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I was attempting to merge coverage reports on a different machine than what generated them, and I was ending up with empty reports. It looks like the filter does a file_exists() check on each file, which was failing for me.
Is there some reason we have to validate the file exists, instead of just assuming the file names are valid? If so, it would be good if here or in the phpcov CLI tool the 'merge' command documented this caveat.