No runtime includes

The title is a slight misnomer. This pull request does a few things that turned out to be coupled:

- Fix the windows build, which once again tracks trunk llvm

- Update nacl version to pepper_35 and track trunk pnacl llvm (fixes a bug in test_memoize on win32 under pnacl llvm)

- Avoid system includes (even the -ffreestanding ones - didn't work with pnacl on windows). Now uses compiler built-in macros for the stdint types, which should be more robust than the old old method.