Simplifies the GlobalContext constructor so that a future
change may just set up the flags and the GlobalContext
before calling into what is currently "main".
Namely this change:
https://codereview.chromium.org/997773002/

This also moves all uses of LLVM's CommandLine.h to
a single file, so that in the future we may be able
to simplify the flags parsing (especially for the
minimal build).

BUG= https://code.google.com/p/nativeclient/issues/detail?id=4091
BUG= https://code.google.com/p/nativeclient/issues/detail?id=4084
R=stichnot@chromium.org

Review URL: https://codereview.chromium.org/1024203002