Changed makefiles to allow better clang++ support.

There are 3 other problems that have not yet been checked in, in
order to compile under clang++:

1. mpir needs to have its configure script patched.
2. gran just doesn't compile, so either we need to wait for Anders,
  disable it, or try to fix the compile errors.
3. In the d directory, we need to add -Wno-parentheses-equality
  (A completely stupid warning from clang).

This change allows libfac and factory to compile.
Merge branch 'master' of https://github.com/Macaulay2/M2