docs: backfill CLI reference gaps

[marcus]

Summary

• Backfills CLI reference coverage for init, config, report/logs/stats, service install/uninstall, busfactor, and Cobra help/completion commands.
• Corrects README links that pointed at missing local docs and keeps README pointed at the canonical website docs.
• Adds the existing troubleshooting page to the docs sidebar for discoverability.

Assumptions

• Scope is user-facing CLI documentation/navigation only; no code behavior changes.
• website/docs/cli-reference.md remains the canonical CLI reference.

Verification

• git diff --check
• go test ./...
• npm --prefix website run build
• pre-commit hook: go vet, go build