I am not aware of of any modules to automate user configuration files that can be over-ridden on the command line. (I would be interested to know of any). A few years ago I wrote some code to do it myself, which I am pasting here.

The basic code to read command a config file, and allow that config to be overridden from the command line uses Getopt::Long, with a bit of extra code to first read the config from a file, and then allow the config hash to be over-ridden on the command line:

sub getArgs
{
    # 1. Declare internal defaults to use for any atributes not on the
+ command line or in the user's preferences.
    # Format is: name (hash key), default value, comment (for the stor
+ed config file).
    my $user_prefs_file = $HOME.'/.application_name.prefs';
    my @system_defaults =
    (
        [ 'verbose',             1, "The Verbosenes. The script should
+ be silent if verbose=0" ],
        [ 'parse_schedule_file', 1, "If true, parse the schedule file"
+ ],
        # ... etc.
    );

    # Setup the raw options from the system defaults.
    my $raw_opts;
    my $user_prefs = readDataFile( $user_prefs_file );    # Load user 
+preferences, & over write defaults.

    foreach my $ent ( @$system_defaults )
    {
        my($key, $value, $comment) = @$ent;        # The comment is no
+t used at this stage.
        
        if( defined $user_prefs->{$key} )
        {
            $raw_opts->{$key} = $user_prefs->{$key};
        }
        else
        {
            $raw_opts->{$key} = $value;
        }
    }

    # 3. Parse the command line, overiting options from the user prefs
+ & internal defaults.
    my $store_prefs;
    $raw_opts->{'store_prefs'} = \$store_prefs;
    $raw_opts->{'help'}        = sub{ pod2usage(-verbose=>0) };
    $raw_opts->{'man'}         = sub{ pod2usage(-verbose=>2, -exitstat
+us => 0 ) };

    # Use the store in hash form op GetOptions, with references to exc
+eptions setup above.
    GetOptions( $raw_opts,
        'help|h','man','verbose!','store_prefs','flush_cache', 'parse_
+schedule_file!',
        # ... etc.
    ) or pod2usage(-verbose=>0,  -message => "incorect options");

    # Store the updated user preferences if required.
    if( $store_prefs )
    {
        store_user_prefs( $raw_opts, $user_prefs_file, $system_default
+s );
    }

    # Delete special references
    delete $raw_opts->{'store_prefs'};
    delete $raw_opts->{'help'};
    delete $raw_opts->{'man'};

    # All done, return
    return $raw_opts;
}

sub readDataFile
{
    # Reads a perl data structure from a file.
    my( $fileName ) = @_;
    return undef unless -r $fileName;   # Quick check the file exits.

    open INFILE, "<", $fileName or die "Error, unable to read $fileNam
+e $!";
    my $fileText = join('', <INFILE> );
    close INFILE;

    return eval( $fileText );
}
[download]

In my case, I also needed to allow users to save their prefereces back to the configuration file, so there is an extra bit of code to save preferences in a human readable file format with comments on each field:

sub store_user_prefs
{
    my ( $raw_opts,             # Options hash, amalgamanted from syst
+em defaults, prevously stored preferences, and the command line.
         $user_prefs_file,      # File to store the option in.
         $system_defaults,      # System defaults. Used to provide an 
+ordered list of options to store with comments to store against them.
    ) = @_;

    open OPTS, '>', $user_prefs_file or die "Error saving preferences 
+in $user_prefs_file, $!";

    print OPTS "#!/bin/perl\n";
    print OPTS "#\n";
    print OPTS "# user preferences file. Edit with care.\n";
    print OPTS "\n{\n";

    foreach my $ent ( @$system_defaults )
    {
        my($key, $value, $comment) = @$ent;

        print OPTS "    # $comment\n";

        if( 'ARRAY' eq ref $raw_opts->{$key} )
        {
            my $list = '\''.join('\', \'', @{$raw_opts->{$key}} ).'\''
+;
            printf OPTS "    '%s' => [%s],\n\n", $key, $list;
        }
        elsif( 'HASH' eq ref $raw_opts->{$key} )
        {
            printf OPTS "    '%s' => {\n", $key;
            printf OPTS "        '%s' => '%s',\n", $_, $raw_opts->{$ke
+y}{$_} foreach keys %{$raw_opts->{$key}};
            print  OPTS "    },\n\n";
        }
        elsif( ref $raw_opts->{$key} )
        {
            # Something else, probably the cookie jar. Use data dumper
+.
            my $dumpedInfo  = Dumper( $raw_opts->{$key} );
            $dumpedInfo =~ s/\$VAR1 = //;
            $dumpedInfo =~ s/;$/,/;
            printf OPTS "    '%s' => %s\n", $key, $dumpedInfo,
        }
        else
        {
            # plain string, number etc.
            if( defined $raw_opts->{$key} )
            {
                printf OPTS "    '%s' => '%s',\n\n", $key, $raw_opts->
+{$key};
            }
            else
            {
                printf OPTS "    '%s' => undef,\n\n", $key;
            }
        }
    }
    print OPTS "};\n\n";

    close OPTS;

    return;
}
[download]

In the code above I have stripped out some of the error checking for compactness. I hope it is clear and useful to you.