Improve javadoc in 26 files.

Addresses:
BUKKIT-1643, BUKKIT-1868, BUKKIT-1846, BUKKIT-2632, BUKKIT-3196,
BUKKIT-3187, BUKKIT-3198, BUKKIT-3200, BUKKIT-3201 and BUKKIT-3417.
Spigot POM Changes
Measure the duration of the entire timings run.
Add CustomTimingsHandler for adding new CraftBukkit custom timings