The workflow I would have imagined for versioning data is:
1) Load original data from source into quilt
2) Do transformation
3) Commit transformations to quilt, with commit message
4) Run experiment
5) Do new transformations
6) Commit to quilt
7) Run experiment
Rinse and repeat.
Looking at the video and documentations, this is not emphasised at all, suggesting that edits to data should be saved as a new package.