Auto-fetch mmseqs2, document bare-germline annotation, add arda skill

[mikessh]

mmseqs2 auto-install (zero user bother):

• arda._mmseqs_fetch: download a static MMseqs2 binary into bin/ (packaged so it works for wheel installs too); browser User-Agent avoids GitHub 504s.
• mmseqs.mmseqs_binary() lazily auto-fetches when nothing is found ($ARDA_MMSEQS -> bin/ -> PATH -> fetch). Opt-out $ARDA_NO_AUTO_FETCH; asset override $ARDA_MMSEQS_ASSET. setup.sh --no-conda fetches eagerly.
• scripts/fetch_mmseqs.py CLI wrapper; tests/unit/test_mmseqs_fetch.py.

Bare germline segments: README recipe + docs note + regression test (tests/synthetic/test_germline_segments.py) — a bare V yields FR1-3, a bare J yields FR4 (no coverage filter). This is how mirpy bakes per-allele FR/CDR subsequences into its gene library.

Docs: installation.rst MMseqs2-without-conda section.

Skill: new skills/arda/ (lean SKILL.md router + references for annotation, region/germline segments, mmseqs install, reference build).

[Copilot]

Pull request overview

This PR makes mmseqs2 setup hands-off by adding a packaged auto-fetch mechanism for a static mmseqs binary, documents/locks in “bare germline segment” annotation semantics (V-only → FR1–FR3/CDR1–CDR2/FR3, J-only → FR4), and introduces an arda agent skill with reference docs.

Changes:

• Add arda._mmseqs_fetch + lazy auto-fetch fallback in arda.mmseqs.mmseqs_binary() (with opt-out/env overrides) and an eager-fetch CLI wrapper.
• Add regression tests for mmseqs auto-fetch behavior (offline) and for bare V/J germline segment annotation invariants.
• Expand user-facing docs (README + installation docs) and add skills/arda/ documentation bundle.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/arda/mmseqs.py	Adds lazy auto-fetch fallback and updates binary discovery docs/error message.
src/arda/_mmseqs_fetch.py	New stdlib-only downloader/installer for a static MMseqs2 release asset.
scripts/fetch_mmseqs.py	New CLI wrapper to fetch mmseqs eagerly into bin/.
setup.sh	Eagerly fetches mmseqs in --no-conda installs when not already on PATH.
tests/unit/test_mmseqs_fetch.py	Unit tests for asset selection and binary discovery/opt-out behavior.
tests/synthetic/test_germline_segments.py	Synthetic regression tests for bare V-only and J-only region emission.
README.md	Documents how to annotate bare germline V/J segments.
docs/installation.rst	Documents mmseqs auto-fetch controls for non-conda installs.
skills/arda/SKILL.md	Adds an arda skill router/guide covering annotation semantics and mmseqs setup.
skills/arda/references/annotation.md	Skill reference: runtime API, parameters, and AIRR schema.
skills/arda/references/region-segments.md	Skill reference: region projection + bare germline semantics + junction/CDR3.
skills/arda/references/install-mmseqs.md	Skill reference: discovery order, auto-fetch, env vars, version mismatch.
skills/arda/references/reference-build.md	Skill reference: offline reference-build pipeline and outputs.

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