[clang][deps] Teach dep directive scanner about #pragma clang system_header

This ensures we get the correct FileCharacteristic during scanning. In a
yet-to-be-upstreamed branch this fixes observable failures, but it's
also good to handle this on principle: the FileCharacteristic is a
property of the file that is observable in the scanner, so there is
nothing preventing us from depending on it.

rdar://108627403

Differential Revision: https://reviews.llvm.org/D149777