Pre-registered commitment bundle for certified transition-path measurement: frozen selection rule, thresholds, and sealed prediction contract

Cryptographic pre-registration of the analysis rules, thresholds, and selection criteria for a programme measuring transition-path quantities (committor distribution, route, recrossing) in proteins, deposited before the corresponding measurements are made. The purpose is precedence without trust: the rules are fixed and publicly timestamped before the measurements they govern. Version 3, 9 August 2026. This version corrects the version registered earlier the same day. Section 8 of CALIBRATION_V1.md attributed a systematic 7 percent difference between two reference rates to the choice of estimator. It is the state definition. Running both estimators on both definitions, on identical frame streams, shows the estimators agree to between 0.08 and 0.56 percent when handed the same states, while two ordinary definitions of the same transition differ by 6.45 to 6.96 percent when handed the same estimator; at least 92 percent of the effect is the definition. The correction, how it was found, and the reproduction gates are in CORRECTION_20260809_ESTIMATOR_ATTRIBUTION.md, and the full measurement is in matched_states.json. Sections 1 to 7 are untouched and the calibrated floor of 80 transitions stands, since that calibration used one estimator on one state definition throughout. Section 5 additionally gains "one state definition" in its scope list, an axis it had omitted. Nothing else is withdrawn, and the two earlier records remain public and citable. This record holds 23 files: 21 covered by the manifest, plus MANIFEST.sha256 itself and ROOT_HASH.txt. MANIFEST.sha256 lists the SHA-256 of each of the 21. The single value that commits to the whole bundle is the SHA-256 of that manifest, and it is the number to cite: 225640acec6e3260e1fd862bb14715526277fe0dc4d09b2fd98f0df299504ce0 To verify: download all files into one directory, recompute the SHA-256 of each and compare with MANIFEST.sha256, then recompute the SHA-256 of MANIFEST.sha256 and compare with the value above and with ROOT_HASH.txt. VERIFY.md gives the commands, and running make_manifest.sh --check performs the whole verification and prints the root hash.