Formatting fixes

Hey, can you pull in these formatting fixes? Thanks!

Details of fixes:
 - Change all Windows newlines `\r\n` to Unix newlines `\n`
 - Run formatter with my Bukkit Style settings on it

(Note: There is a single discrepancy between the formatter settings and the style used by Bukkit, and that is that sometimes Javadocs (`/**`) have an extra space at the end of the line.)