fix: resolve test race conditions, add logging, and fix CI deadlock

Re-enables the `numa` feature in CI workflows to prevent container/cgroup deadlocks while preserving validation correctness. Fixes concurrent test race conditions by replacing thread-local parameter storage with process-wide atomics and mutex locks. Integrates `tracing-subscriber` for structured logging and adds thread-ID tracking to debug worker lifecycles. Additionally bumps the crate version, updates `.gitignore`, documents experimental evolutionary distance pipelines, and refactors hardcoded test constants.

docmd/theory/evolutionary_distances.md

@@ -473,6 +473,79 @@ matrix derived from the state graph, `c_ts`/`c_tv`/`c_gl`/`c_ctx` as
 tunable parameters) is directly usable there — no new tooling required
 before testing it.
 
+### Experiment: TNT run on real data (2026-08-11)
+
+**Status:** validated at genus/family/order scale within Bacteria; not
+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
+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
+emits a complete TNT script (`xread` matrix + `smatrix` step-matrix + `hold`/
+`mult` search). No new Rust code was needed for this pass.
+
+**Calibration ("quick option").** Rather than modifying
+`write_raw_snp_distance_csv` to emit raw counts, `c_ctx` was approximated as
+the unweighted mean of the pairwise `snp/(snp+shared)` ratios already
+present in `rawsnp.csv`, restricted to the relevant taxon subset. Used
+values: `mu = gamma = 10`, `c_ctx = 18` (ratio `c_ctx/mu = 1.8`, consistent
+with the observed pairwise ratios for genomes within Enterobacteriaceae/
+Eubacteria, which cluster around 1.5-2 and barely move as the taxon set
+widens — the context signal is stable, not sensitive to which subset is
+chosen). The more principled route (raw counts, weighted `p_hat`, Ts/Tv
+split) remains a follow-up, not yet done.
+
+**Run 1 — Enterobacteriaceae (11 taxa: 4 *E. coli*, 4 *Salmonella enterica*,
+3 *Klebsiella pneumoniae*).** All three genera recovered as monophyletic.
+Initial read of the exported (unrooted, TNT/Nexus `[&U]`) tree as showing a
+genus-arrangement disagreement with known systematics (*Escherichieae*:
+*Escherichia*+*Salmonella* sister vs. more distant *Klebsielleae*) was
+**wrong** — diagnosed via `force = (taxa);` monophyly-constraint test
+(identical score constrained vs. free ⟹ no real disagreement). Root cause of
+the misreading: with exactly 3 clades and no outgroup, an unrooted tree has
+only **one possible topology** (a single trifurcation) — there is no
+internal arrangement to get right or wrong. This run cannot test
+inter-genus relationships at all; it can only test intra-genus monophyly
+(which held).
+
+**Run 2 — Eubacteria (18 taxa: run 1 + *Acidobacterium capsulatum*,
+*Opitutus terrae*, *Bacillus subtilis*, *Shouchella clausii*, *Wolbachia*
+endosymbiont, *Proteus mirabilis*, *Yersinia ruckeri*).** The
+Enterobacteriaceae substructure from run 1 is reproduced identically, now
+correctly rooted by real outgroups, resolving the tribal arrangement left
+undetermined in run 1: *Escherichia*+*Salmonella* sister, *Klebsiella* more
+distant — matching known systematics. Outgroup placement: `(Bacillus,
+Shouchella)` sister pair (Firmicutes/*Bacillales*) splits from all
+Proteobacteria — a correct phylum-level split; `Wolbachia`
+(Alphaproteobacteria) splits from the Gammaproteobacteria block
+(`Proteus`, `Yersinia`, Enterobacteriaceae) — a correct class-level split.
+Lower confidence: the fine nested order `(Proteus, (Yersinia,
+Enterobacteriaceae))` and the relative position of `Acidobacterium` vs.
+`Opitutus` — plausible, not independently verified against current
+Enterobacterales family-level literature.
+
+**Run 3 — full domain set (20 taxa: run 2 + *Candidozyma auris* [yeast] and
+*Saccharolobus islandicus* [archaeon]).** The bacterial clade from run 2 is
+reproduced **unchanged and intact** — a real robustness signal, the method
+does not fragment the ingroup when unrelated deep taxa are added. But the
+result carries **no information on Bacteria/Archaea/Eukarya relationships**:
+with exactly one eukaryote, one archaeon and one bacterial clade, the
+unrooted tree is again forced into the single 3-clade trifurcation from run
+1's caveat — there is no second representative of either outgroup domain to
+resolve internal arrangement, so nothing about their relative position can
+be read from the topology (a "ladder" ordering in the exported tree is
+serialization, not signal). Independently, `rawsnp.csv` shows *why* this
+character type cannot reach further: pairwise ratios involving
+*Candidozyma*/*Saccharolobus* are almost all `NA` (no central-position
+family shared at all) or saturated at `1.0` (every shared family differs) —
+central-position families require literal 31 bp context conservation, which
+simply does not survive domain-level divergence. Cross-domain placement
+would need conserved-marker characters (rRNA, ribosomal proteins), not this
+estimator.
+
 ## Heterozygosity, ploidy, and consensus-assembly inputs
 
 A within-genome multiplicity signal (more than one of the 4 central forms