Register Bukkit API entity wrappers after all mods loaded. Part of fix #1272.

Similar to the Biome wrappers, we register the Entity wrappers now after
all the mods have loaded, just before the plugins are enabled. This now
picks up all of the registered modded entities (388 vs 365, +22 on a test server).
Use entity ID for Bukkit API entity type id. Fixes #1272

If a modded entity class has an ID in EntityList's classToIDMapping
or IDtoClassMapping, use it as the type ID in the Bukkit API.