refactor(cli): address code review feedback

- Extract checkup command helpers (prepareOutputDirectory, prepareUploadConfig,
  uploadCheckupReports, writeReportFiles, printUploadSummary) reducing action
  handler from ~230 to ~90 lines
- Add JSDoc documentation to public API functions in checkup-api.ts
- Add bunfig.toml with default 30s test timeout
- Remove redundant individual timeout settings from init.integration.test.ts

Author: NikolayS