Place binaries and intermediates in folders that include OS

Place binaries and intermediates in folders that include OS

Rework the output paths so that the OS may appear in them.  This then follows the same form as corefx.  This solves a number of problems:
    1) When building unix mscorlib after the regular build, we would use the wrong intermediates for incremental.
    2) When testing windows after building unix mscorlib we'd use the wrong outputs and fail.

This change removes our cmake directory and moves cmake generated files into intermediates (under OS/arch paths)
The reason is that the intermediates go under here when actually doing the build, and on unix based systems, we need to generate the cmake files for different builds into different directories for the purpose of preserving incremental builds.

Change clean behavior

Clean should simply delete the root binary.  We also should not make assumptions about
whether necessary directories are available when we begin to build and should create them every time if
necessary.

Create directories as needed.