Add pathlib.Path to CutomEncoder

See merge request !4

This comes up if the project repo is cloned with git. Then the output repo is missing. Now, during the first instantiation of a ProjectRepo class, the missing output repo is cloned

Change directory when running study

See merge request !3

Replace benedict with addict
replace Options.hash with Options.get_hash()

Fix reading empty status files
Catch KeyboardInterrupts in batch_runner

fixup! Refactoring and code cleanup