\documentclass[letterpaper]{book}
\usepackage{makeidx}
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\makeindex
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\begin{document}
\begin{titlepage}
\vspace*{7cm}
\begin{center}
{\Large Reference Manual}\\
\vspace*{1cm}
{\large Generated by Doxygen 1.4.4}\\
\vspace*{0.5cm}
{\small Thu Jun 12 02:27:18 2008}\\
\end{center}
\end{titlepage}
\clearemptydoublepage
\pagenumbering{roman}
\tableofcontents
\clearemptydoublepage
\pagenumbering{arabic}
\chapter{CMX Generated Documentation }
\label{index}\hypertarget{index}{}\input{index}
\chapter{Directory Hierarchy}
\input{dirs}
\chapter{Data Structure Index}
\input{annotated}
\chapter{File Index}
\input{files}
\chapter{Directory Documentation}
\input{dir_000002}
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\include{dir_000003}
\include{dir_000008}
\include{dir_000005}
\include{dir_000004}
\include{dir_000007}
\include{dir_000006}
\chapter{Data Structure Documentation}
\input{union__QGFC__RSD__V0__stageEnergy}
\include{struct__QGFC__RSD__V0__stageEnergy__bf}
\include{union__QGFC__RSD__V1__stageEnergy}
\include{struct__QGFC__RSD__V1__stageEnergy__bf}
\include{union__QGFC__RSD__V2__stageEnergy}
\include{struct__QGFC__RSD__V2__stageEnergy__bf}
\chapter{File Documentation}
\input{QDFC__rsd__check_8c}
\include{QDFC__rsd__v0_8h}
\include{QGFC__rsd__check_8c}
\include{QGFC__rsd__v0_8h}
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\include{QGFC__rsd__v2_8h}
\include{QHFC__rsd__check_8c}
\include{QHFC__rsd__v0_8h}
\include{QMFC__rsd__check_8c}
\include{QMFC__rsd__v0_8h}
\printindex
\end{document}