[codex] Refactor large modules and fix runtime errors

[binaricat]

Summary

• Split oversized source files into focused modules so all source files are at or below 1000 lines.
• Cleared the reported lint warnings and tightened the split module wiring.
• Fixed startup and connection regressions, including the missing storage adapter, focus mode initialization, and SSH start dependency wiring.

Validation

• npm run lint -- --max-warnings=0
• npm run build
• npm test
• Source file line-count scan for files over 1000 lines
• SSH start probe reached the connection layer without the previous buildAlgorithms is not defined failure

Notes

• Draft PR because this is a broad mechanical refactor plus targeted runtime fixes and will benefit from review before merge.