Makefile updates

Most of the changes on this pull-request are related to issue 239 on repo cv32e40p (create a single manifest). This manifest is now on the master branch of cv32e40p, so its time to bring this one in.

As part of the effort to use a single manifest, the following changes to the simulation Makefiles have been made:

• The Makefile variables to build compile-time arguments to compile the RTL have been removed.
• Common elements of the Makefiles have been moved to a Common.mk that is included by all simulation Makefiles.
• Add Makefile variables to control which repo, branch and hash is used to clone the RTL.
• All Makefiles not under sim have been removed.