Handles patch-reversed-included-from-destination files specially in the merge algorithm. Since these files have already been patched successfully or resolved by the user, they never constitute a conflict in the merge phase. Essentially the conflict has already been resolved.
Adds the temp dir containing patch-reversed files as a source directory for the include action. This is necessary for the "include" action to see the patch-reversed file instead of the unpatched file.
Add a bunch of tests for upgrading with patch reversal.
This builds on #547.
This PR does a few things: