cleanup

[rvosa]

• use shorter file names
• do not use spaces in file names
• provide a README.md file in every directory describing the directory contents
• do not commit OS-specific helper files such as Thumbs.db
• use descriptive commit messages, not "Commit message"
• do not dump everything in one folder. For example, script is for scripts only
• make the ipynb files viewable, i.e. not too big
• use comma- (or tab-) separated files instead of Excel spreadsheets

[rvosa]

There are still spaces in the *.py files because I wasn't sure if the notebooks depend on them, but these names also should be fixed.