Our organization does not use "master" as the default branch. We host projects under Diffusion and set the default branch as appropriate. This works for the web interface and it's all great.
When a user clones the repo the following warning is generated
warning: remote HEAD refers to nonexistent ref, unable to checkout.
This requires the user to issue a checkout command like git checkout correct-branch before their clone is usable. Ultimately this isn't a big deal, but it would be nice if setting the default branch in Diffusion for a hosted repo would also set the bare repo's HEAD to point to that branch.
Having access to the bare repo I can fix it with git symbolic-ref HEAD refs/heads/correct-branch as in http://stackoverflow.com/a/3302018/859353