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Maybe the way the plugin checks if the repository is empty is not correct. The problem above can be fixed by setting the HEAD of the bare repository to a branch that actually contains something. This is a detail that should be said somewhere in the documentation and/or in the empty repository page (along with the instructions).
It raises the question thought: Is a repository empty when the master branch doesn't contain any file?
When using another branch than the master one, the repository page says the repository is empty.
When using the default git adapter, the repository is not empty.
Example (taken from git flow):
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