[DimaMolod]

A fold's output directory had grown a scatter of AlphaPulldown's own JSON files next to AlphaFold's outputs. They now go in two subdirectories, and AlphaFold's own files stay where AlphaFold, AlphaJudge and users expect them.

<fold>/
  …AlphaFold outputs, unchanged…
  completed_fold.txt              (the workflow's sentinel, unchanged)
  alphapulldown/
    prediction.json               fold record (was alphapulldown_prediction.json)
    inference_kernels.json        which kernels ran (was at the top)
    feature_metadata/             copied feature metadata (was at the top)
  debug/                          only with --debug_msas / --debug_templates
    templates/                    (AF2's was templates_debug/)

• Bug fix along the way: AF3 wrote its --debug_templates mmCIFs, and a note on any template that failed to convert, into the current working directory. They now go to the fold's debug/templates/.
• One kernel-record writer for AF2 and AF3 (prediction/inference_kernels.py). It writes atomically and never fails a finished prediction; AF2's used to write in place and could raise.
• Older folds keep working.
  • A 2.10-era top-level inference_kernels.json is moved into alphapulldown/ on its next entry.
  • ModelCIF conversion and AF3 ModelCIF metadata still read feature metadata copied to the top.
  • alphapulldown_prediction.json was never released, so it needs no compatibility.
• Nothing downstream reads the moved files. Checked AlphaJudge and AlphaPulldownSnakemake: neither reads the kernel record, the fold record or the metadata copies.

Verification

• CPU equivalence harness, the 15 AF3 inputs with debug MSAs and templates on: all 107 files main writes are byte-identical at their new locations (76 moved). The only new files are the 3,317 AF3 template debug mmCIFs that used to land in the working directory.
• Unit + integration, both release images, branch wrappers on both sides: identical to main, plus 5 new tests (layout, kernel-record migration, metadata lookup in both places). AF2 image: 979 passed. AF3 image: 1049 passed.
• GPU: the cluster checks are updated to the new layout. The AF3 resume check now simulates 2.10's layout, so the compatibility path runs on GPU too. Full AF2 and AF3 suites run on main once this round is merged.

🤖 Generated with Claude Code

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