fix(tune): omit -crf in libx264 two-pass encoding and update state.md

[lusoris]

Summary

Fixes open bug T-VMAFTUNE-TWOPASS-CRF-INVALID-2026-08-30 from docs/state.md where libx264 multi-pass encoding emitted conflicting rate control flags (-crf and -pass), causing FFmpeg to reject pass 2 (CRF/CQP is incompatible with 2pass.). In multi-pass mode (pass_number != 0), -crf is omitted across both Go (pkg/codecadapter, pkg/ffencode, pkg/corpus) and Python (vmaftune.codec_adapters.x264, vmaftune.encode). Also records verification of T-SPEED-GPU-REGISTRY-ORPHAN-2026-06-19, which was already resolved on master via PR #1004 (commit a0bf83c214).

Type

• fix — bug fix

Checklist

• Commits follow Conventional Commits (the commit-msg hook enforces this).
• make format && make lint is green locally.
• Unit tests pass: meson test -C build.
• If I touched any SIMD/GPU code path, I ran /cross-backend-diff and the worst ULP is <= 2.
• If I touched a feature extractor with SIMD/GPU twins, I either updated every twin or listed the gap under "Known follow-ups" below.
• If I added a new .c / .cpp / .cu / .h / .hpp, it has the appropriate license header (see CONTRIBUTING.md).
• If this is a breaking change, the commit message uses ! or BREAKING CHANGE: and the migration path is documented below.
• If this PR adds an ADR, the ADR row lives in docs/adr/_index_fragments/<NNNN-slug>.md and the slug is appended to docs/adr/_index_fragments/_order.txt — do not edit docs/adr/README.md directly (regenerated by scripts/docs/concat-adr-index.sh; see ADR-0221).

Bug-status hygiene (ADR-0165)

• docs/state.md updated in this PR with rows in Recently closed for T-VMAFTUNE-TWOPASS-CRF-INVALID-2026-08-30 and T-SPEED-GPU-REGISTRY-ORPHAN-2026-06-19.

Netflix golden-data gate (ADR-0024)

• I did not modify any assertAlmostEqual(...) score in the Netflix golden Python tests.

Deep-dive deliverables (ADR-0108)

• Research digest — no digest needed: bug fix for conflicting FFmpeg rate-control flags.
• Decision matrix — no alternatives: only-one-way fix.
• AGENTS.md invariant note — no rebase-sensitive invariants.
• Reproducer / smoke-test command — pasted below under "Reproducer".
• CHANGELOG fragment — changelog.d/fixed/vmaftune-twopass-crf-conflict.md added.
• Rebase note — docs/rebase-notes.md updated with entry for fix/vmaftune-state-bugs.

Reproducer

go test -v ./pkg/ffencode/... ./pkg/codecadapter/... ./pkg/corpus/...
pytest tools/vmaf-tune/tests/test_codec_adapter_x265_two_pass.py -v