chore: Improve repository cleanup and artifact management

[eshaffer321]

Summary

This PR improves the make clean target to properly remove ALL build artifacts, not just the bin/ directory. It also removes a redundant .gitignore file in the mcp-server directory.

Changes Made

Enhanced Makefile clean target

• ✅ Added removal of coverage.txt (root coverage file)
• ✅ Added removal of mcp-monarch binaries (root and cmd/mcp-server/)
• ✅ Added removal of test_*.go files (ad-hoc test files)
• ✅ Added removal of security-report.json (from make security)
• ✅ Added removal of *.bak files (backup files)

Cleanup

• ✅ Removed redundant cmd/mcp-server/.gitignore
  • Root .gitignore already covers mcp-monarch binary
  • Subdirectory .gitignore had wrong binary name (monarch-mcp-server vs mcp-monarch)

Why This Matters

Before this PR: Running make clean would only remove the bin/ directory and coverage.out/coverage.html files, leaving behind:

• coverage.txt (36KB)
• mcp-monarch binary (11MB)
• test_*.go files
• *.bak backup files
• security-report.json

After this PR: make clean removes ALL artifacts consistently.

Testing

• ✅ All tests pass (51/51)
• ✅ make clean successfully removes all artifacts
• ✅ Verified artifacts are properly gitignored (not committed)

Notes

This addresses the issue where make clean didn't remove coverage.txt and other artifacts that were left in the working directory. The .gitignore was already correctly configured to ignore these files - we just needed the clean target to remove them properly.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 43.18%. Comparing base (6f8ff75) to head (521beba).
⚠️ Report is 1 commits behind head on main.

❌ Your project status has failed because the head coverage (43.18%) is below the target coverage (70.00%). You can increase the head coverage or adjust the target coverage.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #16   +/-   ##
=======================================
  Coverage   43.18%   43.18%           
=======================================
  Files          15       15           
  Lines        2239     2239           
=======================================
  Hits          967      967           
  Misses       1198     1198           
  Partials       74       74           

Flag	Coverage Δ
unittests	43.18% <ø> (ø)

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