docs: sync docs with rust/rayon migration, fill api.md gaps, add docs-audit gate

[d-laub]

Summary

Audits and syncs user-facing docs against recent gvl changes (Phase 5: numba read-path deleted → Rust-only, awkward → _core migration, new rayon threading env vars), fills a large api.md gap, adds a docs-audit gate to CLAUDE.md, and removes an obsolete docs task.

Changes

Docs consistency

• faq.md: rewrote the "Ragged objects" answer — dropped the false "subclass of Awkward Arrays / numba JIT'd functions" claim; describes the seqpro.rag.Ragged (_core.Ragged, Rust) backend and notes awkward is no longer a dependency.
• faq.md: new entry documenting the threading env vars (GVL_NUM_THREADS, GVL_FORCE_PARALLEL, RAYON_NUM_THREADS override) — previously undocumented.
• README.md: replaced the stale tbb/pyomp-for-numba install note with "parallelism is built-in Rust/rayon, tune via GVL_NUM_THREADS".
• SKILL.md: _core.Ragged "Rust+numba backend" → "Rust backend" (rag layer is numba-free).

api.md ↔ __all__ drift (18 missing public symbols)

• Insertion fill: InsertionFill, Constant, FlankSample, Interpolate, Repeat5p, Repeat5pNormalized
• Flat containers: FlatRagged, FlatAnnotatedHaps, FlatIntervals, FlatVariants, FlatAlleles, FlatVariantWindows
• Variant windows: VarWindowOpt, DummyVariant
• Dataset maintenance: migrate, migrate_svar_link
• Writing: update; PyTorch interop: to_nested_tensor
• Verified: 39/39 __all__ symbols now present in api.md.

Process

• CLAUDE.md: new "Docs audit before feature/breaking-change PRs" gate, including an explicit api.md ↔ __all__ sync check with a one-liner.

Cleanup

• pixi.toml: removed the obsolete install-e docs task. It editable-installed sibling seqpro/genoray from hardcoded absolute cluster paths but was never required — they are transitive deps and the locked seqpro 0.20.0 already provides every symbol gvl imports. The docs build only broke when an env drifted stale from the lock (fixed by pixi install -e docs).

Verification

• Docs build cleanly on darwin (osx-arm64) with the plain PyPI wheels after reconciling the env; api.html renders and the new autodoc entries produce no new warnings/errors.
• Programmatic __all__ ↔ api.md diff reports no missing symbols.
• docs/source/changelog.md intentionally untouched (auto-generated from commits).

🤖 Generated with Claude Code

[d-laub]

Rebased onto origin/main: this PR now contains only its 4 docs commits (the rayon thread-cap commits it had picked up belong to #265). ⚠️ Merge #265 first — the new threading FAQ entry documents GVL_FORCE_PARALLEL and the RAYON_NUM_THREADS override, which land in #265; merging this before #265 would briefly document unshipped env vars.