Darfoune:

While a heredoc is fixed length (barring variable substitution), you can still do multiple writes to the file. So the heredoc could have the basic header for your script. Then as the user selects other modules, you can continue to add them to the script.

open my $FH, '>', 'afile.pl';
print $FH <<EOHDR;
Some header stuff
EOHDR

while (<>) {
    if (/^RPT/) { print $FH, "another line of your script" }
    elsif (/^FOO/) { print $FH, "something completely different" }
    elsif (/^Q/) { last; }
}
[download]

Alternatively, you can use a heredoc to load a variable, then continue to add data to the variable:

my $SCRIPT = <<EOHDR
Some header stuff
EOHDR;

$SCRIPT .= "More script stuff";
[download]

...roboticus

When your only tool is a hammer, all problems look like your thumb.