Using this code gets me almost exactly what I needed. There still was a few bugs: the link in the main text were sometime not working. Either the file:/// part was missing in a link or some directories were lost from the path to the html files.
I did this: in the pod2html method around line 735
my $p = Pod::Simple::HTML->new();
my $fn = substr ( $args, 10 );
open FH, ">" . $fn or die("can't open $fn for writing $!");
$fn = substr ( $args, 9) ;
$p->parse_file( $fn ) or die("can't open $fn to parse $!");
and in the head of the script
#use Pod::Html qw( 1.04 );
With this modification, the link in the text part are working, and the ennoying "manpage" are removed.
Pod::Master is very useful and that's a pity its author never put it on CPAN.
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Want more info? How to link or
or How to display code and escape characters
are good places to start.