docs: backfill cli command reference

[marcus]

Summary

• expand the CLI reference to cover all visible top-level Nightshift commands, including Cobra-generated completion and help
• document newer run/task flags including branch, timeout, and no-color
• add concise examples for budget snapshots, log filters, reports, daemon, install, busfactor, and shell completion
• correct stale README documentation links that pointed at missing local files

Verification

• go test ./...
• npm --prefix website run build
• git diff --check

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Automated by nightshift