Fix a bug that -isysroot is completely ignored on Unix

-isysroot is the flag which set the system root directory.
This bug report https://bugs.llvm.org//show_bug.cgi?id=11503
shows that -isysroot is not handled at all on Unix, so fixed this bug.

After this diff, I could get this result https://pastebin.com/TeCmn9mj .

Differential Revision: https://reviews.llvm.org/D31495

llvm-svn: 301998