The directories beos/apps, beos/bin and beos/preferences are essentially identical to system/apps, system/bin and system/preferences and so can be replaced by links. However there was one omission is system/bin - mkdepend was omitted, and I'm unsure whether this was intentional.
The directories beos/etc and beos/system should be left in situ for the moment to avoid problems with apps looking for stuff at absolute locations.
Rob
