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.