Fix setting nested config variables

Should fix #372 (closed)

If I see correctly, the issue here was that the nested config setting (e.g. setting the main configs "git_remote_preferences" key to the config for remote preferences) was instead setting the nested value to itself (so "git_remote_preferences" was pointing to the "top-level" config).

Please review if that makes sense, but it fixed #372 (closed) for me