Describe flow of things to do with examples... switches to be defined in the mathematica file and default analysis
\subsection{Input Mathematica file \& User analysis}
\section{Description and usage of the internal modules}
\subsection{Automatic modules}
...describe how to turn on and off modules which are automatic.
\subsubsection{Local stability}
\subsubsection{Tree-level unitarity}
\subsubsection{Block diagonal detection}
\subsection{User defined extensions}
...describe functions that need to be defined and their aim
\subsubsection{VEV space user user defined constrains}
\subsubsection{Mixing matrix user defined constrains}
\subsubsection{Coupling/Mass user defined constrains}
\subsubsection{RGE running module}
\section{Using external interfaces}
\subsection{SuperIso}
\subsection{HiggsBounds/Signals}
\subsection{SuShi}
\subsection{Micromegas}
\subsection{Examples}
\section{Using the source as a library}
\subsection{Basic classes and their usage}
\subsection{Examples}
\section{Summary}
\section*{Acknowledgements}
We would like to thank Augusto Barroso, Pedro Ferreira and Jo\~ao P. Silva for
comments and suggestions.
The work of R.C., M.S. and R.S. is supported in part by the Portuguese
\textit{Funda\c{c}\~{a}o para a Ci\^{e}ncia e a Tecnologia} (FCT)
under contract PTDC/FIS/117951/2010 and by FP7 Reintegration Grant, number PERG08-GA-2010-277025. R.S. is also partially supported by PEst-OE/FIS/UI0618/2011.
R.C. is funded by FCT through the grant SFRH/BPD/45198/2008.
M.S. is funded by FCT through the grant SFRH/BPD/ 69971/2010.