When adding a new entry to an existing manifest and then calling regenerate without first clone the new repository, the tool just complains about a failing lstat:
Unable to eval symlinks for /home/user/graylog/graylog-project-repos/graylog-plugin-foo: lstat /home/user/graylog/graylog-project-repos/graylog-plugin-foo: no such file or directory
Make this a bit friendlier to explain what happened (and suggest that a checkout might solve this problem).