[xbuild]: Fix 4.0/4.5 repo layout.

4.0/Microsoft.Common.* was not installed anywhere, so it could safely
be deleted, and 4.5/M.C.* was previously being installed into
$(prefix)/lib/mono/4.0.  It's now in 4.0/M.C.* to match xbuild's
tool version.

This patch does not affect how things are installed, it simply cleans
up the source layout.