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c1e52fc807
Our logic to decide if a file needs to be checked out from the previous commit or deleted because it didn't exist in the previous commit didn't work for submodules. We were using `git cat-file -e` to ask whether the file existed, but this returns an error for submodules, so we were always deleting those instead of reverting them back to their previous state. Switch to using `git ls-tree -- file` instead, which works for both files and submodules.