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CommitController: don't mutate array we enumerate when refreshing index
There was a nasty bug in handling the finishing of the index change.
This code path was changed when I simplified the file tracking, but
as a result the code now mutated the files array, over which
we were also enumerating. This can cause all sorts of bad stuff, like
files that aren't really deleted from the view, to wrong files that
are deleted, to a crash of the system for wrong memory access.
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