perf: pool HMM (kofam/sulfur) via -T bit-score prefilter [HOLD until campaign done]

[tpall]

⛔ HOLD — do not merge until the current eluring campaign finishes

The 3 finished cohorts (samples_65_74_new, samples_12_18_new, dengl2025) and the in-flight ones (chulenbayeva → wu_rampelli → sajased-aftekas → curated_metagenomic) all run on the -E per-genome path. Merging this changes HMM (kofam/sulfur) output (-E→-T, +0.08% kofam), so it must wait until the campaign is done — then it becomes the default for the next campaign (everything -T-pooled, consistent from the start).

Why this PR exists

PR #11 was stacked on perf/search-bundling and merged into that branch after PR #10 had already merged perf/search-bundling → dev. So #11's HMM commits never reached dev. This PR brings them in: it's exactly the 4 commits perf/search-bundling is ahead of dev:

ad9a0a78 Merge pull request #11
0034dc9b docs: reword O()
c9665817 docs: -T bit-score validated
03f0f5d8 experiment: HMM pooling via -T

What it does

Adds HMM (kofam/sulfur) to --pool_searches by switching hmmsearch from the Z-dependent e-value prefilter to a Z-independent bit-score prefilter:

hmmsearch -T 10 --domT 10   (was: -E 1e-5)

hmm_parser already filters on per-profile bit-score thresholds, so -E was the only search-space-size-dependent step. 10 sits below kofam's lowest profile threshold (15.07), so nothing a real threshold would keep is pre-cut. Bit score is identical alone vs pooled, so pooled HMM == per-genome HMM.

Validation (extraves)

per-genome(-T) vs pooled-chunked(-T), all 5 DBs: RESULT: IDENTICAL (141270 rows; kofam fanned to 8 chunks). With this, the entire annotation path (mmseqs + HMM) pools byte-identically.

• Drift vs -E: +63 kofam calls (~0.08%) — the bit-score-significant hits -E 1e-5 silently dropped (arguably a latent-bug fix).
• Output size unchanged (final annotations same; only transient domtblout grows).
• -Z/--domZ doesn't work for a multi-genome pool (one -Z can't match variable per-genome sizes).
• Full record: docs/dev/search-bundling.md.

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