Minecraft wiki entry for Development_versions, associated text: .minecraft directory structure is changed:
assets folder; stores resources such as language packs and sounds.
All music discs now use .ogg format instead of .mus format.
library folder; stores Java libraries such as LWJGL and jinput.jar.
versions folder; there are files version.json (meta data) and folders that stores minecraft.jar for each versions (but its name is the same as its version; the jar for 13w16a is versions/13w16a/13w16a.jar).