prepare-staging

Prepare Staging

Use this after reproduce-results. The input is the working repo plus working/reproduction/reproduction-report.md. The output is a self-contained APP candidate tree at publication-staging/.

Explain to the author that publication-staging/ is a draft public repository inside the private repo; it is not public yet.

Process

1. Read working/reproduction/reproduction-report.md.
2. Create or revise publication-staging/:
   • first release: create from scratch;
   • revision: start from previous public release or coherent existing staging, whichever is cleaner;
   • preserve/summarize any old staging before replacing generated files.
3. Show the author the copy plan and get confirmation before copying.
4. Organize approved files under APP layout:
   • paper/, code/, data/, environment/, supplementary/, skills/;
   • exactly one canonical public location per file;
   • no private parent-repo dependencies or absolute private paths.
5. Create data/README.md whenever any dataset is used, local or external.
6. Prepare the environment following environment.md.
7. Create/copy LICENSE following licensing.md.
8. Copy only approved supplementary materials:
   • extracted chat context;
   • authors-note.md drafted from author intent;
   • know-how.md or materials the author wants public/sandbox-visible;
   • concise experiment notes, lab reports, design notes, or follow-up notes when they are publication-safe and directly help readers interpret figures, reproduce checks, understand parameter choices, or design next sanity checks;
   • slides, posters, tutorials, or paper-specific skills. Select notes rather than copying whole scratch trees. Exclude virtual environments, caches, build products, private paths, credentials, abandoned drafts, and notes whose status or authorship is unclear. If a note is useful but too broad or private, create a short reader-facing summary in supplementary/ and cite the exact staged code/data/paper anchors it explains.
9. Migrate reproduction wrappers:
   • follow figure-wrapper-migration.md;
   • create publication-staging/code/figure-reproduction/README.md;
   • rerun scripts from staging root when safe.
10. Run /validate-publication --stage structure with publication-staging/ as effective root.
11. Verify from staging root when safe:

• environment setup;
• paper compilation;
• figure/table scripts marked reproduced;
• tests, notebooks, imports;
• parent/private path checks.

12. Give the author a plain-language staging summary:

• what is in each top-level folder;
• what stayed outside staging;
• what is ground truth (paper/, staged code/data) versus optional context (supplementary/);
• remaining blockers or decisions before paper-agent drafting.

Do not write process checklists into publication-staging/; keep workflow status in chat/internal notes.