LaTeX Scaffold

Convert an approved Markdown draft into a minimal, compilable LaTeX project. This is a deterministic format conversion — prose quality should already be addressed in the source draft.

When to Use

• Converting a literature review, survey, or report from Markdown to LaTeX for PDF output
• Turning meeting notes or drafts into a formatted document
• Bootstrapping a LaTeX project from an existing outline
• Any time you need md→tex without rewriting content

Inputs

• A Markdown file (.md) — the draft to convert
• A .bib file (optional) — if the draft contains citations

Outputs

• A .tex file ready to compile with latex
• The fail-closed canonical .latexmkrc if one does not already exist. Invoke the latex pre-flight to copy the canonical artifact; never synthesize selected directives.

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Workflow

Step 1: Analyse the Draft

Read the Markdown file and inventory:

• Heading structure (determine \section / \subsection depth)
• Citations ([@Key] or [@Key1; @Key2] patterns)
• Tables (Markdown pipe tables)
• Math blocks ($...$ inline, $$...$$ display)
• Figures (![caption](path))
• Code blocks (fenced with language)
• Whether an abstract section exists

Step 2: Create the LaTeX File

Apply these conversion rules:

Markdown	LaTeX
# Title (first H1)	\title{...}
## Section	\section{...}
### Subsection	\subsection{...}
#### Subsubsection	\subsubsection{...}
## Abstract	\begin{abstract}...\end{abstract}
Headings starting with Appendix	\appendix once, then \section{...}
**bold**	\textbf{...}
*italic*	\emph{...}
`code`	\texttt{...}
[@Key]	\citep{Key}
[@Key1; @Key2]	\citep{Key1,Key2}
@Key (inline)	\citet{Key}
$...$ / $$...$$	Pass through unchanged
- item	\begin{itemize}\item ...\end{itemize}
1. item	\begin{enumerate}\item ...\end{enumerate}
> quote	\begin{quote}...\end{quote}
	\begin{figure}[htbp]\includegraphics{path}\caption{caption}\end{figure}
Pipe tables	\begin{table}[htbp]\begin{tabular}{...}...\end{tabular}\end{table}
Fenced code blocks	\begin{verbatim}...\end{verbatim}
--- (horizontal rule)	\bigskip\hrule\bigskip or omit

Preamble Template

\documentclass[a4paper,11pt]{article}

\usepackage[a4paper,margin=1in]{geometry}
\usepackage{hyperref}
\hypersetup{colorlinks=true,linkcolor=blue,citecolor=blue,urlcolor=blue}
\usepackage{booktabs}
\usepackage{tabularx}
\usepackage{graphicx}
\usepackage{amsmath,amssymb}
\usepackage{enumitem}
\usepackage[backend=biber,style=authoryear,natbib=true]{biblatex}
\addbibresource{references.bib}

\title{...}
\author{...}
\date{\today}

\begin{document}
\maketitle
% content here
\printbibliography
\end{document}

Adjust the preamble based on what the draft actually uses (e.g., skip graphicx if no figures). The natbib=true option provides \citet/\citep compatibility. If the project already uses natbib (e.g., with a journal .bst file), keep natbib — but for new scaffolds, biblatex is the default.

Step 3: Strip Markdown Residue

After conversion, scan the .tex file for any remaining Markdown syntax:

• ## heading markers
• ** bold markers
• [@ citation markers
• Pipe | table syntax
• ![ image markers

These indicate incomplete conversion — fix them.

Step 4: Wire Bibliography

• If a .bib file exists in the project, point \addbibresource{} to it
• If the project has a references.bib, use that
• If no .bib exists but citations are present, create placeholder comments: % TODO: create .bib with keys: Key1, Key2, ...
• Ensure \printbibliography is at the end of the document (not \bibliography{})

Step 5: Compile and Verify

Run latex to compile. Verify:

• Document compiles without errors
• All citations resolve (or are marked as TODO)
• Tables render correctly
• Math renders correctly
• Page count is reasonable

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Rules

• No content rewriting — this is format conversion only. Do not improve prose, fix grammar, or reorganise sections.
• Preserve all content — every paragraph, figure reference, and citation in the draft must appear in the .tex output.
• Strip heading numbering — if the draft has numbered headings like 1.2 Methods, let LaTeX handle the numbering (just use \subsection{Methods}).
• Use latex for compilation — never bare pdflatex or latexmk without out/ directory.
• Bold caption lines like **Table 1. Description** immediately before a pipe table should become \caption{Description} inside a table float.

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Cross-References

Skill	When to use alongside
latex	Compile the scaffolded .tex file
latex	For manual compilation config and .latexmkrc setup
bib-validate	After scaffolding to verify all citation keys resolve
proofread	After scaffolding for grammar and consistency check
latex-template	After scaffolding to verify preamble aligns with the working paper template

Citation Contract

1. Paperpile is the only source of truth for committed citation keys and BibTeX metadata.
2. Before writing \cite{key}, verify with paperpile get-item key and paperpile export-bib key.
3. Resolve unknowns in order: DOI lookup → Paperpile substring search → refpile semantic search → Paperpile verify.
4. A DOI miss is not non-membership; continue with title/author search and refpile.
5. If unresolved, write \CiteTodo{slug}{title/author/year/DOI hint} — never a guessed key.
6. Drafting sub-agents must not write/edit the active .bib; only the orchestrator regenerates it from Paperpile exports.
7. Stage genuine new refs under .paperpile-import/ for manual Paperpile import; don't cite until Paperpile mints the key.
8. Run scripts/bib/citation_lint.py before commit; zero placeholders, zero non-Paperpile keys, zero hand-authored metadata.

See rules/paperpile-citations.md for the full workflow.