Oh, okay. Well, if you are doing a require to get the configuration in there, I'd suggest putting everything in the configuration file into a subroutine, then call it when you've done all the necessary set up.

For example, your config file may look like this:

# config file
sub initConfig {
    $foo = "$user - bar";
    # ... whatever...
}
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Where your program file may look like this:

# program
require 'configuration_file';
print "Username:";
chomp($user = <STDIN>);
# now $user exists, although you'd wanna check it for validity
&initConfig();
# ... continue processing...
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Does that solve your problem? I've done it this way in the past, and it has worked out well.
Hope that helps!