fix missing import: `read_nb`; check output dir

[maschlr]

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Running the functions provided by tools/clean.py gave me an error. This is probably due to an update in any of the globally imported libraries? Next error was the missing clean directory (it's still referenced in the README)

N.b. I don't know if that's supposed to be a little riddle for student to sharpen their problem-solving skills in the real word :)

Thx for creating the awesome course! I'm a big fan of the work.