Improved general usage and added CMake integration

[Pseudomanifold]

Dear authors,

I improved the general usage of the runMLG application by implementing proper loading and processing for arbitrary data sets. Moreover, I added generic CMake integration such that building the tool should now be easier.

Hope you like this pull request; let me know if I can improve it in any way. Thank you very much for providing your code in the first place, I really appreciate it!