There are two CheckoutConflictException classes:

org.eclipse.jgit.errors.CheckoutConflictException which is used internally in jgit and by all user's not using the API in org.eclipse.jgit.api.

org.eclipse.jgit.api.errors.CheckoutConflictException which should be the only checkout exception thrown by the API in org.eclipse.jgit.api.

Since you are using the API you should ideally use the exception in org.eclipse.jgit.api. A good example how it should look like is in MergeOperation.java (line 120). But there seems to be a bug in MergeCommand.java that it throws org.eclipse.jgit.errors.CheckoutConflictException instead of org.eclipse.jgit.api.errors.CheckoutConflictException. Maybe we have to solve this first. The change http://egit.eclipse.org/r/#change,4178 is addressing this ... but not yet accepted. I'll try to trigger that this change solves the problem.