Exclude deleted files in tooling/bin/find_changes

What does this MR do and why?

We actually used to exclude deleted files with !78045 (merged).

But it was changed, probably inadvertently with !96485 (merged).

This started to be a problem after !107996 (merged) was merged (e.g. https://gitlab.com/gitlab-org/gitlab/-/jobs/3591875306 for !107989 (merged)).

MR acceptance checklist

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• I have evaluated the MR acceptance checklist for this MR.