Runtime Rerun Refusals

A rerun refusal is a positive runtime decision: the retained environment, inputs, provider boundary, artifacts, or downstream evidence do not support the requested replay claim. The refusal preserves the best supported lane without describing a weaker reconstruction as faithful execution.

flowchart TD
    request["requested rerun claim"] --> lane{"governed lane exists?"}
    lane -->|no| refuse["refuse and name missing lane"]
    lane -->|yes| environment{"environment and inputs reconstructable?"}
    environment -->|no| refuse
    environment -->|yes| replay{"artifacts and invalidation cases pass?"}
    replay -->|no| refuse
    replay -->|yes| scope{"claim inside current evidence ceiling?"}
    scope -->|no| narrow["complete replay; narrow the claim"]
    scope -->|yes| accept["record rerun-ready disposition"]

Current family posture

Family	Rerun ready	Present refusal	Blocked claim

| dda | no | faithful rerun still stops at imported MaxQuant and comparator exports because the repository does not own a raw DDA search execution lane; external-engine behavior remains proprietary or out-of-repository for the strongest DDA package | raw DDA search parity; full outsider-auditable DDA rerun language | | dia | no | the shipped DIA lane is raw-executable in runtime terms but still depends on library-conditioned exported reports rather than chromatogram-native replay | chromatogram-native DIA parity; broad vendor-parity DIA authority | | lfq | yes | none | none | | multiplex | no | multiplex remains below outsider-auditable trust because runtime rerun strength still outruns family-level consequence and challenge closure | outsider-auditable multiplex trust | | ptm | yes | none | none | | targeted | yes | none | none |

Rerun-ready means the checked Runtime lane can be reopened under its named contract. It does not establish raw-vendor parity, scientific transfer, decision validity, or laboratory consequence beyond that contract.

Family evidence

dda

• rerun ready: no
• refusal reasons: faithful rerun still stops at imported MaxQuant and comparator exports because the repository does not own a raw DDA search execution lane, external-engine behavior remains proprietary or out-of-repository for the strongest DDA package
• blocked claims: raw DDA search parity, full outsider-auditable DDA rerun language
• next evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/package_manifest.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/failure_replay.json
• note: The refusal ledger names exactly why a workflow family still stops short of a stronger rerun claim instead of letting maintainers narrate around the gap.

dia

• rerun ready: no
• refusal reasons: the shipped DIA lane is raw-executable in runtime terms but still depends on library-conditioned exported reports rather than chromatogram-native replay
• blocked claims: chromatogram-native DIA parity, broad vendor-parity DIA authority
• next evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/package_manifest.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/failure_replay.json
• note: The refusal ledger names exactly why a workflow family still stops short of a stronger rerun claim instead of letting maintainers narrate around the gap.

lfq

• rerun ready: yes
• refusal reasons: none
• blocked claims: none
• next evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/package_manifest.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/failure_replay.json
• note: The refusal ledger names exactly why a workflow family still stops short of a stronger rerun claim instead of letting maintainers narrate around the gap.

multiplex

• rerun ready: no
• refusal reasons: multiplex remains below outsider-auditable trust because runtime rerun strength still outruns family-level consequence and challenge closure
• blocked claims: outsider-auditable multiplex trust
• next evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/package_manifest.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/failure_replay.json
• note: The refusal ledger names exactly why a workflow family still stops short of a stronger rerun claim instead of letting maintainers narrate around the gap.

ptm

• rerun ready: yes
• refusal reasons: none
• blocked claims: none
• next evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/package_manifest.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/failure_replay.json
• note: The refusal ledger names exactly why a workflow family still stops short of a stronger rerun claim instead of letting maintainers narrate around the gap.

targeted

• rerun ready: yes
• refusal reasons: none
• blocked claims: none
• next evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/package_manifest.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/failure_replay.json
• note: The refusal ledger names exactly why a workflow family still stops short of a stronger rerun claim instead of letting maintainers narrate around the gap.

Close or preserve a refusal

Refusal source	Evidence required before reconsideration
no repository-owned lane	implementation, public entrypoint, retained fixtures, negative paths, and ownership review
imported or proprietary upstream step	governed source custody plus executable or independently comparable upstream evidence
missing environment or tool	versioned environment contract and clean-environment replay
unstable or incomplete artifacts	complete inventory, stability classification, and successful invalidation challenges
claim exceeds Runtime authority	scientific, Knowledge, Intelligence, or Lab evidence from the responsible owner

A refusal is superseded only by a new record that cites the prior refusal, identifies the added evidence, replays the negative path, and states the new claim ceiling. Until then, operators preserve the refusal and use the strongest supported lane rather than narrating around the missing proof.