* fix(sec): upgrade vulnerable deps
* feat: add comprehensive logging to upgrade tests
- Modify VersionRunner to write server logs to /tmp/upgrade-test-*.log files
- Add pytest hook to automatically dump server logs on test failure
- Add CI workflow step to show upgrade test logs (always runs)
- Improves debuggability when upgrade tests fail in CI
This addresses the issue where upgrade test failures in CI were
impossible to debug because API server logs were not visible.
* misc: add mcp integration tests and increase test coverage
* misc: add mcp integration tests and increase test coverage
* misc: add mcp integration tests and increase test coverage
