sync-tex

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

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Source SKILL.md: https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/blob/HEAD/skills/29-quarcs-lab-project20XXy/dot-claude/skills/sync-tex/SKILL.md

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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

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