Improve how filepaths are handled, especially for resources

[johnjasa]

HOPP currently assumes that filepaths provided for resources are either relative to the HOPP package or absolute.
This causes issues when inputting filepaths through GreenHEART.
We should develop a robust and general way of handling filepaths for all files, not just resources.

I propose we check in this order:

1. relative to the config file
2. absolute path