Code reorganization

[ondrejkrejci]

• All the other running scripts from the examples (and root) and have only PPSTM_simple.py to run those. The only exception should be IETS, which is not used, but should be available for future development if needed.

• running scripts (GUI.py,PPSTM_simple.py,SUM_Orb_Contrib.py,PPdos_simple.py and IEST_test_FePc.py )should be put into a new directory cli

• optionally API for a database creation could be added there.

Should be done after [ ] #33