Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.
This commit improves memory management by respecting Linux cgroup v1/v2 limits and introduces a configurable memory budget for the new `rebuild` subcommand to prevent OOM during index reconstruction. The rebuild process now supports filtering, compaction, and parallelization. Diagnostic capabilities are expanded with debug-level tracing for partition merges, k-mer expansion tracking, and utility flags for label renaming, matrix size breakdowns, per-genome counts, and partition distribution reporting. Accessor methods for active and remaining memory have also been added to the stats struct.
Replace the documented direct combined indexing command with a two-step workflow. This involves building separate exact indexes per genome, merging them into a single multi-genome index via `obikmer merge`, and keeping the approximate index conversion unchanged.
Fix a stray prefix in the README heading and update documentation to reflect the query pipeline's operation on `s-mers` (`s = k - z + 1`) with post-partition z-window filtering. Clarify the Findere trick, including k-mer size reduction, consecutive match requirements, and false positive rate calculations. Additionally, expand input format documentation to cover supported file extensions, gzip compression, recursive directory handling, and `query` command specifications.
Eric Coissac