Clarify types for molecule.util:merge_types

[Qalthos]

• Type merge_dicts with a bound TypeVar so that it is clearer about what it accepts and that it returns the same thing it takes in.
• write_file was missed in the Path update. This updates the method to accept Paths and simplifies the method by using Path internally.
  • This got included in Add type hints for state.py #4294

NestedDict can probably take the place of any nonspecific dict[str, Any] we have, though it might also be overly specific.