git merge “deleted by us”

Here is a partial solution:

1. Resolve all non deleted merge conflicts by hand, which you have to do anyway

2. Type git diff --name-only --diff-filter=U to get a list of all remaining files in conflict. These files must be the ones you want deleted. Save the list of removed files as filesToRemove.txt

3. Then do cat filesToRemove.txt | xargs git rm to remove all the files.