Extends `KmerIndex::finalize_indexed` to accept a `sparse` boolean parameter, enabling control over whether output presence matrices are packed in a compact sparse format or stored densely. The merge command now exposes a `--dense` flag to invert this setting, defaulting to the existing sparse representation. Call sites in select and rebuild modules pass `false` to preserve current behavior. A benchmark lock file is also added for dependency tracking.
Eric Coissac
cbf6893f38