The comsol directory should be empty because it contains big comsol file stored in locale. (pick the FWM_template.empty.mph and change its parameters. Run with comsol and then save it in the comsol/ folder)
To run matlab files you should be in the files' folder. For example to run the extractor one should be in the comsol-extractor/ folder, to run the phase matching file should be in the phase-matching/ folder
In data/ are stored data files estracted from .mph files
There are stored .tex files for the thesis.