Propagate llvm::vfs::FileSystem from driver_env to Clang (#4537)

As discussed in #4530 . This required switching to using
`llvm::IntrusiveRefCntPtr` in a number of places.

---------

Co-authored-by: Josh L <josh11b@users.noreply.github.com>

toolchain/driver/clang_runner.cpp

@@ -26,7 +26,6 @@
 #include "llvm/Support/LLVMDriver.h"
 #include "llvm/Support/Path.h"
 #include "llvm/Support/Program.h"
-#include "llvm/Support/VirtualFileSystem.h"
 #include "llvm/TargetParser/Host.h"
 
 // Defined in:
@@ -42,9 +41,12 @@ auto clang_main(int Argc, char** Argv, const llvm::ToolContext& ToolContext)
 namespace Carbon {
 
 ClangRunner::ClangRunner(const InstallPaths* install_paths,
-                         llvm::StringRef target, llvm::raw_ostream* vlog_stream)
+                         llvm::StringRef target,
+                         llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem> fs,
+                         llvm::raw_ostream* vlog_stream)
     : installation_(install_paths),
       target_(target),
+      fs_(std::move(fs)),
       vlog_stream_(vlog_stream),
       diagnostic_ids_(new clang::DiagnosticIDs()) {}
 
@@ -123,10 +125,10 @@ auto ClangRunner::Run(llvm::ArrayRef<llvm::StringRef> args) -> bool {
   clang::DiagnosticsEngine diagnostics(
       diagnostic_ids_, diagnostic_options.get(), &diagnostic_client,
       /*ShouldOwnClient=*/false);
-  auto vfs = llvm::vfs::getRealFileSystem();
-  clang::ProcessWarningOptions(diagnostics, *diagnostic_options, *vfs);
+  clang::ProcessWarningOptions(diagnostics, *diagnostic_options, *fs_);
 
-  clang::driver::Driver driver(clang_path, target_, diagnostics);
+  clang::driver::Driver driver(clang_path, target_, diagnostics,
+                               "clang LLVM compiler", fs_);
 
   // Configure the install directory to find other tools and data files.
   //