Arduino files are found in 3 locations: The installation folder, the sketchbook folder, and the Arduino15

folder. The installation folder should be removed when you uninstall but the other two folders remain so
you will need to remove those also to get a completely clean install. The Arduino15 folder is located at:
On Mac OS X:
/Users/(username)/Library/Arduino15

On Windows:
Arduino IDE 1.6.5r5 and previous:
C:\Users\(username)\AppData\Roaming\Arduino15
Arduino IDE 1.6.6 and later:
C:\Users\(username)\AppData\Local\Arduino15

On Linux:
/home/(username)/.arduino15 (a.k.a. ~/.arduino15)

If you delete this folder then you will need to reinstall any Boards you have installed using Boards
Manager after you reinstall the Arduino IDE.

The sketchbook folder location is set in File > Preferences if you have any sketches or libraries that you
want to save in there then back them up before removing it.