mex does have a function form as well as command form, but for some reason this doesn't appear to be documented in the help so I have also had difficulties understanding how to convert command form into function form for doing something like this. I assume it is possible.
e.g. without flags you can just do:
mex( 'myfile.cpp' )
so I assume you can pass some kind of property, value pairs to this too which would allow a dynamic string.
mex( 'myfile.cpp', '-g' )
works, for example, so maybe you can do the same for -I and pass your folder name as the following argument.
I don't really have a test case handy to try out myself.
