Repair 16 comprehensive fixture patches and add a patch-apply CI check (#541)

[amirbena]

Fixes #541

What

• Behavior / contracts: Repairs the 16 comprehensive fixtures whose input.patch did not apply to their own input.base (wrong hunk-header counts, drifted context/indentation, and missing base files in risk-depth-diffsize-elevated-refactor). Adds test_benchmark_corpus_patch_applies.py, a corpus-wide git apply sweep through the runner's own patch materialization, so drift fails in CI instead of a scheduled run. _materialize_patch / _PatchDidNotApply become public materialize_patch / PatchDidNotApply (no behavior change). Patch-apply validation and fail-closed completion verification are unchanged; no case is skipped or excluded.
• Governance / policy: None
• Packaging / portability: None
• Changelog: generated at release from the two lines below — never edit CHANGELOG.md (see docs/RELEASE.md)
• Release category: none
• Release entry:

Validation

• Relevant validation was run, or the reason it could not be run is stated.
• Corpus-wide git apply --check sweep: 16 failures before, 0 after.
• New test plus runner, corpus, and specialist/repo-intel/risk-depth/semantic suites pass.
• All 108 patch-bearing comprehensive fixtures materialize through the runner's materialize_patch path (108/108).
• Repaired fixtures run through the real run_benchmark.py --case-id path, all executed, no patch-did-not-apply: database-migration-deepening-additive-nullable-column-clean (the triggering hunk-header fixture), database-migration-deepening-expand-contract-safe-clean (context/start-line), risk-depth-diffsize-elevated-refactor (missing base files), semantic-implication-single-dimension-persistence (other sub-corpus). Two more repaired fixtures also ran cleanly before the sample was cut short.
• Not run: the full Comprehensive lane. The defect is fixture materialization, settled before any reviewer runs, so the full lane adds no evidence for it; the next scheduled Comprehensive routine gives operational confirmation. Comprehensive corpus: 16/108 fixture patches fail git apply against their own base (fail-closed, blocks lane sealing) #541's acceptance criterion is updated to say so. Edited fixtures get new per-case digests, treated as per-case incomparable.

Review

local-code-review on 51dbe10: REVIEW CLEAN, 0 P0/P1/P2 (an earlier pass's two P2s were fixed in that commit).

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