Found this today when I joined my server and checked the console.
[12:35:59] [User Authenticator #2/INFO]: UUID of player Scrufdog is 6895abcb-14b8-45f5-8df1-be66accea83a
[12:35:59] [Server thread/INFO]: Scrufdog[/66.87.82.211:38174] logged in with entity id 534 at ([ScrufLand3] -210.85133516383928, 69.0, 260.477902868787)
[12:35:59] [pool-10-thread-1/ERROR]: /var/games/minecraft/servers/ScrufLand3/plugins/Essentials/userdata/6895abcb-14b8-45f5-8df1-be66accea83a.yml (Permission denied)
java.io.FileNotFoundException: /var/games/minecraft/servers/ScrufLand3/plugins/Essentials/userdata/6895abcb-14b8-45f5-8df1-be66accea83a.yml (Permission denied)
at java.io.FileOutputStream.open(Native Method) ~[?:1.8.0_25]
at java.io.FileOutputStream.<init>(FileOutputStream.java:213) ~[?:1.8.0_25]
at java.io.FileOutputStream.<init>(FileOutputStream.java:162) ~[?:1.8.0_25]
at com.earth2me.essentials.EssentialsConf$WriteRunner.run(EssentialsConf.java:415) [Essentials-2.x-SNAPSHOT.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_25]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_25]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_25]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_25]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_25]
It seems all Essentials functions still work. Is this a file permissions thing or something else?
Thanks