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.

src/obikmer/src/cmd/mod.rs

@@ -4,7 +4,7 @@ pub mod pack;
 pub(crate) mod predicate;
 pub mod select;
 pub mod utils;
-pub mod distance;
+pub mod phylo;
 pub mod dump;
 pub mod estimate;
 pub mod index;

src/obikmer/src/cmd/phylo/mod.rs

@@ -55,7 +55,7 @@ impl From<MetricArg> for DistanceMetric {
 }
 
 #[derive(Args)]
-pub struct DistanceArgs {
+pub struct PhyloArgs {
     /// Index directory
     pub index: PathBuf,
 
@@ -220,7 +220,7 @@ pub struct DistanceArgs {
     pub output: Option<PathBuf>,
 }
 
-pub fn run(args: DistanceArgs) {
+pub fn run(args: PhyloArgs) {
     let idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
         eprintln!("error opening index: {e}");
         std::process::exit(1);

src/obikmer/src/main.rs

@@ -30,8 +30,9 @@ enum Commands {
     Dump(cmd::dump::DumpArgs),
     /// Add or update genome metadata from a CSV file; or dump metadata as CSV
     Annotate(cmd::annotate::AnnotateArgs),
-    /// Compute pairwise distance matrix between genomes; optionally build NJ/UPGMA trees
-    Distance(cmd::distance::DistanceArgs),
+    /// Compute pairwise evolutionary-distance proxies between genomes (metric matrix, NJ/UPGMA
+    /// trees, SNP/Sankoff calibration, TNT/PhyG/IQ-TREE exports)
+    Phylo(cmd::phylo::PhyloArgs),
     /// Dump unitigs from a built index to stdout (debug)
     Unitig(cmd::unitig::UnitigArgs),
     /// Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing
@@ -71,7 +72,7 @@ fn main() {
         Commands::Select(args)    => cmd::select::run(args),
         Commands::Query(args)     => cmd::query::run(args),
         Commands::Annotate(args)  => cmd::annotate::run(args),
-        Commands::Distance(args)  => cmd::distance::run(args),
+        Commands::Phylo(args)     => cmd::phylo::run(args),
         Commands::Unitig(args)    => cmd::unitig::run(args),
         Commands::Estimate(args)  => cmd::estimate::run(args),
         Commands::Reindex(args)   => cmd::reindex::run(args),