manuscript-guard

Write the analysis plan in design/plan.md before the analysis exists, and record every deviation from it as it happens. Use at the start of a paper project, when check reports no-analysis-plan, plan-section-missing or plan-section-empty, or when the analysis is about to do something the plan did not say.

Look at a rendered figure and record whether it is honest, complete and consistent with the results and the manuscript. Use when `manuscript-guard check` reports figure-unreviewed or figure-review-stale, after re-rendering a figure, or before a submission build.

Choose a target journal with the author, then read that journal's instructions for authors and fill the annotated profile template with its limits, required sections and required statements. Use when choosing where to submit, when check reports journal-profile-missing or journal-profile-stale, or before submitting to a different journal.

Retrieve a source, extract a value with its verbatim quote, and record it so the chain from manuscript to published sentence can be verified. Use when adding a number from the literature, when check reports literature-source-missing or quote-not-in-source, or when a citation needs a stored source.

Draft or revise manuscript prose that reads as though a person wrote it. Use when writing any section, when check reports ai-phrasing, ai-cadence or vague-attribution, or when revising text that was drafted quickly.

Write or reconcile a Methods section against the analysis code that was actually run. Use when drafting Methods, when check reports methods-drift or methods-never-reconciled, or after the analysis changes.

Check the numbers in a paper that was not written with manuscript-guard against the analysis outputs, and report honestly what a match is worth. Use when handed an existing .docx or Markdown manuscript whose numbers were typed by hand, before resubmitting an old paper, or before moving one into a manuscript-guard project.

Start a manuscript-guard paper project and run its daily loop, from analysis plan to built .docx, and find which skill deals with a given finding. Use when starting a new paper, when adding manuscript-guard to an existing analysis repository, when paper.yaml or authors.yaml need filling in, or when unsure what to do next in a project that has a paper.yaml.

Retrieve a reporting guideline's official checklist (STROBE, CONSORT, PRISMA, RECORD, SPIRIT, TRIPOD, ARRIVE and others) and record it so the build can check that every item is addressed. Use when check reports checklist-not-retrieved, or when adopting a new guideline.

Publish values from the analysis through the Python or R emitter, write them into the manuscript as bindings, and get an unbound number out of the red. Use when writing or changing an analysis script in a manuscript-guard project, when putting a result, table or figure into the text, or when check reports unclassified-number, unresolved-binding, value-splits-paragraph, unquoted-result, hand-authored-table, results-edited, script-newer, input-changed or duplicate-quantity.

Assemble a review panel for a manuscript, run the reviews, and record them. Use before submission, when check reports no-review or review-missing, or when a round is complete and a second is due.

Answer a journal's reviewers point by point, with every claimed revision checked against the manuscript as it was sent. Use when a decision letter with reviewer comments arrives, before revising anything, when check reports point-unanswered, response-claims-nothing, claimed-change-did-not-happen, claimed-change-missed-the-point or anchor-unrecorded, or before resubmitting.

Assemble everything a journal asks for and write the covering letter. Use when a manuscript is ready to submit, or when check --submission is close to clean and you want to see what remains.

Send a co-author a Word document built from the Markdown source, and bring their edits and comments back without letting a hand-typed number or citation in. Use when a co-author wants a .docx to edit, when an edited .docx comes back, or before running manuscript-guard import.