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For this reason, projects under version control tend to be stored within a single directory to correspond with a single Git repository.  For strategies on how to best organize your own projects, see Noble, 2009 \cite{19649301}.  \textbf{Figure \ref{fig:Fig1}. The git add/commit process.}  To store a snapshot of changes in your repository, first \verb|git add| any files to the staging area you wish to commit (for example, you've updated the \verb|process.sh| file).  Second, type \verb|git commit| with a message. Only files added to the staging area will be committed.  All past commits are located in the hidden \verb|.git| directory in your repository.  \begin{verbatim}  $ cd ~/thesis  $ ls