feat(C3.9): Add project documentation extraction from markdown files

- Scan ALL .md files in project (README, docs/, etc.)
- Smart categorization by folder/filename (overview, architecture, guides, etc.)
- Processing depth: surface=raw copy, deep=parse+summarize, full=AI-enhanced
- AI enhancement at level 2+ adds topic extraction and cross-references
- New "Project Documentation" section in SKILL.md with summaries
- Output to references/documentation/ organized by category
- Default ON, use --skip-docs to disable
- Add skip_docs parameter to MCP scrape_codebase_tool
- Add 15 new tests for markdown documentation features

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

src/skill_seekers/cli/main.py

@@ -315,6 +315,7 @@ For more information: https://github.com/yusufkaraaslan/Skill_Seekers
     analyze_parser.add_argument("--skip-test-examples", action="store_true", help="Skip test examples")
     analyze_parser.add_argument("--skip-how-to-guides", action="store_true", help="Skip guides")
     analyze_parser.add_argument("--skip-config-patterns", action="store_true", help="Skip config")
+    analyze_parser.add_argument("--skip-docs", action="store_true", help="Skip project docs (README, docs/)")
     analyze_parser.add_argument("--no-comments", action="store_true", help="Skip comments")
     analyze_parser.add_argument("--verbose", action="store_true", help="Verbose logging")
 
@@ -609,6 +610,8 @@ def main(argv: list[str] | None = None) -> int:
                 sys.argv.append("--skip-how-to-guides")
             if args.skip_config_patterns:
                 sys.argv.append("--skip-config-patterns")
+            if args.skip_docs:
+                sys.argv.append("--skip-docs")
             if args.no_comments:
                 sys.argv.append("--no-comments")
             if args.verbose: