[VFS] Port tooling to use the in-memory file system.

This means file remappings can now be managed by ClangTool (or a
ToolInvocation user) instead of by ToolInvocation itself. The
ToolInvocation remapping is still in place so users can migrate.

Differential Revision: http://reviews.llvm.org/D13474

llvm-svn: 249815