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.