きっと今後未来の自分がエラーに躓くのでメモしとく。

結論

２段階認証の設定をしたときは
git clone https://hoge.gitではなく
git clone git://hoge.gitを使ってね。

# NG
~/hogeProject:user1 git clone https://github.com/hoge/hoge-branch.git
Cloning into 'hoge-branch'...
Username for 'https://github.com': user1
Password for 'https://user1@github.com': 
remote: Invalid username or password.
fatal: Authentication failed for 'https://github.com/hoge/hoge-branch.git/'

# OK
~/hogeProject:user1 git clone git@github.com:hoge/hoge-branch.git
Cloning into 'hoge-branch'...
warning: You appear to have cloned an empty repository.