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The github for mac tool generates .git repositories without setting the 'repository version' in the config file. I reported this several months ago to them but I don't know if they fixed it yet. Currently jgit parses the config file and does this check at line 187 in FileRepository.java if (!"0".equals(repositoryFormatVersion)) This means jgit is incapable of reading repositories created by the github tool. We have been running with a patch to change this line into the equivalent of: if (!IsNullOrEmpty (repositoryVersion) && !"0".equals(repositoryFormatVersion)) It makes sense to treat a lack of value as being the same as meaning the default value of '0' has been set. This allows jgit to open github for mac repositories correctly.
Proposed fix pushed to https://git.eclipse.org/r/#/c/5217
Fixed in master now.