Supposed, we got the YAGNI case, and all you need is

• all config vars can be set in the config file and the command line
• the command line will have the highest priority
• the user can set the config file location at the command line

In that case, you could do it like this:

use Getopt::Std;
my %opts;

getopts( 'dhc:', \%opts );      # usw, -c for cfg-file
$opts{'c'} and $opts{'c'} !~ m{^/([\w\.]+/)*[\w\.]+$} and &usage;

my $cfg = $opts{'c'} ? $opts{'c'} : '/default/path/to.conf';

open CFG, '<'.$cfg or die;
while(<CFG>) {
   # do sth like ...
   /^\s*(.*?)\s*: (.*)$/;  
   $cfg{ $1 } = $2;
}
foreach (keys %cfg) {
   $opts{$_} and $cfg{$_} = $opts{$_};
}
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You can do this "overriding" as many times you like, using a list of config file locations. The script would eat one file after another, starting with the "weakest", most global one, and finishing with the command line options.

The overriding process could be done in the manner indicated in the code above.