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Remove duplicate entries from theme picker
It is possible to overwrite the runtime themes that come with Helix by putting a theme with the same name in the .config/helix/themes directory. This creates duplicate entries in the theme picker that both point to the same theme:

Best solution would be just to remove the duplicate entries.
I generally agree, but is it that more complicated to maybe have it like
bogster bogster(user)
To have them both and mark the user theme?
That might be a problem for choosing a theme in your config.toml: do you write theme = "bogster(user)"? It could work but it doesn't seem very elegant.
It looks like both "bogster"s activate same theme (the user one) because of the theme loading rules. I think the simplest way to make this less confusing would be to deduplicate the theme completion but in the long-run we may want to support multiple themes with the same name for the sake of https://github.com/helix-editor/helix/pull/3067. You may want to make a small modification to a built-in theme locally and name it the same thing.