docs: backfill missing CLI documentation

[marcus]

Summary

• Expanded the command reference to cover the currently public top-level CLI surface, including notes, config, feature flags, sync/auth, sync-project, doctor, directory associations, last, and diagnostics.
• Added focused docs pages for notes, configuration, sync CLI setup/operations, and directory associations.
• Added sidebar entries and narrow discovery links from getting started, AI integration, and the command reference.

Validation

• npm run build (from website) passed
• Targeted go run . --help checks passed for note, config, feature, auth, sync, sync-project, doctor, config associations, last, stats, and serve
• go test ./... passed when rerun with TD_FEATURE_SYNC_AUTOSYNC and TD_FEATURE_SYNC_CLI removed from the test environment; the first run failed in internal/features because those shell overrides were set

[marcus]

Iteration 2 update:\n\n- Corrected the sync CLI enablement docs: hidden sync/auth/config commands are registered by the process-level TD_FEATURE_SYNC_CLI=true gate, not by td feature set sync_cli true.\n- Removed examples implying sync.enabled exposes or enables the CLI surface.\n- Validation: npm run build from website; targeted go run . help checks for sync/auth/config with and without the env gate; env -u TD_FEATURE_SYNC_CLI -u TD_FEATURE_SYNC_AUTOSYNC go test ./....