You have to explicitly tell Devel::Cover what files to cover. See the docs for specifics, but something along the lines of (note it sets the output to go into /tmp/covertest/): 
/usr/bin/perl -MDevel::Cover=-db,/tmp/covertest,-silent,0,-ignore,.,-s
+elect,/home/you/your_pm index.cgi

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In reply to Re^3: Finding bottlenecks in the code by davidrw
in thread Finding bottlenecks in the code by punkish

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