[Tooling] Produce diagnostics for missing input files.

Summary:
This was disabled way back in 2011, in the dark times before Driver was VFS-aware.

Also, make driver more VFS-aware :-)

This breaks one ClangTidy test (we improved the error message), will fix when
submitting.

Reviewers: ioeric

Subscribers: cfe-commits, alexfh

Differential Revision: https://reviews.llvm.org/D53958

llvm-svn: 346414