Clean-up and consistency check

[viatkin]

Hi everyone!
I did a bit of cleanup of the project folders, including model folders.
Details are in this commit message: 6877f2e
Please pull the changes before continuing to work on your models.
I moved some of the files into "deprecated" folder in each model. If you need some old files you may find them there.
Please check if your codes, e.g. inspectModel.py are working. In case of any issues, please let me or Markus know.
Cheers!
Kostia