Available but not executable: transparency-audit and containerized re-execution artifacts for code-available dysphagia and swallowing AI

Reproducibility artifacts for the meta-research study "Available but not runnable out of the box: an audit of execution prerequisites and label reporting in shared code for dysphagia and swallowing artificial intelligence." The protocol keeps the working title it was written under. We audited whether published swallowing/dysphagia-AI code is not only available but re-runnable, and we release the full measurement pipeline so the audit is itself reproducible ("we practice what we audit"). Contents: multi-source open-API search & enrichment scripts (01–06), repository discovery / intake / code-link mining / census synthesis (07–10), a blind screening-reliability re-coding (11), post-hoc robustness checks (12–18: search-truncation measurement, backward-citation coverage, reference verification, and full author-list verification against Crossref), and the measurement scripts behind the environment pinning/portability audit, the run-instruction audit and every reported proportion (19–21), whose machine-readable outputs are archived under results/; the transparency rubric, codebook, and RS1–RS6 clinical reference-standard taxonomy; the containerized re-execution harness (Dockerfile templates) with per-repository build/run logs and verdicts; the dated study protocol, a self-audit checklist applying this study's own minimum-reporting recommendation set to itself, the PRISMA-ScR checklist (transparently declined, with its rationale), and that recommendation set; record-level bibliographic corpus metadata; and the candidate-repository inventory at three stages (raw discovery, code-link-mining additions, and the vetted inventory carrying the inclusion decision and reason for every candidate) together with the objective per-repository intake table behind each verdict. Non-distributive: only artifacts produced by the authors are included. Audited third-party repositories—their code, trained weights, and any human-derived (e.g. VFSS/FEES) data—are not re-hosted; each is referenced to its original repository/DOI. Dual license: code (scripts/, harness) under MIT (LICENSE-CODE); data & text under CC-BY-4.0 (LICENSE-DATA). Changes in v1.1.6. Counts the release whose codes come from an accepted manuscript. One audited release has no open published version, and its codes were assigned from the version its authors deposited in an institutional repository, which the deposit records as the version accepted for publication. The row was held outside the clinical denominator while it already carried a confirmed absence for label reliability, which the study's own rule does not allow. It is now counted, its spectrum cell is filled from the same source, and the denominator moves from six to seven with the reliability count from 0 of 5 to 0 of 6, since one release has no rater. Script 21 now reads that denominator from the coding file instead of printing it as a constant. The recommendation set still carried the sample data count from before the rule was corrected in August, and the July intake log presented its figures as current and now says what superseded them. No other number changes. Changes in v1.1.5. A corrective release. Script 31 derived the point shifts of the screening sensitivity from figures that had already been rounded, which moved two of them by 0.1 point, and reported the largest increase only over the signals with a nonzero count, leaving out the larger shift a zero row can take. Both bounds are now computed from the exact fractions and rounded away from zero, and the increase over every signal is recorded beside the earlier figure. In the adapted reporting checklist, the item on unadjusted estimates pointed only at the footnote that explains the row given without an interval, not at the table body or the results subsection that carry the proportions, and the funding item named only the title page heading while the statement also stands under Declarations in the manuscript. The archive documents name the article's sections as the articl…