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.

UserDocMD/architecture.md

@@ -20,7 +20,7 @@ An index directory is organized as `KmerIndex → partitions → layers`, with a
 
 ## Parallel execution and NUMA awareness
 
-Partition-level work (index construction, `merge`, `filter`, `reindex`, `select`, `distance`'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:
+Partition-level work (index construction, `merge`, `filter`, `reindex`, `select`, `phylo`'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:
 
 - On a multi-socket / multi-NUMA-node machine, one thread pool is pinned per NUMA node, and each partition is processed entirely by threads pinned to one node — keeping the memory a partition touches local to that node's DRAM. This matters because touching kmer data across NUMA nodes without pinning can degrade throughput by an order of magnitude or more on large multi-socket machines.
 - On a single-socket machine, Apple Silicon, or if hwloc cannot report NUMA topology, all cores are treated as one node with no pinning and negligible overhead — this is the default behavior on macOS.

UserDocMD/index.md

@@ -24,7 +24,7 @@ All functionality is exposed through a single binary, `obikmer`, organized as su
 | [`query`](usage/query.md) | Query an index with sequences and annotate matches |
 | [`dump`](usage/dump.md) | Dump indexed kmers as CSV |
 | [`annotate`](usage/annotate.md) | Add, update, or dump genome metadata |
-| [`distance`](usage/distance.md) | Compute pairwise distance matrices and phylogenetic exports |
+| [`phylo`](usage/phylo.md) | Compute pairwise evolutionary-distance proxies, trees, and phylogenetic exports |
 | [`unitig`](usage/unitig.md) | Dump the unitigs of an index as FASTA |
 | [`estimate`](usage/estimate.md) | Estimate approximate-index parameters before indexing |
 | [`reindex`](usage/reindex.md) | Convert an index's evidence representation (exact ↔ approximate) |

UserDocMD/usage/phylo.md

@@ -1,9 +1,9 @@
-# distance
+# phylo
 
-Compute pairwise distance matrices between the genomes stored in an index, optionally build trees (NJ/UPGMA), and optionally derive a central-position SNP model with exports for external phylogenetic tools (TNT, PhyG, IQ-TREE).
+Compute pairwise evolutionary-distance proxies between the genomes stored in an index — a plain distance matrix, optionally trees (NJ/UPGMA), and optionally a central-position SNP model with exports for external phylogenetic tools (TNT, PhyG, IQ-TREE).
 
 ```bash
-obikmer distance INDEX [OPTIONS]
+obikmer phylo INDEX [OPTIONS]
 ```
 
 ## Arguments