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/mcp/tools/scraping_tools.py

@@ -464,6 +464,7 @@ async def scrape_codebase_tool(args: dict) -> list[TextContent]:
             - skip_test_examples (bool, optional): Skip test example extraction (default: False)
             - skip_how_to_guides (bool, optional): Skip how-to guide generation (default: False)
             - skip_config_patterns (bool, optional): Skip config pattern extraction (default: False)
+            - skip_docs (bool, optional): Skip project documentation extraction (default: False)
 
     Returns:
         List[TextContent]: Tool execution results
@@ -497,6 +498,7 @@ async def scrape_codebase_tool(args: dict) -> list[TextContent]:
     skip_test_examples = args.get("skip_test_examples", False)
     skip_how_to_guides = args.get("skip_how_to_guides", False)
     skip_config_patterns = args.get("skip_config_patterns", False)
+    skip_docs = args.get("skip_docs", False)
 
     # Build command
     cmd = [sys.executable, "-m", "skill_seekers.cli.codebase_scraper"]
@@ -526,6 +528,8 @@ async def scrape_codebase_tool(args: dict) -> list[TextContent]:
         cmd.append("--skip-how-to-guides")
     if skip_config_patterns:
         cmd.append("--skip-config-patterns")
+    if skip_docs:
+        cmd.append("--skip-docs")
 
     # Adjust timeout based on enhance_level
     timeout = 600  # 10 minutes base