Ask yourself what is clean code? Is it something you read in a book? Does using a pattern help or hurt? Write more code. Learn different languages and how paradigms different in each language and framework. Take some of those things you learned and decide which ones you can apply in new frameworks and projects and which ones don't.
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Yes
Yes exactly why this is actually quite problematic. There's a lot of HTTPS Git pull remotes around and random software that uses raw.githubusercontent.com to fetch data. All of that is now subject to the 60 req/hr limit and not all of it will be easy to fix.