Patch Set 3: I would prefer that you didn't submit this

Why don't we fix it that these commands do really throw 
org.eclipse.jgit.api.errors.CheckoutConflictException 

The intention behind wrapping org.eclipse.jgit.errors.CheckoutConflictException inside a org.eclipse.jgit.api.errors.CheckoutConflictException was that "all" JGit API commands only throw GitAPIException and RuntimeExceptions. If you start using jgit api you can always start  with

try {
  mergeCmd.include(...).call()
} catch (GitAPIException e) {
  System.out.println("git problem: "+e.toString();
....
}

As a beginner who doesn't know how to react on all the different low-level JGit exceptions you should not be forced to catch dozens of exceptions just to do a "git log". Therefore we collect all possible exceptions in wrappers extending GitAPIException allowing you to write 
code catching only one exception type.

And then, if you get more experienced with Git exceptions, you still have the chance to catch the specific subclasses of GitAPIException exceptions.