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sync-tex

Transfers prose edits from latex/index.tex (Overleaf) back into index.qmd. Use after pulling LaTeX edits from a collaborator.

Published by brycewang-stanford ↗brycewang-stanford/Auto-Empirical-Research-Skills

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sync-tex

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Use sync-tex to transfer collaborator prose edits from latex/index.tex into index.qmd using the existing LaTeX baseline, preserve all embed shortcodes, summarize transferred and untransferred changes, and render to verify the result.

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    SKILL.md

    name: sync-texdescription: Transfers prose edits from latex/index.tex (Overleaf) back into index.qmd. Use after pulling LaTeX edits from a collaborator.disable-model-invocation: trueallowed-tools: Bash, Read, Write, Edit, Glob, Grep

    Sync LaTeX Edits to QMD

    Transfer prose changes made by collaborators in latex/index.tex (e.g., via Overleaf) back into index.qmd.

    Prerequisites

    • latex/.baseline.tex must exist (auto-created by bash scripts/render.sh)
    • latex/index.tex must contain collaborator edits (pulled from Overleaf / GitHub)

    Steps

    1. Read these three files:

      • latex/.baseline.tex — the LaTeX snapshot from the last render (before edits)
      • latex/index.tex — the LaTeX after collaborator edits
      • index.qmd — the current QMD manuscript source
    2. Compare latex/.baseline.tex vs latex/index.tex to identify changes. Focus on the document body only (everything between \begin{document} and \end{document}). Ignore the preamble (lines before \begin{document}) — these are auto-generated by Quarto.

    3. For each section (identified by \section{...}\label{...} and \subsection{...}\label{...} markers), check if the prose text changed between baseline and modified.

    4. For each changed section, apply the edits to the corresponding section in index.qmd:

      • Convert LaTeX formatting to QMD equivalents:
        • \textbf{...} → **...**
        • \textit{...} or \emph{...} → *...*
        • \href{url}{text} → [text](url)
        • Section~\ref{sec-id} → @sec-id
        • Figure~\ref{fig-id} → @fig-id
        • Table~\ref{tbl-id} → @tbl-id
        • \cite{key} or \citep{key} → [@key]
        • \citet{key} → @key
        • Footnotes: \footnote{...} → ^[...]
      • CRITICAL: Preserve all {{< embed >}} shortcodes exactly as they are in the QMD. Do NOT replace them with \includegraphics, \begin{figure}, \begin{longtable}, or any LaTeX equivalents. These shortcodes pull live outputs from notebooks and must remain intact.
      • If a collaborator edited a figure/table caption in LaTeX (\caption{...}), note the change in the summary report but do NOT modify the embed shortcodes — captions are defined in the notebook source cells.
    5. After applying all changes, show a summary:

      • List each section that was modified
      • For each, show a brief description of what changed (e.g., "Added two sentences to Introduction", "Rewrote paragraph 2 in Methods")
      • Note any changes that could NOT be transferred (e.g., caption edits, preamble changes, new LaTeX packages)
    6. Render the manuscript with bash scripts/render.sh to verify the round-trip is clean (no warnings, no errors).

    Error handling

    • If latex/.baseline.tex does not exist, tell the user to run /project:render first.
    • If latex/.baseline.tex and latex/index.tex are identical, report "No changes detected" and stop.
    • If a section label in the LaTeX does not match any section in index.qmd, flag it and skip.