Try to shorten system header paths when using -MD depfiles

GCC tries to shorten system headers in depfiles using its real path
(resolving components like ".." and following symlinks). Mimic this
feature to ensure that the Ninja build tool detects the correct
dependencies when a symlink changes directory levels, see
https://github.com/ninja-build/ninja/issues/1330

An option to disable this feature is added in case "these changed header
paths may conflict with some compilation environments", see
https://gcc.gnu.org/ml/gcc-patches/2012-09/msg00287.html

Note that the original feature request for GCC
(https://gcc.gnu.org/bugzilla/show_bug.cgi?id=52974) also included paths
preprocessed output (-E) and diagnostics. That is not implemented now
since I am not sure if it breaks something else.

Differential Revision: https://reviews.llvm.org/D37954

llvm-svn: 316193