#! /usr/bin/perl
use strict;
use warnings;

# use Getopt::Long;
# use CGI;

my %foo;

while ( my $line = <DATA> ) {

    if ( my ( $var, $wert ) = $line =~  m{set\s+([^=]+)=(.+)$} ) {

        if ( $wert =~ m/%/ ) {
            $wert =~ s/%([^%]+)%/$foo{$1}/g;
        }

        $foo{$var} = $wert;
    }
}

use Data::Dumper;
print Data::Dumper->new( [ \%foo ], [ '*foo' ])->Sortkeys(1)->Dump;


__DATA__
set Variable1=c:/ursprungspfad/site1
set Variable2=%Variable1%/info
set Variable3=verzeichnis
set Variable4=%Variable1%/%Variable3