To make this easier to extend with similarity based matching code, I would just do:

  added = tempAdded

Here, and then above in getEntries() just before you set done, I would do something like:

  entries.addAll(added);
  entries.addAll(deleted);
  added = null;
  deleted = null;
  done = true;
  Collections.sort(entries, ...);

Then we can just plug in the similarity pass by invoking a new similarity pass method after the findExactRenames() method is run.