This was happens in my server Centos7 in the Google Cloud Platform.
Initially the plugin printed the message of error in execution of the file ssh-inc.
I deactivate the selinux temporably with setenforce 0 and clicked in the "Fetch repository".
In this moment, majority of the plugins and themes was deleted.
I see in the file inc/class-git-wrapper.php:644 have rm -rf.
I suggest to change it, it is too dangerous.