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So, should we be using RSS? Or Atom?

It seems like Atom is better, but RSS as a name is more well known?

I'm guessing adding a button on your website which says "Subscribe via RSS" but which actually points to an Atom feed would be confusing and bad?

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Like you said, atom is slightly better, and based on RSS (hence why everyone just uses 'RSS'). It should be fine to say "Subscribe via RSS" and point to an atom feed instead, almost any tooling will be able to handle both. You can also say "Subscribe to atom feed" to be more explicit.

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