warning: remote HEAD refers to nonexistent ref, unable to checkout

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The warning: remote HEAD refers to nonexistent ref, unable to checkout. means that the remote (bare) repository contains branch reference in the file called HEAD with a value that does not match any published branch in the same repository. In practice, that file defines which branch should be checked out by default after cloning the repository.

Note that the warning only means that git didn’t do checkout. The cloned repository is otherwise just fine. Just do git branch -a to see possible branches and git checkout the-branch-you-want to workaround the issue.

This usually happens because the default contents for that file (.git/HEAD or plain HEAD for bare repositories) is ref: refs/heads/master which says that if somebody is going to clone this repository, they should by default clone the branch refs/heads/master. By default Git will create local branch without the refs/heads/ prefix (that is, master by default). Try git help symbolic-ref for more information.

The problem with this situation is that Git does not provide a method for modifying remote symbolic refs so either you use something the Git hosting provider has implemented (e.g. Settings – Default branch in GitHub if you have admin rights) or you have to use branch name master as the default branch (because that’s the default content for the file HEAD and if you cannot modify that file, you’ll be stuck with master forever).

If you have a shell access to your remote git repo, you can simply cd path/to/git/repo; git symbolic-ref HEAD refs/heads/XYZ where XYZ is the branch name you want to use by default.

One way to hit this issue is to create a new remote bare repo with no commits and then do git push name-of-the-remote my-special-branch-name which will result in bare repository containing a single branch my-special-branch-name but the HEAD symbolic ref still contains the default value pointing to master. As a result, you’ll get the aforementioned warning. If you cannot modify the remote HEAD file, you can publish your branch using syntax git push name-of-the-remote my-special-branch-name:master meaning that your local branch called my-special-branch-name should be published as branch master on the remote.

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