I replied to your issue but just to mention here as well, in 1.22 (currently in beta), you can logout explicitly which will let you enter another token.
In the meantime, the token was likely saved by a program on your computer that stores credentials (e.g. Keychain Access on macOS). What operating system are you running?
I suppose that the “token” I had to type was the password, but I cannot find a way to enter it.
I’m beginning to think that that “token” is something else, but… what???
The token is an Oauth token which lets the GitHub package access your repositories on your behalf. In the GitHub panel, after you click the Login button, you should see this:
Click on the link and you’ll be taken to atom.io where you login with your GitHub credentials, and then you’ll be given a token that you can copy and paste into the GitHub package.
So if you can let me know what OS you’re using, hopefully we can figure out how to clear the saved token so you can go through the login process again.