This what MorphOS does in a very neat way. All the typical directories are pretty much empty, for example SYS:Libs, but LIBS: is assigned to SYS:Libs MOSSYS:Libs, and the lattet comtains all of MorphOS native libraries. Any libraries installed by programs or user, goes to SYS:Libs (since it is first in path of the Libs: assign), and libs in SYS:Libs will also be loaded before equally named libs in MOSSYS:Libs.
And all these directories came from TRIPOS btw.