wondered why the diff was so large, turns out the file in the repo uses CRLF

I assume its easier to fix for you manually, so I didn't create a PR. Can do that tho. 

Quick test (without git so auto.crlf and stuff dont apply...):

martin@glados:# wget https://hub.spigotmc.org/stash/projects/SPIGOT/repos/craftbukkit/raw/src/main/java/org/bukkit/craftbukkit/util/permissions/CommandPermissions.java -q           

martin@glados:# file CommandPermissions.java
CommandPermissions.java: ASCII text, with CRLF line terminators