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?

Independent Review Contract¶

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

flowchart LR
    manifest["public package manifest"]
    source["copied-source locator and checksum"]
    request["runtime entrypoint and declared mode"]
    bundle["checked run bundle"]
    lineage["stage lineage"]
    failure["failure replay"]
    comparison["declared comparison verdict"]
    manifest --> source --> request --> bundle
    bundle --> lineage --> comparison
    bundle --> failure --> comparison

A reviewer should be able to resolve every node without private credentials, undocumented files, or a maintainer choosing which differences to ignore.

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

Rerun Closure Record¶

Record	Closure condition
package identity	manifest and copied-source checksums resolve to the reviewed public package
execution identity	entrypoint, runtime version, mode, provider, and environment contract are recorded
run history	state transitions, retries, resume or rehydrate events, and terminal disposition are coherent
artifact inventory	required outputs, fingerprints, lineage, and declared absences agree with the lane
replay pressure	failure replay and invalidation challenges produce the expected governed verdict
comparison	byte, value, review, and permitted-environment differences are classified
authority handoff	runtime conclusion and every stronger blocked claim are named separately

The rerun closes when these records agree. Similar-looking outputs without a resolved package, run history, or comparison policy do not close it.

Runtime Execution Boundary¶

Independent Review Contract¶

Shortest Rerun Route¶

What To Open Next¶

dda¶

dia¶

lfq¶

multiplex¶

ptm¶

targeted¶