Adds support for function definitions with ...'s in them.
Fixes the terrible tabbing situation that was in preprocess.pl.
Adds documentation to the main doxygen page, describing how to make doxygen, some useful commands, and adds a few links.
update submodules
Merge pull request #90 from andybarry/doxygen

Doxygen updates
Implement the MATLAB version of FootStepConstraint, will work on C++ implementation
Rename 'FootStepConstraint' to 'FootStepRegionConstraint'