists():
             try:
                 content = desc_file.read_text(encoding="utf-8")