Convert to Path insted of raw strings

Adding type hinting has revealed that some classes are accepting raw strings for filenames and locations. This is fine, but combined with starting to use Path instead, it is revealing some untidyness. Best to go through and 1) update to use Path explicitly and 2) incorporate type hinting when not already done in relevant functions.

Start by locating classes and relevant functions that accept raw strings for filenames or locations, then review existing Path usage and type hints. Done means those locations use Path explicitly and the relevant functions have appropriate type hints.

Written by the indexing model from the issue text.