I downloaded PermissionsEx on my server and everything went fine. I created the server groups in PermissionsEx.yml and created a prefix for Chatex. Then I went to my server and wanted to add myself to the server group. Unfortunately, that did not work and not in the console either. Then I entered / pl and the plugin was red. But I have the same version. Then I went into my data manager and the plugin was not there. I downloaded the plugin again and it was still not there. I use Spigot 1.8.8 on the hoster PloudOs.
And how should we help you without permissions.yml or other?
Do you need the Yml or what?
Drive down the server, plugin upload, restart server, then the folder permissionsEx is generated and you can ingame with / pex you show the possibilities.
