a) Enable the possibility to remove the "air bubble" around submerged collision object. This feature is enabled as standard for new files. The code was found in elbeem by nudelZ, coded and provided by Nils Thürey (thanks!)
b) Old baked files gets deleted if a new bake gets started (were overwritten before and resulted in weird old bake + new bake mixture) (idea by nudelZ)
ui/ --> startup/bl_ui
op/ --> startup/bl_operators
scripts/startup/ is now the only auto-loading script dir which gives some speedup for blender loading too.
~/.blender/2.56/scripts/startup works for auto-loading scripts too.