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>

tests/test_analyze_command.py

@@ -74,7 +74,8 @@ class TestAnalyzeSubcommand(unittest.TestCase):
             "--skip-patterns",
             "--skip-test-examples",
             "--skip-how-to-guides",
-            "--skip-config-patterns"
+            "--skip-config-patterns",
+            "--skip-docs"
         ])
         self.assertTrue(args.skip_api_reference)
         self.assertTrue(args.skip_dependency_graph)
@@ -82,6 +83,7 @@ class TestAnalyzeSubcommand(unittest.TestCase):
         self.assertTrue(args.skip_test_examples)
         self.assertTrue(args.skip_how_to_guides)
         self.assertTrue(args.skip_config_patterns)
+        self.assertTrue(args.skip_docs)
 
     def test_backward_compatible_depth_flag(self):
         """Test that deprecated --depth flag still works."""