paper-build-output-hygiene

name	paper-build-output-hygiene
description	Use this skill when validating AutoLabOS-generated TeX/PDF/paper bundles and keeping test/output coherent without manually substituting artifacts.
contract_version	1
contract_kind	codex_skill
runtime_contract	true
gate	paper_build_artifact_integrity
validation	paper_build_output_hygiene_review

Paper Build Output Hygiene

Purpose

Ensure that AutoLabOS itself generates the paper-facing artifacts and that test/output/ remains a clean, operator-facing bundle.

This skill is about artifact integrity and output structure, not about overstating research quality.

Use this skill when

Use this skill when the user asks to:

• inspect generated TeX/PDF outputs
• clean up paper output structure
• remove duplicate or confusing bundles
• verify page-budget compliance
• determine whether TeX→PDF is wired correctly
• ensure the canonical output path is coherent
• verify that a live validation run used the intended brief, template, and workspace-local paper inputs
• investigate citation/reference ordering, repeated citations, bibliography style, or template-surface regressions in generated papers

Required validations

Always report:

1. current output structure
2. unnecessary file/folder status
3. duplicate artifact status
4. required artifact coverage
5. TeX status
6. PDF status
7. page-budget compliance status
8. wiring/path changes needed
9. active brief/template/source workspace used for the generated paper
10. rendered-page inspection status for layout, table overflow, figure presence, references, author metadata, font/template consistency, and text alignment
11. bibliography-style status, including whether ACL templates use the expected ACL-compatible style and whether numeric references follow first-citation order
12. repeated-citation-bundle status, especially whether the same \cite{...} bundle is mechanically repeated across many paragraphs

Required principles

• AutoLabOS should generate the canonical paper artifacts itself.
• Do not manually substitute externally written TeX/PDF as if it were system output.
• Prefer one coherent canonical bundle over many partially overlapping bundles.
• Keep operator-facing outputs easy to inspect.
• Manuscript templates and style files used for live validation belong in the validation workspace, not in the repository, unless the project explicitly adds a public example template.
• The manuscript is not complete merely because TeX or PDF exists; inspect the rendered PDF when the user is evaluating paper quality.
• Tables must fit within the rendered text block. If a table visually crosses margins or covers body text, treat that as a paper-build blocker.
• Expected paper components include author metadata, references/citations, quantitative tables, and figures or charts when the brief or results require them.
• Algorithmic or conceptual figures may be generated by the workflow when appropriate, but they must be referenced, captioned, and checked against claims/results.

Guardrails

• Do not manually author TeX/PDF as a substitute for system output.
• Do not hand-patch generated main.tex, .bib, or PDF as the final fix for output-quality defects. Fix the AutoLabOS generator, validator, review gate, or harness handoff, then rerun generation.
• Do not multiply output folders unless the contract explicitly requires it.
• Do not break canonical runtime paths while cleaning structure.
• Distinguish between "artifact exists" and "artifact is correctly wired and usable".
• Do not treat a fallback built-in preamble as equivalent to the requested submission template.
• Do not treat template_applied=true as sufficient if the final rendered main.tex no longer preserves the requested template package/class (for example \usepackage[review]{ACL2023}) or if required sibling .sty/.bst files were not copied into the paper build directory.
• Do not inject template-absent front-matter elements such as an explicit Keywords: line when a concrete manuscript template is supplied, unless the template itself asks for that surface.
• If the template package name and available .sty filename differ by case, call it out as a build-risk and fix it in the workspace before rerunning.
• Do not mark paper-generation complete until rendered inspection has checked the concrete complaints or quality criteria the user raised.

Citation and Reference Hygiene

• Treat hardcoded \bibliographystyle{plain} as a defect for submission-template output unless the template explicitly asks for it; plain can make numeric references appear alphabetically instead of in first-citation order.
• For ACL-style templates preserving \usepackage[review]{ACL2023}, the generated TeX should preserve or infer an ACL-compatible bibliography style such as acl_natbib, and the build directory should include the sibling .bst file when available.
• If a concrete template contains \bibliographystyle{...}, preserve that exact style in the generated paper unless the user explicitly requests a different one.
• Repeated citation bundles are a render-quality issue: the same \cite{a,b,c} should not be appended to many paragraphs in the same section as a traceability fallback.
• paper/render_validation.json, paper/citation_consistency.json, and review artifacts should expose bibliography-style mismatches and repeated citation bundles so meta-harness can route the problem back to the responsible node instead of treating it as cosmetic paper polish.

AutoLabOS-Owned Fix Loop

When the problem is in generated output:

1. Reproduce or inspect the generated artifact that shows the defect.
2. Identify the AutoLabOS source path that emitted or failed to validate it.
3. Add the smallest generator/validator/review-gate change that prevents recurrence.
4. Add or update a targeted test around the system behavior.
5. Rerun the relevant generation, harness, or render validation path when practical.
6. Report any remaining gap explicitly; do not present manual artifact edits as completion.