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And then use a inheriting theme that overrides the necessary bits in the core application repo

Watea and starter are CWP built themes, you can find them on GitHub... 🙂

It provides a base theme to work off, and you can inherit from that 🙂

But if you don't want that, you are obviously free to use whatever you like

In your case, I refer to my previous comment, use the base theme and have the modifications together with the code 🙂

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Any ideas to what the issue is with Solr, if no search results show up on the website, but doing a query from the Solr admin panel works fine?