Pipeline: major changes to Features Sheet and Paths File

[AlexTate]

Edit 10/15: this issue is too large. I've created a separate issue to address the repurposing of tagged counting.
Edit 10/27: this issue is still too large. I've created a separate issue for the new Source/Type Filter approach.

Feature Sources and Per-GFF Preferences
The Feature Source and Alias by... columns will be moved from the Features Sheet to the Paths Sheet. This is because the other columns define selection rules that pertain to all GFF files, not just the GFF file they share a row with, whereas the Alias by... column applies only to its corresponding GFF file. The Paths Sheet is a more appropriate place for these since other file inputs are defined there. This move toward consistency should help alleviate some confusion and open up the Features Sheet for other selectors.

[AlexTate]

Update 10/15: this issue was too large. I've created a separate issue to address the repurposing of tagged counting.