Runtime Execution Boundary

Start here when the question is: how would an independent reviewer reopen a shipped workflow family without asking maintainers what to trust next?

How An Independent Reviewer Should Use This Route

• start from the public benchmark manifest, not from runtime prose
• reopen the checked bundle before deciding whether the lane still deserves a stronger sentence
• use stage lineage and failure replay to test whether the execution story is robust enough to survive scrutiny without maintainer narration

Shortest Rerun Route

workflow family	start from	runtime entrypoint	checked bundle	current limit
dda	packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/package_manifest.json	bijux_proteomics_runtime.workflows.paths.run_reviewable_import_path	packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/run_bundle.json	dda replay is real for the shipped imported-result lane, but it still refuses broader raw-engine rerun claims.
dia	packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/package_manifest.json	bijux_proteomics_runtime.workflows.benchmark_runs.run_benchmark_dia_review_path	packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/run_bundle.json	DIA replay is real for the shipped runtime lane, but it still refuses chromatogram-native and broader vendor-parity claims.
lfq	packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/package_manifest.json	bijux_proteomics_runtime.workflows.benchmark_runs.run_benchmark_lfq_review_path	packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/run_bundle.json	lfq replay is real for the shipped runtime lane, but it still inherits the same benchmark and downstream claim limits as the checked bundle.
multiplex	packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/package_manifest.json	bijux_proteomics_runtime.workflows.benchmark_runs.run_benchmark_multiplex_review_path	packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/run_bundle.json	multiplex replay is real for the shipped runtime lane, but it still inherits the same benchmark and downstream claim limits as the checked bundle.
ptm	packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/package_manifest.json	bijux_proteomics_runtime.workflows.benchmark_runs.run_benchmark_ptm_review_path	packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/run_bundle.json	ptm replay is real for the shipped runtime lane, but it still inherits the same benchmark and downstream claim limits as the checked bundle.
targeted	packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/package_manifest.json	bijux_proteomics_runtime.workflows.benchmark_runs.run_benchmark_targeted_review_path	packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/run_bundle.json	targeted replay is real for the shipped runtime lane, but it still inherits the same benchmark and downstream claim limits as the checked bundle.

What To Open Next

dda

• start from the public benchmark manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/package_manifest.json
• confirm copied-source scope in: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/source_locator_manifest.json
• reopen the checked runtime bundle: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/run_bundle.json
• challenge stage-to-stage continuity with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/stage_lineage.json
• challenge replay and invalidation with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/failure_replay.json
• rerun refusal summary: 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

dia

• start from the public benchmark manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/package_manifest.json
• confirm copied-source scope in: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/source_locator_manifest.json
• reopen the checked runtime bundle: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/run_bundle.json
• challenge stage-to-stage continuity with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/stage_lineage.json
• challenge replay and invalidation with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/failure_replay.json
• rerun refusal summary: the shipped DIA lane is raw-executable in runtime terms but still depends on library-conditioned exported reports rather than chromatogram-native replay

lfq

• start from the public benchmark manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/package_manifest.json
• confirm copied-source scope in: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/source_locator_manifest.json
• reopen the checked runtime bundle: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/run_bundle.json
• challenge stage-to-stage continuity with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/stage_lineage.json
• challenge replay and invalidation with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/failure_replay.json
• rerun refusal summary: none

multiplex

• start from the public benchmark manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/package_manifest.json
• confirm copied-source scope in: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/source_locator_manifest.json
• reopen the checked runtime bundle: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/run_bundle.json
• challenge stage-to-stage continuity with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/stage_lineage.json
• challenge replay and invalidation with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/failure_replay.json
• rerun refusal summary: multiplex remains below outsider-auditable trust because runtime rerun strength still outruns family-level consequence and challenge closure

ptm

• start from the public benchmark manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/package_manifest.json
• confirm copied-source scope in: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/source_locator_manifest.json
• reopen the checked runtime bundle: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/run_bundle.json
• challenge stage-to-stage continuity with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/stage_lineage.json
• challenge replay and invalidation with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/failure_replay.json
• rerun refusal summary: none

targeted

• start from the public benchmark manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/package_manifest.json
• confirm copied-source scope in: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/source_locator_manifest.json
• reopen the checked runtime bundle: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/run_bundle.json
• challenge stage-to-stage continuity with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/stage_lineage.json
• challenge replay and invalidation with: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/failure_replay.json
• rerun refusal summary: none

What This Route Proves And What It Does Not

• it proves that a reviewer can reopen the shipped runtime lane from named public roots
• it does not prove that execution alone upgrades benchmark, grounding, recommendation, or lab authority
• it should hand off once the question becomes whether the reopened lane still deserves stronger language beyond runtime traceability