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Fix blessing of new reference files
Adding of new reference files wasn't handled correctly. It was trying to read a file that didn't exist yet. Instead of unwrapping, we now treat a missing reference file as empty (`Vec::new`). This makes the following conditional work. We then also have to re-read the reference file after it was being copied. This second read is technically the same as in the old shell script, but wasn't really obvious. The shell script did a `-s` test which reads the file.
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