Sync Tex

---
name: sync-tex
description: Transfers prose edits from latex/index.tex (Overleaf) back into index.qmd. Use after pulling LaTeX edits from a collaborator.
disable-model-invocation: true
allowed-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.