Well, why did you do that?

bioseq or https://metacpan.org/pod/bioseq leads to https://metacpan.org/pod/release/ROCKY/Bio-BPWrapper-1.02/lib/Bio/BPWrapper/bioseq.pod

Delete or change the pod to

=head1 NAME

Bio::BPWrapper::bioseq - desc
[download]

And it "bioseq" should now lead to https://metacpan.org/pod/distribution/Bio-BPWrapper/bin/bioseq

bioseq is a command-line program just like lwp-request. In the distribution tarball it is located in the bin directory.

The name suggested, Bio::BPWrapper:bioseq, is wrong. That may be where metacpan may find it, but that is not the name. It doesn't have a package namespace of Bio::BPwrapper.

As for why I did that, it is because I want the POD which is long to be separate from the code so that the same file can be put on a shared wiki, but combined with the distribution just before release.

The name suggested, Bio::BPWrapper:bioseq, is wrong.

Then why does https://metacpan.org/pod/release/ROCKY/Bio-BPWrapper-1.02_02/lib/Bio/BPWrapper/bioseq.pod exist with the =head1 NAME bioseq?

The file doesn't belong, its not https://metacpan.org/pod/release/ROCKY/Bio-BPWrapper-1.02_02/bin/bioseq.pod

You need unique names.

You need unique names.

You need unique names.

Ok. That was an inadvertent mistake on my part and explains some of the weirdness. Having gone through the possibilities listed elsehwere, I think I understand the best I can do for merging in the concerns of cpan.org and convinient wiki editing. Again this is spelled out elsewhere in this thread.