Correctly classify main file includes if there is a prefix added

Summary:
Prevents misclassifying includes based on the command-line filename (e.g. if a project is in a subdirectory).

This is slightly more robust than the additional duplicate detection, however the current classification scheme is still kind of brittle for a lot of code.

Reviewers: hokein, alexfh

Subscribers: cfe-commits, #clang-tools-extra

Patch by Julian Bangert!

Differential Revision: https://reviews.llvm.org/D26015

llvm-svn: 291767