Applying patch files get added to the index by default #104

We can see that the indexes are being updated when we apply the patch when we commit the changes in the DirCache class. The file gets added to the diff when we move it over when its renamed (inside the tmp.commit call). I'm uncertain how we handle ignored files in other cases but it must be done much earlier because I didn't see any validation around if the file should or shouldn't be added to the commit

public boolean commit() {
  final LockFile tmp = myLock;
  requireLocked(tmp);
  myLock = null;
  if (!tmp.commit()) {
	  return false;
  }
  snapshot = tmp.getCommitSnapshot();
  if (indexChangedListener != null
		  && !Arrays.equals(readIndexChecksum, writeIndexChecksum)) {
	  indexChangedListener.onIndexChanged(new IndexChangedEvent(true));
  }
  return true;
}