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Finding the root cause for me took hours. First I tried to reproduce it locally but I couldn't.
Then tried to check things in frontend of commons. With the debug=true, I realized it's line 331 of wikibase.client.PageConnector.js which means wb.sites.getSite( firstSiteId ) is failing. This needs to return value for both commons and enwiki. Trying it out, it works for enwiki but not commons.
If you dig in the code, it's based on mw.config.get( 'wbSiteDetails' ) config variable that gets injected using SitesModule.php and SitesModuleWorker.php in WikibaseLib. If you ask for the config variable, it doesn't have any special wiki in commons but it has in wikidata or other wikis.
This php module, reads specialSiteLinkGroups from \Wikibase\Settings::singleton() in which combines repo and client settings. So the problem is that repo setting of specialSiteLinkGroups is set to [] per default but it's correct for clients (but it got overriden once commons turned to be a repo). The fix is easy, add wikidata specialSiteLinkGroups repo setting to commons too and that's what I did in the patch.
Cc: Ladsgroup, Liuxinyu970226, SJu, Lymantria, Ghouston, Addshore, Lucas_Werkmeister_WMDE, Michael, Mbch331, hoo, Lydia_Pintscher, Robby, Aklapper, Nandana, Lahi, Gq86, GoranSMilovanovic, QZanden, LawExplorer, Poyekhali, _jensen, Jonas, Wong128hk, Wikidata-bugs, aude, El_Grafo, Dinoguy1000, Steinsplitter
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