I don't know if everyone knows about this, but you can dump some of those files you mentioned into a dot github directory to keep them out of the repo root. I think .travis.yml might be able to go there too, depending on your prefs.

https://github.com/Homebrew/brew/tree/master/.github

Multiple issue templates are supported as well:

https://github.com/tutao/tutanota/tree/master/.github/ISSUE_TEMPLATE

In effect, when a user clicks "new issue", they are presented with 3 different options.

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