Pass directories explicitly in example workflow

[ElliottKasoar]

Resolves #6

[ElliottKasoar]

A few further changes:

• Pass the QE directory explicitly to write_n2p2_data_qe, since it's already passed in prepare_qe, which may result in inconsistencies if only one were changed
• Pass n2p2 directory to CP2K and QE notebooks, as this is the most likely directory to vary in name
• Pass the LAMMPS and active learning directories in the workflow, reducing current hardcoding of directory names/potential for inconsistencies