Just noticed the existence of Pathlib, which seems nice, and worth switching to. Also need to improve some file management stuff so we can make a slightly more integrated PR out of this.

• Use Pathlib for directory management
  • Now that I'm using this more, it creates a nice point where we can separate out all the paths from the monolithic DictConfig and start passing them around individually to subroutines. So I am now endeavouring to do a bigger push with this.
• Save data from analyses so they may be plotted outside of a simulation
• Fix some bugs/refine directory structure