If one image is used as an input more than once, each run will overwrite the marked area
Fixed by keeping the leftovers in memory the whole run, then writting them to disk after the rest of processing is done.
Clipping marks the whole area, instead only of the clipped part
Fixed by using the box used for clipping for marking leftovers as well.
This is actually two separate issues:
Before:
After:
Fixes #9.