Confusingly, Wikidata.org and WikimediaBadges have very similarly named images (resources/images/wb-badges-notproofread.png vs resources/images/badge-notproofread.png) except they're totally different.

Wikidata.org is deployed to wikidata repos only
WikimediaBadges is deployed to the clients.

The badges stuff from wikidata.org can probably live in the WikimediaBadges repo and the message stuff can probably live in the messages extension.

I'll give the team a poke and see if anyone has any other issues with this.

The idea of the Wikidata.org extension is to contain bits that are not true for all Wikibase installations but only for wikidata.org, and are not configuration (but code and binary files). This is especially true for the badge graphics, as they depend on particular item IDs that only exist on wikidata.org.

WikimediaBadges is the counterpart. It holds the same number of graphics representing badges along with some CSS, just from the point of view of the client wikis (all Wikimedia wikis except wikidata.org itself).

Logically the two belong together. They could be merged into one codebase. This combined extension must then be deployed on all wikis including wikidata.org. Just make sure this does not create any unwanted load, e.g. code that is executed when not needed, or unwanted files being transfered.

In theory all this could even be merged into WikimediaMessages. I just don't like this idea because a) this extension is already very messy as it contains messages and other stuff for dozens of extensions and b) CSS and binary files are not really "messages". The first issue could be made much better by introducing a i18n/wikibase directory.

All that said, I personally don't support the idea to merge any of these code repositories. They all have crystal clear boundaries. If the issue is a lack of documentation, we can fix this.