refactor: install skills directly to skills folder instead of nested path

- Add source_directory field to Skill class to store full path in repo
- Change directory field to store just the skill folder name for installation
- Update _fetch_skills_from_repo to set both fields correctly
- Update _download_and_install_skill to use source_directory for source location
- Fix tests to match new behavior

Before: ~/.factory/skills/devops/terraform-module-builder/skills/terraform-module-builder/
After:  ~/.factory/skills/terraform-module-builder/

Author: zhujian0805

code_assistant_manager/skill_repos.json

@@ -30,6 +30,7 @@
     "owner": "jeremylongshore",
     "name": "claude-code-plugins-plus",
     "branch": "main",
-    "enabled": true
+    "enabled": true,
+    "skillsPath": "plugins"
   }
 }

code_assistant_manager/skills.py

@@ -94,6 +94,7 @@ def __init__(
         repo_branch: Optional[str] = None,
         skills_path: Optional[str] = None,
         readme_url: Optional[str] = None,
+        source_directory: Optional[str] = None,
     ):
         self.key = key
         self.name = name
@@ -105,6 +106,8 @@ def __init__(
         self.repo_branch = repo_branch or "main"
         self.skills_path = skills_path
         self.readme_url = readme_url
+        # source_directory stores full path in repo; directory is just the skill folder name for installation
+        self.source_directory = source_directory
 
     def to_dict(self) -> Dict:
         """Convert to dictionary."""
@@ -125,6 +128,8 @@ def to_dict(self) -> Dict:
             data["skillsPath"] = self.skills_path
         if self.readme_url:
             data["readmeUrl"] = self.readme_url
+        if self.source_directory:
+            data["sourceDirectory"] = self.source_directory
         return data
 
     @classmethod
@@ -141,6 +146,7 @@ def from_dict(cls, data: Dict) -> "Skill":
             repo_branch=data.get("repoBranch"),
             skills_path=data.get("skillsPath"),
             readme_url=data.get("readmeUrl"),
+            source_directory=data.get("sourceDirectory"),
         )
 
 
@@ -395,17 +401,19 @@ def _download_and_install_skill(self, skill: Skill, install_dir: Path) -> None:
 
         try:
             # Determine the source path within the downloaded repo
+            # Use source_directory if available (full path in repo), otherwise fall back to directory
+            source_dir = skill.source_directory or skill.directory
             if skill.skills_path:
-                source_path = temp_dir / skill.skills_path.strip("/") / skill.directory
+                source_path = temp_dir / skill.skills_path.strip("/") / source_dir
             else:
-                source_path = temp_dir / skill.directory
+                source_path = temp_dir / source_dir
 
             if not source_path.exists():
                 raise ValueError(
                     f"Skill directory not found in repository: {source_path}"
                 )
 
-            # Copy to install directory
+            # Copy to install directory using just the skill folder name (directory field)
             dest_path = install_dir / skill.directory
             if dest_path.exists():
                 shutil.rmtree(dest_path)
@@ -643,14 +651,17 @@ def _fetch_skills_from_repo(self, repo: SkillRepo) -> List[Skill]:
                 meta = self._parse_skill_metadata(skill_md)
 
                 try:
-                    # Calculate relative path from scan_dir
+                    # Calculate relative path from scan_dir (full path in repo relative to skills_path)
                     rel_path = skill_dir.relative_to(scan_dir)
-                    directory = str(rel_path).replace("\\", "/")
+                    source_directory = str(rel_path).replace("\\", "/")
 
                     # Skip if SKILL.md is at the root of scan_dir (directory == ".")
                     # to avoid conflicts when installing to the root of skills directory
-                    if directory == ".":
+                    if source_directory == ".":
                         continue
+
+                    # The install directory is just the skill folder name (last part of path)
+                    directory = skill_dir.name
                 except ValueError:
                     continue
 
@@ -659,8 +670,8 @@ def _fetch_skills_from_repo(self, repo: SkillRepo) -> List[Skill]:
                 readme_path = str(path_from_repo_root).replace("\\", "/")
 
                 skill = Skill(
-                    key=f"{repo.owner}/{repo.name}:{directory}",
-                    name=meta.get("name", directory.split("/")[-1]),
+                    key=f"{repo.owner}/{repo.name}:{source_directory}",
+                    name=meta.get("name", directory),
                     description=meta.get("description", ""),
                     directory=directory,
                     installed=False,
@@ -669,6 +680,7 @@ def _fetch_skills_from_repo(self, repo: SkillRepo) -> List[Skill]:
                     repo_branch=actual_branch,
                     skills_path=repo.skills_path,
                     readme_url=f"https://github.com/{repo.owner}/{repo.name}/tree/{actual_branch}/{readme_path}",
+                    source_directory=source_directory,
                 )
                 skills.append(skill)
                 logger.debug(f"Found skill: {skill.key}")

tests/test_skills_recursive.py

@@ -53,21 +53,24 @@ def test_fetch_skills_recursive(self, mock_download, skill_manager):
             # Verify results
             assert len(skills) == 2
 
+            # directory is now just the skill folder name for installation
             skill_map = {s.directory: s for s in skills}
 
             # Check Skill 1
             assert "skill1" in skill_map
             s1 = skill_map["skill1"]
             assert s1.name == "Skill One"
             assert s1.key == "owner/repo:skill1"
+            assert s1.source_directory == "skill1"
             assert s1.readme_url.endswith("/skills/skill1")
 
             # Check Skill 2
-            # directory should use forward slashes
-            assert "category/skill2" in skill_map
-            s2 = skill_map["category/skill2"]
+            # directory is just the folder name, source_directory has full path
+            assert "skill2" in skill_map
+            s2 = skill_map["skill2"]
             assert s2.name == "Skill Two"
             assert s2.key == "owner/repo:category/skill2"
+            assert s2.source_directory == "category/skill2"
             assert s2.readme_url.endswith("/skills/category/skill2")
 
     @patch("code_assistant_manager.skills.SkillManager._download_repo")
@@ -95,5 +98,8 @@ def test_fetch_skills_root_structure(self, mock_download, skill_manager):
 
             # Should find nested skill but skip root skill
             assert len(skills) == 1
-            assert skills[0].directory == "nested/skill"
+            # directory is now just the folder name for installation
+            assert skills[0].directory == "skill"
+            # source_directory has the full path
+            assert skills[0].source_directory == "nested/skill"
             assert skills[0].name == "Nested"

tests/unit/test_skills.py

@@ -321,8 +321,10 @@ def test_manager_sync_installed_status(self, temp_config_dir, temp_install_dir):
             "code_assistant_manager.skills.SKILL_INSTALL_DIRS",
             {"test_app": temp_install_dir},
         ):
-            # Create skill1 directory in install location
-            (temp_install_dir / "skill1").mkdir(parents=True)
+            # Create skill1 directory in install location with SKILL.md
+            skill1_dir = temp_install_dir / "skill1"
+            skill1_dir.mkdir(parents=True)
+            (skill1_dir / "SKILL.md").write_text("---\nname: Skill 1\n---\n# Skill 1")
 
             manager.sync_installed_status("test_app")