Expected Behavior
coverage/ folder being excluded even when not present from the exclude list.
Observed Behavior

See comment made at #502 (comment).
Bonus Points! Code (or Repository) that Reproduces Issue
Look at https://github.com/thelounge/lounge/blob/master/.nycrc (that gets run with npm run coverage). We removed coverage/ from the exclude list of The Lounge here but I have just noticed that it is not ignored anymore.
Forensic Information
Operating System: macOS 10.11.6
Environment Information: Result of sh -c 'node --version; npm --version; npm ls'