- Remove atime field from proto schema (field 304 reserved)
- Omit createdAt timestamp by default for deterministic output
- Add --include-timestamps flag to gen and freshen commands to opt in
- Add Builder.SetIncludeTimestamps() and ScannerOptions.IncludeTimestamps
- Rate-limit Checker progress updates to once per second (matching Scanner)
- Add tests for all changes
Closes design decisions: deterministic-by-default, atime removal.