The most likely cause of the prototype mismatch errors is that require happens at run-time, which is long after prototypes checks are applied. You need to force the require to happen at compile time by putting it in a BEGIN block:

BEGIN { require 'commons.pl' }

For the uses in commons.pl to work properly, you should make sure that they are executed with package main:

# in commons.pl...
package main;
use DBI;  
use Date::Calc qw( Decode_Date_US Add_Delta_Days);
use File::Copy;
# etc.
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Unfortunately, you can't use lexical variables at all this way since they are file scoped, not package scoped. You'll have to use package variables instead, and predeclare them in main.cgi:

# in main.cgi...
our $q, $variables;
# or, for < 5.6:
#use vars qw/$q $variables/;

BEGIN { require 'commons.pl' }
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# in commons.pl, _AFTER_ package main LINE!
our $q = new CGI;
our $variables; # etc.
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Hope that helps. :-)

bbfu
Seasons don't fear The Reaper.
Nor do the wind, the sun, and the rain.
We can be like they are.