Patch Set 3:

"wrapping org.eclipse.jgit.errors.CheckoutConflictException inside a org.eclipse.jgit.api.errors.CheckoutConflictException" is something that already exists or is it a solution to be implemented? I don't see such relation in the current code. 

The idea behind my latest patch was to remove one of the exceptions with as little changes as possible but I agree that leaving the one from the *.api.errors package makes more sense.