Upgrade Conflicts - Questions For Cs-Cart Development

So I upgraded my development area from 4.3.1 to 4.3.2 (this is a straight demo store with only addon changes, not core file changes). The upgrade said there were a whole bunch of “local modifications” to files. However, none of these files has every been touched.

Couple of questions:

  1. Why is upgrade identifying files as modified when in fact they haven't been
  2. In older versions, conflicts were stored and we could 'diff' the files to see what's changed in the newest release so that any real custom modifications could be identified and then re-applied. How is this done now? Now I check a box saying I agree my changes will be totally lost. So how is someone supposed to identify those changes and then take appropriate action? Is there no longer a useful tool as part of the upgrade that allows me to review what's changed and what's different between the two releases on a file by file basis?

    Seems the upgrade process (while prettier) is taking big steps backward in functionality and useability.

    Hopfully I'm just missing something obvious.