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.

docmd/theory/evolutionary_distances.md

@@ -205,7 +205,7 @@ single-copy at that locus.
 
 ## Context, detectability, and a 3-way ordinal distance per pair
 
-Empirical follow-up to the pseudo-alignment idea above: `obikmer distance
+Empirical follow-up to the pseudo-alignment idea above: `obikmer phylo
 --snp` was run on a real 20-genome benchmark index and the resulting FASTA
 fed to `raxml-ng`. Two problems surfaced, both traced back to conflating
 distinct notions under one symbol.
@@ -552,7 +552,7 @@ informative across domains with this character type. Exploratory only —
 run entirely outside the repo (`/tmp/tnt_run`, TNT installed locally under
 `TNT/`), no new Rust code. Kept here as the record of what was learned.
 
-**Pipeline.** `obikmer distance --snp` emits one IUPAC-coded pseudo-alignment
+**Pipeline.** `obikmer phylo --snp` emits one IUPAC-coded pseudo-alignment
 row per genome (`snp_pseudo_alignment`, one column per family with
 `family_size() >= 2`). A small external Python script decodes IUPAC back to
 the 16-state bitmask, applies the set-edit-distance formula above, and
@@ -630,7 +630,7 @@ it, no external script needed. `∅` is an ordinary 16th state throughout
 (never `-`), specifically to avoid gap-semantics confusion in downstream
 tools — see "A concrete Sankoff cost matrix" above for why.
 
-**TNT (`--tnt`).** `write_sankoff_tnt` (`obikmer/src/cmd/distance.rs`)
+**TNT (`--tnt`).** `write_sankoff_tnt` (`obikmer/src/cmd/phylo/mod.rs`)
 recodes to TNT's own `0-9A-F` xread alphabet (its default reader rejects
 the wider IUPAC set otherwise), scales and rounds costs to integers
 (`smatrix`/`cost` reject decimals), then re-runs integer Floyd-Warshall on
@@ -902,7 +902,7 @@ sections below, which implement and then substantially revise this.
 
 ### `R`/`π` implemented; `--exclude-genome` added; rogue-taxon test negative (2026-08-12)
 
-`write_iqtree` (`obikmer/src/cmd/distance/iqtree.rs`) implements exactly
+`write_iqtree` (`obikmer/src/cmd/phylo/iqtree.rs`) implements exactly
 the `R = exp(-cost)` / empirical-`π` design above: writes
 `<prefix>_iqtree.model` (lower-triangular `R`, PAML order, then `π`) and
 `<prefix>_iqtree.fasta` (alignment recoded to the compact `0..k-1`
@@ -949,7 +949,7 @@ tell: with `n_eligible=1`, the ratio can only be exactly `0` or `1`, so
 possibly ascertainment bias — see below — or possibly a few genuinely
 ultra-conserved loci; not resolved).
 
-**`--exclude-genome LABEL`** (repeatable, `obikmer distance`) added for
+**`--exclude-genome LABEL`** (repeatable, `obikmer phylo`) added for
 exactly this kind of test: zeroes the excluded genome's row/column in
 `RawSnpDistanceOutput` after `raw_snp_distance` runs (a pair with zero
 counts is already skipped by `calibrate_p_hat`/`base_pair_tally` — no
@@ -1165,7 +1165,7 @@ silently wrong data for TNT/PhyG, and a hard failure for IQ-TREE's `+ASC`
 (verified: excluding 2 taxa on the benchmark left 116,351 such columns —
 matches the manual `+ASC` failures hit earlier in this same investigation,
 before `--exclude-genome` existed). Fixed in `drop_excluded`
-(`obikmer/src/cmd/distance/mod.rs`): after dropping excluded rows,
+(`obikmer/src/cmd/phylo/mod.rs`): after dropping excluded rows,
 re-scan each column among the *surviving* sequences and drop any that are
 now constant. Verified: 908,723 → 792,372 sites after excluding 2 taxa,
 zero monomorphic columns remain, `π` recomputed from the corrected
@@ -1582,7 +1582,7 @@ index, not of any single genome — it cannot be computed correctly at
 mono-genome build time (a family may gain siblings, or its minorant may
 change, once more genomes are merged in later). Computing it eagerly at
 every `merge` would also waste work on intermediate merged states nobody
-ever queries. Instead: compute it lazily, on first `distance` call against a
+ever queries. Instead: compute it lazily, on first `phylo` call against a
 given index, and persist the result alongside that index for subsequent
 calls — the same lazy-derived-cache pattern `PersistentBitMatrix` already
 uses for `Columnar` -> `Packed`. This requires no explicit invalidation for
@@ -1745,7 +1745,7 @@ above) is observed anywhere in the index — fixes both:
    own 3 lookups independently," not a strict improvement to adopt by
    default.
 4. **Trigger and caching** (`obikindex::KmerIndex`/`distance.rs`): compute
-   lazily on first `distance` call for an SNP-family metric against a given
+   lazily on first `phylo` call for an SNP-family metric against a given
    index; check for an existing annex file first (mirrors
    `PersistentBitMatrix::open()`'s auto-detect-and-fall-back,
    `bitmatrix.rs:264-287`); if absent, run step 3 and persist; if present,
@@ -1765,7 +1765,7 @@ above) is observed anywhere in the index — fixes both:
    slots are never looked up cross-partition during the sweep.
 
 Cost: `3 * N_distinct` existence-only lookups, computed once per index
-state and amortised over every subsequent `distance` call that reuses the
+state and amortised over every subsequent `phylo` call that reuses the
 cached annex — cheaper per-lookup than the sweep itself (hit/miss only, no
 column fetch).
 
@@ -1795,11 +1795,11 @@ intermediate). Two options, to decide:
   Keeps one CLI surface (`--metric jukes-cantor`), at the cost of a branch in
   `distance()` that ignores the `LayeredStore` it built.
 - **(b)** A dedicated pathway (`KmerIndex::snp_distance`) and a distinct CLI
-  entry, if mixing a cross-partition sweep into the partition-local `distance`
+  entry, if mixing a cross-partition sweep into the partition-local `phylo`
   command is judged architecturally muddy.
 
 Recommendation: (a) for user ergonomics (all pairwise distances under
-`distance`, all feeding NJ/UPGMA/`--shared-kmers` unchanged), but compute the
+`phylo`, all feeding NJ/UPGMA/`--shared-kmers` unchanged), but compute the
 sweep lazily only when an SNP-family metric is requested, so the existing
 metrics keep their partition-local fast path untouched.