$/ = undef;
open DOC, "manual2.tex";
$doc = <DOC>;

#$doc =~ s/(http\:\/\/\S+?)([\.\)]\W|\s)/\\htmladdnormallink{$1}{$1}$2/g;

$doc =~ s/\\IfFileExists\{url\.sty\}.+\n.+/\\usepackage{url}/;
$doc =~ s/\\url\|(.+?)\|/\\url\{$1\}/g;
$doc =~ s/(?<!\\newcommand{\\doubledash}{)-\\\/-/\\doubledash{}/g;

open DOC, ">manual.tex";
print DOC $doc;