[clang] Fix ASTUnit working directory handling

Fix a couple of issues with the handling of the current working directory in ASTUnit:

- Use `createPhysicalFileSystem` instead of `getRealFileSystem` to avoid affecting the process' current working directory, and set it at the top of `ASTUnit::LoadFromCommandLine` such that the driver used for argument parsing and the ASTUnit share the same VFS. This ensures that '-working-directory' correctly sets the VFS working directory in addition to the FileManager working directory.
- Ensure we preserve the FileSystemOptions set on the FileManager when re-creating it (as `ASTUnit::Reparse` will clear the currently set FileManager).

rdar://110697657

Reviewed By: bnbarham, benlangmuir

Differential Revision: https://reviews.llvm.org/D154134