rename distance subcommand to phylo

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.

README.md

@@ -66,9 +66,11 @@ Non-ACGT characters act as hard breaks between k-mer segments in all formats.
                Annotates each sequence with per-genome k-mer match counts
                and optional per-position coverage vectors (--detail).
                Parallel over sequence chunks.
-    distance   Compute a pairwise Bray-Curtis or Jaccard distance matrix
-               between all indexed genomes.
-               Optionally outputs a Newick NJ or UPGMA tree.
+    phylo      Compute pairwise evolutionary-distance proxies between all
+               indexed genomes (Bray-Curtis, Jaccard, etc.), optionally
+               a Newick NJ/UPGMA tree, and optionally a central-position
+               SNP/Sankoff calibration with exports for external
+               phylogenetic tools (TNT, PhyG, IQ-TREE).
     annotate   Add or update genome metadata (taxonomy, etc.) from a CSV
                file; or dump the current metadata as CSV.
     estimate   Dry-run: resolve and print approximate-index parameters
@@ -106,7 +108,7 @@ obikmer reindex --approx -z 5 --evidence-bits 8 index/
 obikmer query index/ reads.fq.gz > annotated.fa
 
 # Pairwise distances
-obikmer distance index/ > distances.tsv
+obikmer phylo index/ > distances.tsv
 ```
 
 ## Parameter constraints