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Refactor code to make it interfacable

Stef Smeets requested to merge stefsmeets/predicrystal:instamatic into master

Some more updates to clean the code a bit:

  • Restructure the project directory
  • Refactor code to separate functions so they can be called from outside
  • Tune the command line interface to make it more consistent
  • Remove some redundant lines from 'settings.yaml'
  • Streamline output to stdout

For the rest, I tried to keep everything as much as it was, so that it works in the same way.

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