docs: add comprehensive examples and close stale issues

Examples:
- Add real-world usage patterns for all MCP tools
- Include workflow examples (new feature, bug investigation, code review)
- Add tips for search quality and token management
- Document integration patterns for Cursor and Claude Code

Issue cleanup:
- Closed #33 (Integration Testing - completed)
- Updated #31 (Adapter Discovery - partial, moved to backlog)
- Updated #25 (Automation Layer - shelved per philosophy)

All polish tasks now complete!

Author: prosdev

PLAN.md

@@ -137,7 +137,7 @@ Focus on quality, documentation, and developer experience before adding new feat
 | CLI reference docs | ✅ Done | 🟡 Medium |
 | Configuration guide | ✅ Done | 🟡 Medium |
 | Troubleshooting guide | ✅ Done | 🟡 Medium |
-| Examples for new tools | 🔲 Todo | 🟢 Low |
+| Examples for new tools | ✅ Done | 🟢 Low |
 
 ### Code Quality
 
@@ -151,8 +151,8 @@ Focus on quality, documentation, and developer experience before adding new feat
 
 | Task | Status | Priority |
 |------|--------|----------|
-| Close completed epics | 🔲 Todo | 🟡 Medium |
-| Update stale issues | 🔲 Todo | 🟢 Low |
+| Close completed epics | ✅ Done | 🟡 Medium |
+| Update stale issues | ✅ Done | 🟢 Low |
 
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