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.
Introduces directory-level locking to prevent concurrent index operations from corrupting shared directories, along with explicit APIs for acquiring, probing, and releasing locks. Restructures the index cache crate to use a layered store architecture that eagerly initializes metadata and provides fast hierarchical lookups. Updates dependent modules, test suites, and CLI commands to align with the refactored API surface, and adds an end-to-end smoke test for validation.
Eric Coissac