The old MediaWiki page had http://biopython.org/wiki/Special:AllPages in the sidebar which was useful when browsing the content, and for ensuring search engines found everything. For now we can browse the source at https://github.com/biopython/biopython.github.io/tree/master/wiki
This can probably be done quite easily with the same liquid templating as used on the recreated wiki tag/category pages via https://github.com/biopython/biopython.github.io/blob/master/_layouts/tagpage.html
See also https://www.mediawiki.org/wiki/Special:SpecialPages - there may be others worth resurrecting.
Note we'd want to white-list wiki/Special:AllPages again in robots.txt
This touches another problem: There is a number of sites that are 'unreachable', i.e. they are not linked from within biopython.org. Here is a list I made approx. one week ago:
Some of these are (outdated?) drafts (e.g. PDBParser), some may be linked as 'cookbook' entries (e.g. Degenerated_Codons) others as usual 'wiki' entries (e.g. Gene_Ontology). We have already discusse the User_XXX pages here #61
Yes, this is what the related special page wiki/Special:LonelyPages was for.
All these 'hidden' pages should be reviewed (separate issue), e.g. I've removed File_talk_Contig_class.png.md with ca5845c (I deliberately didn't include the talk pages for normal wiki and user pages) and in 6a72982 you added Degenerated_Codons.md to the cookbook category.