As long as the index *somehow* knows about these new files, they are
removed.
The situation is:
(0) you start from a HEAD that does not have path xyzzy;
(1) you attempt to merge a rev that has path xyzzy;
(2) the merge conflicts, leaving higher staged index entries for the
path.
(3) you decide not to conclude the merge by saying "reset --hard".
The old logic for "reset" was to remove paths that exist in the index at
stage #0 (i.e. cleanly merged) and not in HEAD. The patch changes the
rule to remove paths that exist in the index at any stage (i.e. including
the ones that have conflicted and not resolved yet) and not in HEAD.
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