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 2, 9 August 2026. This version amends the deposit of 6 August 2026 under the amendment clause of SELECTION_RULE.md section 8, which permits amendment before unsealing by depositing a new registration while the earlier one remains public and permanent. The seal has not been opened, and no measured value from either sealed family has been read. Four files are added: CALIBRATION_V1.md, registering a calibrated admission floor for a rate estimated from a single unweighted trajectory by direct transition counting; calibration.json and certification.json, the measurement that floor was read from; and CHANGES_SINCE_20260806.md, a file-by-file diff against the previous version. All 14 files covered by the previous manifest are carried over byte-identical. Nothing is withdrawn. This record holds 20 files: 18 covered by the manifest, plus MANIFEST.sha256 itself and ROOT_HASH.txt. MANIFEST.sha256 lists the SHA-256 of each of the 18. The single value that commits to the whole bundle is the SHA-256 of that manifest, and it is the number to cite: 6e83e2fb8473e19e2b63684aa5731a2429caa54b60de93f85e6178a156ba58e1 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.