fix: Fix local repo extraction limitations (code analyzer, exclusions, enhancement)

This commit fixes three critical limitations discovered during local repository skill extraction testing:

**Fix 1: Code Analyzer Import Issue**
- Changed unified_scraper.py to use absolute imports instead of relative imports
- Fixed: `from github_scraper import` → `from skill_seekers.cli.github_scraper import`
- Fixed: `from pdf_scraper import` → `from skill_seekers.cli.pdf_scraper import`
- Result: CodeAnalyzer now available during extraction, deep analysis works

**Fix 2: Unity Library Exclusions**
- Updated should_exclude_dir() to accept and check full directory paths
- Updated _extract_file_tree_local() to pass both dir name and full path
- Added exclusion config passing from unified_scraper to github_scraper
- Result: exclude_dirs_additional now works (297 files excluded in test)

**Fix 3: AI Enhancement for Single Sources**
- Changed read_reference_files() to use rglob() for recursive search
- Now finds reference files in subdirectories (e.g., references/github/README.md)
- Result: AI enhancement works with unified skills that have nested references

**Test Results:**
- Code Analyzer: ✅ Working (deep analysis running)
- Unity Exclusions: ✅ Working (297 files excluded from 679)
- AI Enhancement: ✅ Working (finds and reads nested references)

**Files Changed:**
- src/skill_seekers/cli/unified_scraper.py (Fix 1 & 2)
- src/skill_seekers/cli/github_scraper.py (Fix 2)
- src/skill_seekers/cli/utils.py (Fix 3)

**Test Artifacts:**
- configs/deck_deck_go_local.json (test configuration)
- docs/LOCAL_REPO_TEST_RESULTS.md (comprehensive test report)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

src/skill_seekers/cli/github_scraper.py

@@ -301,9 +301,29 @@ class GitHubScraper:
         except GithubException as e:
             logger.warning(f"Could not fetch languages: {e}")
 
-    def should_exclude_dir(self, dir_name: str) -> bool:
-        """Check if directory should be excluded from analysis."""
-        return dir_name in self.excluded_dirs or dir_name.startswith('.')
+    def should_exclude_dir(self, dir_name: str, dir_path: str = None) -> bool:
+        """
+        Check if directory should be excluded from analysis.
+
+        Args:
+            dir_name: Directory name (e.g., "Examples & Extras")
+            dir_path: Full relative path (e.g., "TextMesh Pro/Examples & Extras")
+
+        Returns:
+            True if directory should be excluded
+        """
+        # Check directory name
+        if dir_name in self.excluded_dirs or dir_name.startswith('.'):
+            return True
+
+        # Check full path if provided (for nested exclusions like "TextMesh Pro/Examples & Extras")
+        if dir_path:
+            for excluded in self.excluded_dirs:
+                # Match if path contains the exclusion pattern
+                if excluded in dir_path or dir_path.startswith(excluded):
+                    return True
+
+        return False
 
     def _extract_file_tree(self):
         """Extract repository file tree structure (dual-mode: GitHub API or local filesystem)."""
@@ -322,16 +342,29 @@ class GitHubScraper:
             logger.error(f"Local repository path not found: {self.local_repo_path}")
             return
 
-        file_tree = []
-        for root, dirs, files in os.walk(self.local_repo_path):
-            # Exclude directories in-place to prevent os.walk from descending into them
-            dirs[:] = [d for d in dirs if not self.should_exclude_dir(d)]
+        # Log exclusions for debugging
+        logger.info(f"Directory exclusions ({len(self.excluded_dirs)} total): {sorted(list(self.excluded_dirs)[:10])}")
 
-            # Calculate relative path from repo root
+        file_tree = []
+        excluded_count = 0
+        for root, dirs, files in os.walk(self.local_repo_path):
+            # Calculate relative path from repo root first (needed for exclusion checks)
             rel_root = os.path.relpath(root, self.local_repo_path)
             if rel_root == '.':
                 rel_root = ''
 
+            # Exclude directories in-place to prevent os.walk from descending into them
+            # Pass both dir name and full path for path-based exclusions
+            filtered_dirs = []
+            for d in dirs:
+                dir_path = os.path.join(rel_root, d) if rel_root else d
+                if self.should_exclude_dir(d, dir_path):
+                    excluded_count += 1
+                    logger.debug(f"Excluding directory: {dir_path}")
+                else:
+                    filtered_dirs.append(d)
+            dirs[:] = filtered_dirs
+
             # Add directories
             for dir_name in dirs:
                 dir_path = os.path.join(rel_root, dir_name) if rel_root else dir_name
@@ -357,7 +390,7 @@ class GitHubScraper:
                 })
 
         self.extracted_data['file_tree'] = file_tree
-        logger.info(f"File tree built (local mode): {len(file_tree)} items")
+        logger.info(f"File tree built (local mode): {len(file_tree)} items ({excluded_count} directories excluded)")
 
     def _extract_file_tree_github(self):
         """Extract file tree from GitHub API (rate-limited)."""