[clang-scan-deps] Fix for headers having the same name as a directory

Scan deps tool crashes when called on a C++ file, containing an include
that has the same name as a directory.
The tool crashes since it finds foo/dir and tries to read that as a file and fails.

Patch by: kousikk (Kousik Kumar)

Differential Revision: https://reviews.llvm.org/D67091

llvm-svn: 371903