Forced region splitting about pprepair HOT 1 CLOSED

It's possible, but I think you more need a GIS than pprepair to be honest.

In the branch 'new' there's a better version to handle input/output files. What you're looking for is the option PL, for priority list. You'd repair as such

pprepair -i A.shp -i B.shp -r PL --priority prio.txt

and have in the same folder a file prio.txt which contains 3 lines:

datasets
A
B

this gives the priority to use when there are overlapping polygons.

from pprepair.