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