With the introduction of Eclipse SmartHome project and openHAB2 I think it's the right time file system hierarchy standard to be agreed and published so it can be used by all other developers. As I can see so far there are three main directories:
Kai or other core developers could you share your vision about the hierarchy and describe in some more details the purpose of each one of these directories and what can/should be stored in them?
The idea is actually, that Eclipse SmartHome only allows a generic configuration of where certain folders are and a concrete solution (such as openHAB 2) then uses certain folders - so the ones you mention are only relevant for openHAB 2 and as such will be documented in the openHAB documentation.
Nonetheless what is left for Eclipse SmartHome is to document the configuration possibilities. This is actually not yet fully implemented to my satisfaction, see the discussion here: https://github.com/eclipse/smarthome/pull/40#issuecomment-50176861
I plan to adapt this in the coming days and will then also add some section in the documentation about it.