docs: update stale version numbers, MCP counts, and test counts across docs/

Version headers/footers updated to 3.1.0-dev:
- docs/features/BOOTSTRAP_SKILL_TECHNICAL.md (was 2.8.0-dev)
- docs/reference/API_REFERENCE.md (was 2.7.0)
- docs/reference/CODE_QUALITY.md (was 2.7.0)
- docs/guides/TESTING_GUIDE.md (was 2.7.0)
- docs/guides/MIGRATION_GUIDE.md (was 2.7.0, historical tables untouched)

MCP tool count 18 → 26:
- docs/guides/MCP_SETUP.md
- docs/guides/TESTING_GUIDE.md
- docs/reference/CODE_QUALITY.md
- docs/reference/CLAUDE_INTEGRATION.md
- docs/integrations/CLINE.md
- docs/strategy/INTEGRATION_STRATEGY.md

Test count 700+/1200+ → 1,880+:
- docs/guides/MCP_SETUP.md
- docs/guides/TESTING_GUIDE.md
- docs/reference/CODE_QUALITY.md
- docs/reference/CLAUDE_INTEGRATION.md
- docs/features/HOW_TO_GUIDES.md
- docs/blog/UNIVERSAL_RAG_PREPROCESSOR.md

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

docs/integrations/CLINE.md

@@ -292,7 +292,7 @@ In Cline panel, check "Available Tools" - you should see:
 - `list_configs` - List preset configurations
 - `scrape_docs` - Scrape documentation dynamically
 - `package_skill` - Package skills for Cline
-- ... (18 total MCP tools)
+- ... (26 total MCP tools)
 
 **Using MCP Tools**