I'm upgrading from 2012a to 2013a. Assuming matlab doesn't change much then these should apply in the future. Just replace 2012a and 2013a appropriately.
cp ~/.matlab/R2012a/* ~/.matlab/R2013a/
/Applications/MATLAB_R2012a.app/toolbox/local/pathdef.m
and copy custom lines into /Applications/MATLAB_R2013a.app/toolbox/local/pathdef.m
cp /Applications/MATLAB_R2012a.app/bin/mexopts.sh /Applications/MATLAB_R2013a.app/bin/mexopts.sh
add_igl_tab_completion
Note: May have to change that path to the most recent mosek toolbox. For example, /usr/local/mosek/7/toolbox/2013a/
.