Improve or clarify what's supported for custom annotation

[Nick-Eagles]

Our documentation doesn't currently describe the expectations for the internal structure of custom annotation files necessary for SPEAQeasy to run without errors. For example, the GTF is currently assumed to contain specific column names representing specific things. If we can find a way to be more flexible with what annotation file structures are acceptable, that would be ideal, but otherwise we should at least document the expected structure.