docs: add DEPENDENCIES.md recording accepted and declined crates

CONTRIBUTING.md:58 requires that a new dependency, especially a non-Rust one, be raised in an
issue before the PR. That rule covers the decision. What it does not cover is the record: today
the justifications live in comments in Cargo.toml (good ones, for flate2's zlib-rs backend
and for mimalloc) and the rejections live nowhere at all. So a crate that was considered and
turned down in issue #N gets re-proposed six months later and re-litigated from scratch.

Proposal: a DEPENDENCIES.md at the repo root with two tables and one list.

1. Active runtime dependencies — crate, version range, license, what uses it, why it earns its
   place. Seeded from the comments already in Cargo.toml, which are the best material here.
2. Dev-only dependencies — same shape, lower bar (nothing ships).
3. Considered and declined — crate, date, reason, link to the deciding issue.

Declined list, from the August 2026 survey

Draft content for section 3, to be confirmed in the sibling issues:

• Alternative aligners — block-aligner 0.5.1 (adaptive SIMD affine-gap, 5–10x over prior
  methods on its paper's datasets), ksw2rs, parasailors. Faithfulness to STAR's scoring,
  extension and tie-breaks is the product; an aligner that computes alignments differently, even
  better, is a divergence.
• k-mer / minimizer / sketching crates — simd-minimizers, minimizer-iter,
  minimizer-queue, seq-hash, sourmash, nthash. STAR seeds by MMP search in the suffix
  array; sketching changes which seeds exist.
• rust-htslib — brings htslib as a system C dependency; noodles already covers
  SAM/BAM/BGZF with a self-contained build across the five supported platforms.
• rust-bio — broad toolkit, slower readers (allocations, copying, UTF-8 validation), few
  pieces needed.
• Interval libraries — superintervals, coitrees, rust-lapper; see the sibling issue,
  including their non-standard license flags.
• Succinct / rank-select libraries — sucds, vers-vecs, sux, bitm. The packed index
  layout is dictated by STAR's format and there is no rank/select query need.
• rkyv — the index layout is externally specified, not a serialization of our own types.

Checklist

• Write DEPENDENCIES.md with the three sections
• Seed section 1 from the existing Cargo.toml comments, then trim the comments to a pointer
• Link it from CONTRIBUTING.md next to the "new dependencies need prior discussion" rule
• Backfill the decided issues (#162 and the siblings of this one) into section 3 as they close

Start with the dependency comments in Cargo.toml, the rule at CONTRIBUTING.md:58, issue #162, and the sibling issues named in the proposal. Create the root DEPENDENCIES.md with active, dev-only, and considered-and-declined sections; trim Cargo.toml comments to point to it, link it from CONTRIBUTING.md, and backfill decided issues as they close.