docs: backfill missing CLI documentation

[marcus]

Scope

• Expanded the Docusaurus command reference to match the current CLI help, including notes, comments, deleted/resume/check-handoff, sync/auth/project commands, config, feature flags, diagnostics, workflow, and import/export/system commands.
• Added focused user-facing docs for notes, sync and collaboration setup, and system diagnostics.
• Wired the new docs into the sidebar and fixed stale README references for the logo image, SPEC link, docs links, and local-first sync wording.

Validation

• Ran npm run build in website successfully.
• Commit hook ran go vet and go build successfully.
• Skipped go test ./... because this is documentation-only and CLI behavior was verified via Cobra help output.