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Description
Each .cov file has its own filters - whitelists, blacklists, etc. When performing a phpcov merge operation, these filters are ignored, and a default filter is used.
In particular, this results in any processUncoveredFilesFromWhitelist setting being ignored. The filenames are all in the .cov's filter whitelist, but the merge operation ignores them.
Possibly there could be filter options made available to the command line, which would allow filtering the complete set, or perhaps the filter within the file being merged could be used to check against, instead of the default (see PHP_CodeCoverage::merge line which reads:
if (!$this->filter->isFiltered($file)) {
--could potentially check $that->filter()->isFiltered($file) in this instance instead?)
Or some kind of pre-merge on the filters could happen.
I wouldn't be adverse to implementing something if a preferred design was decided upon.