See https://github.com/YunoHost-Apps/dokuwiki_ynh/pull/37#issuecomment-404597751
Just one last thing, if you put the yunohost requirement at 2.7.14 (last jessie version), you can remove any reference to #sub_path_only in nginx into your install script, as well as upgrade and change_url scripts.
This fix, alias_traversal, is now handled by the helper itself.