Reproduce:

1. Start with a branch that has 1 or more untracked files.
2. Merge another branch, like master, into branch, such that conflicts will arise (should NOT be changes that track above file(s)).
3. Merge Conflict dialog pops up.
4. Resolve merge conflicts in editor (do not remove untracked files).
5. Press "Commit Merge" button.
6. See error: "Could not generate a patch for file foo/bar, patch empty".
7. Now you are stuck.

Work arounds:

1. Move (temporarily) the untracked file(s).
2. Run git add foo/bar outside of the app.

Neither are particularly pleasing options.

Preferred Solutions:

1. Quietly skip untracked files for the merge, unless, of course, the merge adds them. Committing anything that didn't come from the merge makes no sense from the merge's perspective. (Preferred)
2. Do (1) and offer options to add or skip untracked. (Ok, but messier merge)
3. Allow me to exit the dialog and commit when I'm ready, which is sort of how it was before the Merge Conflict dialog was added. (Ok, less messy than (2), but not great)
4. Warn me that the merge cannot be started with untracked files present, which is hardly better than doing nothing. (Meh, I'll just end up do work around 1 anyway)