Deduplicate replacements by FileEntry instead of file names.

Summary:
The current version does not deduplicate equivalent file paths correctly.
For example, a relative path and an absolute path are considered inequivalent.
Comparing FileEnry addresses these issues.

Reviewers: djasper

Subscribers: alexshap, klimek, cfe-commits

Differential Revision: https://reviews.llvm.org/D26288

llvm-svn: 286096