When SSO is enabled for your user, your account will not have a password associated with it. Therefore, your username and password will not work with external clients to check out your repos or make a commit.
Instead, you will need to use your username and an API key with repo access. An API key can be obtained by opening your user profile and clicking on the API Applications and Sessions settings on the left sidebar.
Then, check the Repository access checkbox and click the Createbutton to create an API key with repo access to use with two-factor authentication.
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