sync-tex

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

1. 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.

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

1. 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.

1. 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)

1. 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.