# Use the appropriate syntax for your module:
my $root    = ...
my $code    = ...
my $include = ...
my $lib     = ...

foreach ($code, $include, $lib) {
   s/%ROOT%/$root/gi;
   
   # -or-
   #
   # $code =~ s/%([A-Z][A-Z_]*)%/
   #    if ($1 eq 'ROOT') {
   #       $root
   #    } elsif (exists($ENV{$1})) {
   #       $ENV{$1}
   #    } else {
   #       $1
   #    }
   # /eg
}