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Investigate why https://doc.wikimedia.org/Wikibase/master/php/modules.html only lists "Wikibase Client" as a module
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I guess this should either just list Wikibase, or list WikibaseRepo, WikibaseClient & WikibaseLib.

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Random guess. client/WikibaseClient.php has the following bit in the comment around the top of the file:

@defgroup WikibaseClient Wikibase Client

No similar things in other "modules".

That said, opening https://doc.wikimedia.org/Wikibase/master/php/group__WikibaseClient.html got me thinking that probably this module documentation could use some help (but this is a general not on wikibase docs, so nothing new).

Indeed it looks like defgroup is the cause here.

defgroup is only in WikibaseClient.

I guess we should either remove it from there or use it correctly everywhere?

thiemowmde subscribed.

The class index at https://doc.wikimedia.org/Wikibase/master/php/classes.html looks complete. This means the doc generator takes all subdirectories into account. It just does not create entires in the "modules" section, as these are bound to manually maintained @defgroup tags. Honestly, I would remove all these tags and let the directory structure dictate instead.

Change 409906 had a related patch set uploaded (by Thiemo Kreuz (WMDE); owner: Thiemo Kreuz (WMDE)):
[mediawiki/extensions/Wikibase@master] Remove lonely @defgroup tag from WikibaseClient.php

https://gerrit.wikimedia.org/r/409906

Change 409906 merged by jenkins-bot:
[mediawiki/extensions/Wikibase@master] Remove lonely @defgroup tag from WikibaseClient.php

https://gerrit.wikimedia.org/r/409906

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