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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:
Files not being linked from within biopython.org
64-bit_Windows_Biopython
Ace_contig_class.md
Category_People.md
Degenerated_Codons.md
File_talk_Contig_class.png.md
Gene_Ontology.md
GitMigration.md
MotifDev.md
PDBParser.md
PopGen_dev_Statistics.md
ProtParam.md
Struct.md
Subversion_migration.md
User_Alexl.md
User_Blivens.md
User_Davidw.md
User_Edward.Tao.md
User_Gotgenes.md
User_Jblucks.md
User_MarcSaric.md
User_Orbeckst.md
User_ShawnDouglas.md
Some of these are (outdated?)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.
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 inrobots.txt
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