refactor: reorganize project into src layout and update API documentation

Update project structure to use a src/ directory layout and
improve documentation across multiple files.

- Update README.md build command to use ./src
- Add directory structure documentation
- Update status endpoint to include DB health status
- Add pagination support (limit/offset) to whitelist list endpoints
- Document new query parameters with examples
- Update deployment guide to mark API token as required
- Add testing instructions
- Clarify audit log rotation in design documentation

docs/design.md

@@ -106,8 +106,9 @@ If you need persistence across restarts, add a disk-backed store later.
 
 ## Why a background cleanup goroutine?
 
-Checking expiry on every request adds latency (two map lookups per request).
-The cleanup goroutine is a one-time cost that keeps the hot path fast.
+The cleanup goroutine removes expired temporary entries and rotates the audit log.
+It runs every 60 seconds (configurable). The audit log rotation keeps the database
+from growing indefinitely — it maintains a maximum of 100,000 entries.
 
 ## Why poll instead of inotify?