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.

benchmark/Makefile

@@ -89,50 +89,50 @@ $(REF_DIST_CSVS) &: $(REF_NPZS) build_reference_dist.py
 
 reference_dist: $(REF_DIST_CSVS)
 
-# ── obikmer distance (presence index) ────────────────────────────────────────
+# ── obikmer phylo (presence index) ──────────────────────────────────────────
 
 $(OBIKMER_PRESENCE_DIST) &: global_index_presence/index.done $(BINARY)
 	mkdir -p obikmer_dist/presence
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/presence/jaccard \
 		--metric jaccard --shared-kmers --nj \
 		global_index_presence
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/presence/hamming \
 		--metric hamming --nj \
 		global_index_presence
 
 obikmer_dist_presence: $(OBIKMER_PRESENCE_DIST)
 
-# ── obikmer distance (count index) ───────────────────────────────────────────
+# ── obikmer phylo (count index) ─────────────────────────────────────────────
 
 $(OBIKMER_COUNT_DIST) &: global_index_count/index.done $(BINARY)
 	mkdir -p obikmer_dist/count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/jaccard \
 		--metric jaccard --shared-kmers --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/bray_curtis \
 		--metric bray-curtis --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/relfreq_bray_curtis \
 		--metric relfreq-bray-curtis --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/euclidean \
 		--metric euclidean --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/relfreq_euclidean \
 		--metric relfreq-euclidean --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/hellinger \
 		--metric hellinger --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/hellinger_euclidean \
 		--metric hellinger-euclidean --nj \
 		global_index_count

benchmark/build_reference_dist.py

@@ -2,10 +2,10 @@
 """Compute reference pairwise distance matrices from per-specimen .npz kmer indexes.
 
 Reads all .npz files in reference_index/ (each containing sorted uint64 `kmers`
-and uint32 `counts`), computes all distance metrics supported by `obikmer distance`,
+and uint32 `counts`), computes all distance metrics supported by `obikmer phylo`,
 and writes one CSV per metric to reference_dist/.
 
-Output CSV format matches `obikmer distance --output`:
+Output CSV format matches `obikmer phylo --output`:
   - first row: "genome", then specimen names
   - subsequent rows: specimen name, then float or int values
 

benchmark/compare_all_dist.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
-"""Compare all reference distance matrices against obikmer distance outputs.
+"""Compare all reference distance matrices against obikmer phylo outputs.
 
 Reads from:
   reference_dist/   — ground-truth matrices computed by build_reference_dist.py
-  obikmer_dist/     — matrices produced by `obikmer distance`
+  obikmer_dist/     — matrices produced by `obikmer phylo`
 
 Handles label reordering: both matrices are sorted by genome label before
 element-wise comparison, so column/row order differences are irrelevant.