[Tooling] Restore current directory after processing each file.

Summary:
If we actually change directory before processing a file, we need to
restore it afterwards. This was broken in r216620.

Added a comment for the changes in r216620.

Reviewers: klimek

Reviewed By: klimek

Subscribers: klimek, cfe-commits

Differential Revision: http://reviews.llvm.org/D6162