fix: Correctly record missing stages in index for merge conflicts #1907
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Fixes #1833.
I didn't add a test, because it would just be asserting that the Git commands do what they are supposed to, but feel free to ask for a test anyway.
I'm also not sure about the logic when a file did not exist in the previous template version, or was deleted in the latest template version: here I just skip the corresponding stage (2 when created, 3 when deleted) in the index, but maybe the whole index update (all 3 stages) could be skipped for such cases, not sure.
I rewrote the explanation comment above, reusing the wording in the SO answer, as I think it's much more readable than the previous comment.