Use include_directories(SYSTEM ...) consistently
Apparently, at least some compilers treat -isystem differently from -I
in that no matter what the order on the command line is, -I always takes
precedence. This means that some of the
include_directories(BEFORE SYSTEM ...)
did not work correctly, and in particular GMX_EXTERNAL_BOOST=OFF was
broken. Likely also #1539 was (again) broken.
Make all includes that come from outside the source tree use SYSTEM, so
that the include directory for internal boost still takes precedence
over them.
Fixes #1844.
Change-Id: Ib536c24a0d13c6538f78daac145dc8d38135819d