I am running 1.6.5, but the folder says 1.6.3?
1.6.5 is the version of the Arduino IDE.

1.6.3 is the version of the Arduino SAM Boards package that you have installed.


  Does this mean there is a hidden 1.6.5 folder that I am not seeing?


Library/Arduino15 is where your preferences.txt file and Boards Manager index files are stored. Library/Arduino15/packages is where hardware packages installed via Tools > Board > Boards Manager are stored. The Arduino IDE will be located elsewhere on your hard drive. If you need to find it here is an easy way:


Tools > Examples > 01.Basics > BareMinimum
Sketch > Show Sketch Folder - this will open the Examples/01.Basics/BareMinimum subfolder of the Arduino IDE installation folder.



  BTW, this issue surfaced...


That's off the topic of your question and already answered in a comment on your question so I will refrain from answering it.