LaTeX reader not including the results from \input (or anything thereafter)

[pharpend]

I have a rather complicated LaTeX tree, for a book. The entire tree is at https://gitlab.com/lysa/lysa/tree/master/ . The root node of the tree is this LaTeX file.

\documentclass[12pt]{book}

% Append yourself to this list. Aliases are fine (e.g. darkf), but please do
% include an email where people can email you. If applicable, also include your
% middle initial, as is the convention in academia.
\author{
  \pharpend
}

\newcommand{\editors}{
  \aneditor{Randy Brown}{[email protected]}
  \aneditor{Nick Chambers}{[email protected]}
  % \aneditor{Anton Golov}{[email protected]}
  \aneditor{Ng Wei En}{[email protected]}
  \aneditor{Ben Z RF}{[email protected]}
  \aneditor{Alexander G Bauer}{[email protected]}
}

\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsthm}
\usepackage[toc,page]{appendix}
\usepackage[backend=bibtex]{biblatex}
\usepackage{centernot}
\usepackage[answerdelayed]{exercise}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{listings}
\usepackage{mathtools}
\usepackage{relsize}
\usepackage{scrextend}
\usepackage{setspace}
\usepackage{tabu}
\usepackage{ulem}
\usepackage{url}
\usepackage[hidelinks]{hyperref}
\usepackage{cleveref}

\crefname{chapter}{\S}{\S}
\crefname{section}{\S}{\S}
\crefname{subsection}{\S}{\S}
\crefname{subsubsection}{\S}{\S}
\crefname{paragraph}{\S}{\S}
\Crefname{chapter}{\S}{\S}
\Crefname{section}{\S}{\S}
\Crefname{subsection}{\S}{\S}
\Crefname{subsubsection}{\S}{\S}
\Crefname{paragraph}{\S}{\S}

\addbibresource{lysa.bib}
\usepackage{listings}
\usepackage{color}

\definecolor{mygreen}{rgb}{0,0.6,0}
\definecolor{mygray}{rgb}{0.5,0.5,0.5}
\definecolor{mymauve}{rgb}{0.58,0,0.82}

\lstset{ %
  backgroundcolor=\color{white},   % choose the background color; you must add \usepackage{color} or \usepackage{xcolor}
  basicstyle=\footnotesize\tt,     % the size of the fonts that are used for the code
  breakatwhitespace=false,         % sets if automatic breaks should only happen at whitespace
  breaklines=true,                 % sets automatic line breaking
  captionpos=b,                    % sets the caption-position to bottom
  commentstyle=\color{mygreen},    % comment style
  deletekeywords={...},            % if you want to delete keywords from the given language
  escapeinside={\%*}{*)},          % if you want to add LaTeX within your code
  extendedchars=true,              % lets you use non-ASCII characters; for 8-bits encodings only, does not work with UTF-8
  frame=single,                    % adds a frame around the code
  keepspaces=true,                 % keeps spaces in text, useful for keeping indentation of code (possibly needs columns=flexible)
  keywordstyle=\color{blue},       % keyword style
  % Actually, we are using Idris, but Haskell is close enough
  language=Haskell,                % the language of the code
  % morekeywords={*,...},            % if you want to add more keywords to the set
  numbers=left,                    % where to put the line-numbers; possible values are (none, left, right)
  numbersep=5pt,                   % how far the line-numbers are from the code
  numberstyle=\footnotesize\tt,    % the style that is used for the line-numbers
  rulecolor=\color{mygray},        % if not set, the frame-color may be changed on line-breaks within not-black text (e.g. comments (green here))
  showspaces=false,                % show spaces everywhere adding particular underscores; it overrides 'showstringspaces'
  showstringspaces=false,          % underline spaces within strings only
  showtabs=false,                  % show tabs within strings adding particular underscores
  stepnumber=2,                    % the step between two line-numbers. If it's 1, each line will be numbered
  % stringstyle=\color{mymauve},     % string literal style
  tabsize=2,                       % sets default tabsize to 2 spaces
  title=\lstname                   % show the filename of files included with \lstinputlisting; also try caption instead of title
}

% Print-friendly links
\newcommand{\anauthor}[2]
{#1 {\href{mailto:#2}<{\tt #2}>} \\
}
\newcommand{\aneditor}[2]{#1 & {\href{mailto:#2}{<{#2}>}} \\ }
\newcommand{\link}[2]{#2 (\url{#1})}

% Section & Chapter he
\newcommand{\ch}[1]{\chapter{#1}\label{ch: #1}}
\newcommand{\s}[1]{\section{#1}\label{s: #1}}
\renewcommand{\ss}[1]{\subsection{#1}\label{ss: #1}}
\newcommand{\sss}[1]{\subsubsection{#1}\label{sss: #1}}
\newcommand{\pg}[2]{\paragraph{#1}\label{pg: #1}}

% Math shortcuts
\newcommand{\suc}{\mathrm{suc}}
\newcommand{\N}{\mathbb{N}}
\newcommand{\R}{\mathbb{R}}
\newcommand{\Z}{\mathbb{Z}}
\renewcommand{\emptyset}{\varnothing}
% \newcommand{\nil}{\varnothing}
\newcommand{\nil}{\emptyset}
\newcommand{\subof}{\subset}
\newcommand{\subeq}{\subseteq}
\newcommand{\subofnm}{$\subset$}
\newcommand{\subeqnm}{$\subseteq$}
\newcommand{\supof}{\supset}
\newcommand{\supeq}{\supseteq}
\newcommand{\supofnm}{$\supset$}
\newcommand{\supeqnm}{$\supseteq$}
\newcommand{\mset}[1]{\left\{\,#1\,\right\}}
\newcommand{\parens}[1]{\left(\,#1\,\right)}
\newcommand{\brackets}[1]{\left[\,#1\,\right]}
\newcommand{\Qimplies}{\stackrel{?}{\implies}}
\newcommand{\Qimpliedby}{\stackrel{?}{\impliedby}}
\newcommand{\comma}{,\,}
\newcommand{\notimplies}{\centernot\implies}
\newcommand{\notimpliedby}{\centernot\impliedby}
\newcommand{\notiff}{\centernot\iff}
\newcommand{\Qin}{\stackrel{?}{\in}}
\newcommand{\Qiff}{\stackrel{?}{\iff}}
\newcommand{\truenm}{$\true$}
\newcommand{\falsenm}{$\false$}
\newcommand{\true}{\mathrm{True}}
\newcommand{\false}{\mathrm{False}}
\newcommand{\bigand}[1]{\land\brackets{#1}}
\newcommand{\semicolon}{;\;}
\newcommand{\mlist}[1]{\left(\,#1\,\right)}
\newcommand{\sfall}{\semicolon\forall}
\newcommand{\ld}[1]{\lambda\mlist{#1} \to}
\newcommand{\domain}[1]{^{\mathrm{dom}}\brackets{#1}}
\let\dom\domain
\newcommand{\codomain}[1]{^{\mathrm{codom}}\brackets{#1}}
\let\codom\codomain
\newcommand{\bool}{\mathbb{B}}
\newcommand{\boolnm}{$\mathrm{\bool}$}
\newcommand{\bracketset}[1]{\brackets{ #1 }}
\newcommand{\evalat}[2]{#1 _{\,\bracketset{#2}}}
\newenvironment{alignmath}[1]
  {\begin{displaymath}\begin{array}{#1}}
  {\end{array}\end{displaymath}}
\newenvironment{alignedmath}
  {\begin{alignmath}{l}}
  {\end{alignmath}}
\newcommand{\lto}{\lambda\to}
\newcommand{\arc}[1]  {{^{\mathrm{arc}}\brackets{#1}}}
\newcommand{\im}[1]   {{^{\mathrm{im}}\brackets{#1}}}
\newcommand{\preim}[1]{{^{\mathrm{preim}}\brackets{#1}}}
\newcommand{\Set}{\mathbf{Set}}
\newcommand{\Qsubof}{\stackrel{?}{\subof}}
\newcommand{\Qsubeq}{\stackrel{?}{\subeq}}
\newcommand{\Qsupof}{\stackrel{?}{\supof}}
\newcommand{\Qsupeq}{\stackrel{?}{\supeq}}
\newcommand{\notsubof}{\centernot{\subof}}
\newcommand{\notsubeq}{\centernot{\subeq}}
\newcommand{\notsupof}{\centernot{\supof}}
\newcommand{\notsupeq}{\centernot{\supeq}}
\newcommand{\superbracket}[2]{
  {
    ^{
      {#1}
    }
    \brackets{
      {#2}
    }
  }
}

% Miscellaneous
\newcommand{\pharpend}{\anauthor{Peter Harpending}{[email protected]}}
\let\xti\textit %italicize
\let\xtb\textbf %boldface
\newcommand{\code}[1]{{\tt #1}} %boldface
\let\crappycode\code %boldface
\let\terminal\code
\let\tilde\textasciitilde
\setlength{\parskip}{2ex}
\newenvironment{ExcList}
{
  \newpage
  \ss{Exercises}
  \begin{ExerciseList}
}
{
  \end{ExerciseList}
  \newpage
  \sss{Answers}
  \shipoutAnswer
  \newpage
}
\newenvironment{iquote}{\begin{quote}\it}{\end{quote}}

\lstnewenvironment{plainfile}[1][]
  {\lstset{
      numbers=none,
      basicstyle=\small\ttfamily,
      #1
    }}
  {}

\lstnewenvironment{shellsession}[1][]
  {\lstset{
      numbers=none,
      % language=bash,
      basicstyle=\small\ttfamily,
      #1
          }}
  {}

\newcommand{\filepath}{\texttt}


\title{Learn You Some Algebras for Glorious Good!}
\begin{document}
\maketitle

\newpage
\topskip0pt
\vspace*{\fill}

{\footnotesize
  \begin{center}
    Copyright © 2014-2015 \pharpend
  \end{center}
% \noindent
  \begin{center}
    Permission is granted to copy, distribute and/or modify this document under
    the terms of the GNU Free Documentation License, Version 1.3 or any later
    version published by the Free Software Foundation; with no Invariant
    Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the
    license is included in \cref{gfdl}.
  \end{center}
}
\vspace*{\fill}
% \newpage
% \section*{Editors \& Noted Contributors}
% \begin{addmargin}[4em]{2em}
%   \begin{tabular}{l l}
%     \editors
%   \end{tabular}
% \end{addmargin}

\newpage
\tableofcontents
\newpage


\input{1-introduction.ltx}
\input{2-boolean-algebra.ltx}
\input{3-sets-functions.ltx}
\input{4-proofs.ltx}

\begin{appendices}

{\footnotesize
  \setlength{\parskip}{0ex}
  \setlength{\parindent}{0ex}
  \input{fdl.ltx}
}
\input{how-to-learn.ltx}
\end{appendices}

\newpage
\printbibliography
\end{document}

The build script basically copies all of the relevant files into a temporary directory, then compiles the root node with pdflatex, copies the pdf out of the sandbox, and then deletes the sandbox. I want to compile the book into an EPub instead of a PDF. I performed the sandbox-copying steps manually, then used the following command to attempt to generate the epub:

pandoc lysa.ltx -f latex -t epub -o lysa.epub

The EPub only has the first two pages. No TOC or content. The epub can be downloaded here:

http://harpending.org/lysa.epub

By contrast, the correct PDF file is 70-something pages long, and can be seen here:

http://harpending.org/lysa.pdf

Am I missing something here? It seems like Pandoc is completely ignoring the \input commands (and hence no TOC).

[jgm]

What version of pandoc are you using? Recent versions do process
\input.

Are the included files in the directory from which you run pandoc?

+++ Peter Harpending [Jan 15 15 18:44 ]:

I have a rather complicated LaTeX tree, for a book. The entire tree is at https://gitlab.com/lysa/lysa/tree/master/ . The root node of the tree is this LaTeX file.

\documentclass[12pt]{book}

% Append yourself to this list. Aliases are fine (e.g. darkf), but please do
% include an email where people can email you. If applicable, also include your
% middle initial, as is the convention in academia.
\author{
 \pharpend
}

\newcommand{\editors}{
 \aneditor{Randy Brown}{[email protected]}
 \aneditor{Nick Chambers}{[email protected]}
 % \aneditor{Anton Golov}{[email protected]}
 \aneditor{Ng Wei En}{[email protected]}
 \aneditor{Ben Z RF}{[email protected]}
 \aneditor{Alexander G Bauer}{[email protected]}
}

\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsthm}
\usepackage[toc,page]{appendix}
\usepackage[backend=bibtex]{biblatex}
\usepackage{centernot}
\usepackage[answerdelayed]{exercise}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{listings}
\usepackage{mathtools}
\usepackage{relsize}
\usepackage{scrextend}
\usepackage{setspace}
\usepackage{tabu}
\usepackage{ulem}
\usepackage{url}
\usepackage[hidelinks]{hyperref}
\usepackage{cleveref}

\crefname{chapter}{\S}{\S}
\crefname{section}{\S}{\S}
\crefname{subsection}{\S}{\S}
\crefname{subsubsection}{\S}{\S}
\crefname{paragraph}{\S}{\S}
\Crefname{chapter}{\S}{\S}
\Crefname{section}{\S}{\S}
\Crefname{subsection}{\S}{\S}
\Crefname{subsubsection}{\S}{\S}
\Crefname{paragraph}{\S}{\S}

\addbibresource{lysa.bib}
\usepackage{listings}
\usepackage{color}

\definecolor{mygreen}{rgb}{0,0.6,0}
\definecolor{mygray}{rgb}{0.5,0.5,0.5}
\definecolor{mymauve}{rgb}{0.58,0,0.82}

\lstset{ %
 backgroundcolor=\color{white},   % choose the background color; you must add \usepackage{color} or \usepackage{xcolor}
 basicstyle=\footnotesize\tt,     % the size of the fonts that are used for the code
 breakatwhitespace=false,         % sets if automatic breaks should only happen at whitespace
 breaklines=true,                 % sets automatic line breaking
 captionpos=b,                    % sets the caption-position to bottom
 commentstyle=\color{mygreen},    % comment style
 deletekeywords={...},            % if you want to delete keywords from the given language
 escapeinside={\%*}{*)},          % if you want to add LaTeX within your code
 extendedchars=true,              % lets you use non-ASCII characters; for 8-bits encodings only, does not work with UTF-8
 frame=single,                    % adds a frame around the code
 keepspaces=true,                 % keeps spaces in text, useful for keeping indentation of code (possibly needs columns=flexible)
 keywordstyle=\color{blue},       % keyword style
 % Actually, we are using Idris, but Haskell is close enough
 language=Haskell,                % the language of the code
 % morekeywords={*,...},            % if you want to add more keywords to the set
 numbers=left,                    % where to put the line-numbers; possible values are (none, left, right)
 numbersep=5pt,                   % how far the line-numbers are from the code
 numberstyle=\footnotesize\tt,    % the style that is used for the line-numbers
 rulecolor=\color{mygray},        % if not set, the frame-color may be changed on line-breaks within not-black text (e.g. comments (green here))
 showspaces=false,                % show spaces everywhere adding particular underscores; it overrides 'showstringspaces'
 showstringspaces=false,          % underline spaces within strings only
 showtabs=false,                  % show tabs within strings adding particular underscores
 stepnumber=2,                    % the step between two line-numbers. If it's 1, each line will be numbered
 % stringstyle=\color{mymauve},     % string literal style
 tabsize=2,                       % sets default tabsize to 2 spaces
 title=\lstname                   % show the filename of files included with \lstinputlisting; also try caption instead of title
}

% Print-friendly links
\newcommand{\anauthor}[2]
{#1 {\href{mailto:#2}<{\tt #2}>} \\
}
\newcommand{\aneditor}[2]{#1 & {\href{mailto:#2}{<{#2}>}} \\ }
\newcommand{\link}[2]{#2 (\url{#1})}

% Section & Chapter he
\newcommand{\ch}[1]{\chapter{#1}\label{ch: #1}}
\newcommand{\s}[1]{\section{#1}\label{s: #1}}
\renewcommand{\ss}[1]{\subsection{#1}\label{ss: #1}}
\newcommand{\sss}[1]{\subsubsection{#1}\label{sss: #1}}
\newcommand{\pg}[2]{\paragraph{#1}\label{pg: #1}}

% Math shortcuts
\newcommand{\suc}{\mathrm{suc}}
\newcommand{\N}{\mathbb{N}}
\newcommand{\R}{\mathbb{R}}
\newcommand{\Z}{\mathbb{Z}}
\renewcommand{\emptyset}{\varnothing}
% \newcommand{\nil}{\varnothing}
\newcommand{\nil}{\emptyset}
\newcommand{\subof}{\subset}
\newcommand{\subeq}{\subseteq}
\newcommand{\subofnm}{$\subset$}
\newcommand{\subeqnm}{$\subseteq$}
\newcommand{\supof}{\supset}
\newcommand{\supeq}{\supseteq}
\newcommand{\supofnm}{$\supset$}
\newcommand{\supeqnm}{$\supseteq$}
\newcommand{\mset}[1]{\left\{\,#1\,\right\}}
\newcommand{\parens}[1]{\left(\,#1\,\right)}
\newcommand{\brackets}[1]{\left[\,#1\,\right]}
\newcommand{\Qimplies}{\stackrel{?}{\implies}}
\newcommand{\Qimpliedby}{\stackrel{?}{\impliedby}}
\newcommand{\comma}{,\,}
\newcommand{\notimplies}{\centernot\implies}
\newcommand{\notimpliedby}{\centernot\impliedby}
\newcommand{\notiff}{\centernot\iff}
\newcommand{\Qin}{\stackrel{?}{\in}}
\newcommand{\Qiff}{\stackrel{?}{\iff}}
\newcommand{\truenm}{$\true$}
\newcommand{\falsenm}{$\false$}
\newcommand{\true}{\mathrm{True}}
\newcommand{\false}{\mathrm{False}}
\newcommand{\bigand}[1]{\land\brackets{#1}}
\newcommand{\semicolon}{;\;}
\newcommand{\mlist}[1]{\left(\,#1\,\right)}
\newcommand{\sfall}{\semicolon\forall}
\newcommand{\ld}[1]{\lambda\mlist{#1} \to}
\newcommand{\domain}[1]{^{\mathrm{dom}}\brackets{#1}}
\let\dom\domain
\newcommand{\codomain}[1]{^{\mathrm{codom}}\brackets{#1}}
\let\codom\codomain
\newcommand{\bool}{\mathbb{B}}
\newcommand{\boolnm}{$\mathrm{\bool}$}
\newcommand{\bracketset}[1]{\brackets{ #1 }}
\newcommand{\evalat}[2]{#1 _{\,\bracketset{#2}}}
\newenvironment{alignmath}[1]
 {\begin{displaymath}\begin{array}{#1}}
 {\end{array}\end{displaymath}}
\newenvironment{alignedmath}
 {\begin{alignmath}{l}}
 {\end{alignmath}}
\newcommand{\lto}{\lambda\to}
\newcommand{\arc}[1]  {{^{\mathrm{arc}}\brackets{#1}}}
\newcommand{\im}[1]   {{^{\mathrm{im}}\brackets{#1}}}
\newcommand{\preim}[1]{{^{\mathrm{preim}}\brackets{#1}}}
\newcommand{\Set}{\mathbf{Set}}
\newcommand{\Qsubof}{\stackrel{?}{\subof}}
\newcommand{\Qsubeq}{\stackrel{?}{\subeq}}
\newcommand{\Qsupof}{\stackrel{?}{\supof}}
\newcommand{\Qsupeq}{\stackrel{?}{\supeq}}
\newcommand{\notsubof}{\centernot{\subof}}
\newcommand{\notsubeq}{\centernot{\subeq}}
\newcommand{\notsupof}{\centernot{\supof}}
\newcommand{\notsupeq}{\centernot{\supeq}}
\newcommand{\superbracket}[2]{
 {
   ^{
     {#1}
   }
   \brackets{
     {#2}
   }
 }
}

% Miscellaneous
\newcommand{\pharpend}{\anauthor{Peter Harpending}{[email protected]}}
\let\xti\textit %italicize
\let\xtb\textbf %boldface
\newcommand{\code}[1]{{\tt #1}} %boldface
\let\crappycode\code %boldface
\let\terminal\code
\let\tilde\textasciitilde
\setlength{\parskip}{2ex}
\newenvironment{ExcList}
{
 \newpage
 \ss{Exercises}
 \begin{ExerciseList}
}
{
 \end{ExerciseList}
 \newpage
 \sss{Answers}
 \shipoutAnswer
 \newpage
}
\newenvironment{iquote}{\begin{quote}\it}{\end{quote}}

\lstnewenvironment{plainfile}[1][]
 {\lstset{
     numbers=none,
     basicstyle=\small\ttfamily,
     #1
   }}
 {}

\lstnewenvironment{shellsession}[1][]
 {\lstset{
     numbers=none,
     % language=bash,
     basicstyle=\small\ttfamily,
     #1
         }}
 {}

\newcommand{\filepath}{\texttt}


\title{Learn You Some Algebras for Glorious Good!}
\begin{document}
\maketitle

\newpage
\topskip0pt
\vspace*{\fill}

{\footnotesize
 \begin{center}
   Copyright © 2014-2015 \pharpend
 \end{center}
% \noindent
 \begin{center}
   Permission is granted to copy, distribute and/or modify this document under
   the terms of the GNU Free Documentation License, Version 1.3 or any later
   version published by the Free Software Foundation; with no Invariant
   Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the
   license is included in \cref{gfdl}.
 \end{center}
}
\vspace*{\fill}
% \newpage
% \section*{Editors \& Noted Contributors}
% \begin{addmargin}[4em]{2em}
%   \begin{tabular}{l l}
%     \editors
%   \end{tabular}
% \end{addmargin}

\newpage
\tableofcontents
\newpage


\input{1-introduction.ltx}
\input{2-boolean-algebra.ltx}
\input{3-sets-functions.ltx}
\input{4-proofs.ltx}

\begin{appendices}

{\footnotesize
 \setlength{\parskip}{0ex}
 \setlength{\parindent}{0ex}
 \input{fdl.ltx}
}
\input{how-to-learn.ltx}
\end{appendices}

\newpage
\printbibliography
\end{document}

The build script basically copies all of the relevant files into a temporary directory, then compiles the root node with pdflatex, copies the pdf out of the sandbox, and then deletes the sandbox. I want to compile the book into an EPub instead of a PDF. I performed the sandbox-copying steps manually, then used the following command to attempt to generate the epub:

pandoc lysa.ltx -f latex -t epub -o lysa.epub

The EPub only has the first two pages. No TOC or content. The epub can be downloaded here:

http://harpending.org/lysa.epub

By contrast, the correct PDF file is 70-something pages long, and can be seen here:

http://harpending.org/lysa.pdf

Am I missing something here. It seems like Pandoc is completely ignoring the \input commands (and hence no TOC).

---

Reply to this email directly or view it on GitHub:
#1882

[pharpend]

@jgm 1.13.2 , which is the latest version in Hackage.

[jgm]

What about my other question? Are the files to be included
in the working directory from which you run pandoc? Pandoc
will look for them there; it is not smart enough to check
all the paths tex would check.

+++ Peter Harpending [Jan 16 15 20:51 ]:

@jgm 1.13.2 , which is the latest version in Hackage.

---

Reply to this email directly or view it on GitHub:
#1882 (comment)

[pharpend]

Oh sorry, I didn't see that. Yes, they are.

[pharpend]

This also happens when I try to convert to ODT:

[pharpend]

While we are at it, the hierarchy of the temporary directory is as shown:

.:
total 96
-rw-r--r-- 1 pete  9177 Jan 22 21:28 1-introduction.ltx
drwxr-xr-x 2 pete  4096 Jan 22 21:28 2/
-rw-r--r-- 1 pete  3037 Jan 22 21:28 2-boolean-algebra.ltx
drwxr-xr-x 2 pete  4096 Jan 22 21:28 3/
-rw-r--r-- 1 pete  2052 Jan 22 21:28 3-sets-functions.ltx
-rw-r--r-- 1 pete  5936 Jan 22 21:28 4-proofs.ltx
-rw-r--r-- 1 pete 25880 Jan 22 21:28 fdl.ltx
-rw-r--r-- 1 pete  2691 Jan 22 21:28 how-to-learn.ltx
-rw-r--r-- 1 pete  2842 Jan 22 21:28 lysa.bib
-rw-r--r-- 1 pete  9001 Jan 22 21:28 lysa.ltx
-rw-r--r-- 1 pete 10690 Jan 22 21:28 lysa.odt

./2:
total 20
-rw-r--r-- 1 pete 9507 Jan 22 21:28 1-basic-logic.ltx
-rw-r--r-- 1 pete 3372 Jan 22 21:28 2-more-logic.ltx
-rw-r--r-- 1 pete 2565 Jan 22 21:28 3-idris.ltx

./3:
total 52
-rw-r--r-- 1 pete  8847 Jan 22 21:28 1-elements-subsets.ltx
-rw-r--r-- 1 pete 19091 Jan 22 21:28 2-operators-functions.ltx
-rw-r--r-- 1 pete  2057 Jan 22 21:28 3-unions-intersections.ltx
-rw-r--r-- 1 pete     0 Jan 22 21:28 4-natural-numbers.ltx
-rw-r--r-- 1 pete 15975 Jan 22 21:28 garbage.ltx

[pharpend]

Here's what happens when I try to convert it to markdown:

Copyright © 2014-2015 <span><span>Peter Harpending <span>[\<](mailto:[email protected])<span>[email protected]</span>\></span>
</span></span>

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in [gfdl].

I haven't exhaustively tried every output format. That said, I think it's safe to say that this is a problem with the LaTeX reader, and not with any particular output format.

[jgm]

Turns out the code that handles includes in LaTeX only works if the included file has a .sty or .tex extension. This is dumb, and I'll try to make it more flexible. But an easy workaround for you would be to rename your .ltx files .tex..

[pharpend]

Ah, alright. .ltx and .tex mean slightly different things in Emacs, and, for this project, I want the .ltx thing. Good to know it's fixed.