I understand your problem, but the current version don't have an option that could work with multiple forlders.
I can develop a option to select a folder instead of files, but it will take some time.
For now, there is only a workaround I can think about.
1. Name each sprite with a sequencial number.
- Animation 1: 0001.png 0002.png 0003.png
- Animation 2: 0004.png 0005.png 0006.png
- Etc
After that, interpolate all in the same folder.
After the interpolation, get all the output frames and separate them in folder again.
I put in my TODO list to select folders, but it will take a while.