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Sorry to hear you’re facing problems 
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Nextcloud version (eg, 20.0.5): 26.0.1
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The issue you are facing:
I’m trying to create a custom theme for nextcloud which can reside in themes/mytheme.
I know that the example provided in that folder is based on the legacy theme format, which might be phased out in the future.
I’m trying to do some light theming, mainly changing color, title, slogan etc.
Right now, I am sending a server.css with overwritten CSS values for colors, but that requires overwriting the colors by hand. It also has nextcloud still serving the default color scheme from my main theme, which I set up via the admin theming interface.
Since the theming app cannot be disabled anymore, full manual theming does not appear to be present. Creating a custom app would also not work in my use case.
Manually supplying CSS variables doesn’t make use of the automating the theme app provides, namely providing one HEX color and the app does the magic of creating a fitting color scheme, coloring the .svg icons etc.
Thus, the question: Can I provide a value for the primary color, which nextcloud then uses to do its magic?
Background: I’m using domain based theming with a tweak in the config.php which routes to themes/domain