Hide advanced/internal `ktx setup` options from --help output using
.hideHelp() so the command surface is approachable for new users. Remove
the --project, --agent-scope, and --skip-initial-source-ingest flags
that are no longer needed. Update docs and tests to match.
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>