when using Devel::Cover, difference between ./Build test and cover -t

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I'm looking to determine coverage of some unit tests. The project requires a second directory (basically from a GitHub repository) and when running everything, I usually add the 2nd lib directory with

use lib "/path/to/second/dir/lib";

and currently I have this in the Build.PL file (I'm using Module::Build). Running ./Build test gives a nice summary of all of the test (about 10 files-worth), however, running cover -test gives me errors, specifically, a

Can't use an undefined value as a symbol reference at XXX

which is a file in that second directory.

Is this because it appears that the Module::Build tends to copy files to the blib directory? If so, does it use the files there? What are the other differences between running cover -test and ./Build test?

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