Deduplicate replacements from diagnostics.

Summary:
After r329813, clang-apply-replacements stopped deduplicating identical
replacements; however, tools like clang-tidy relies on the deduplication of
identical dignostics replacements from different TUs to apply fixes correctly.

This change partially roll back the behavior by deduplicating changes from
diagnostics. Ideally, we should deduplicate on diagnostics level, but we need to
figure out an effecient way.

Reviewers: bkramer

Subscribers: cfe-commits

Differential Revision: https://reviews.llvm.org/D52264

llvm-svn: 342951