I accidentally stumbled upon ActivePerl::DocTools::Tree::HTML, so now all I do is, and I get no problems with cross/linking like crazyinsomniac does

perl -MActivePerl::DocTools -e ActivePerl::DocTools::UpdateHTML()
perl -MActivePerl::DocTools -e ActivePerl::DocTools::WriteTOC()
[download]

Since all my html docs were messed up, I had to do a

perl -MFile::Path -MConfig -e" rmtree(qq[$Config{installhtmldir}\\bin]
+) "
perl -MFile::Path -MConfig -e" rmtree(qq[$Config{installhtmldir}\\site
+\\lib]) "
[download]

before running the above code

update: John M. Dlugosz , it is a part of ActivePerl::DocTools. The ActivePerl guys commented out the pod a long time ago, so when you say perldoc ActivePerl::DocTools nothing shows up. Anyway, I use Pod::Master now.

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** The Third rule of perl club is a statement of fact: pod is sexy.