[clang][deps] Fix dependency scanning with -working-directory

Stop overriding -working-directory to CWD during argument parsing, which
should no longer necessary after we set the VFS working directory, and
set FSOpts correctly after parsing arguments so that working-directory
behaves correctly.

Author: benlangmuir

clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp

@@ -342,6 +342,9 @@ class DependencyScanningAction : public tooling::ToolAction {
     ScanInstance.getHeaderSearchOpts().ModulesIncludeVFSUsage =
         any(OptimizeArgs & ScanningOptimizations::VFS);
 
+    // FileMgr was created before option parsing; set its FileSystemOptions now.
+    FileMgr->getFileSystemOpts() = ScanInstance.getFileSystemOpts();
+
     ScanInstance.setFileManager(FileMgr);
     // Support for virtual file system overlays.
     FileMgr->setVirtualFileSystem(createVFSFromCompilerInvocation(
@@ -624,9 +627,8 @@ bool DependencyScanningWorker::computeDependencies(
       ModifiedCommandLine ? *ModifiedCommandLine : CommandLine;
   auto &FinalFS = ModifiedFS ? ModifiedFS : BaseFS;
 
-  FileSystemOptions FSOpts;
-  FSOpts.WorkingDir = WorkingDirectory.str();
-  auto FileMgr = llvm::makeIntrusiveRefCnt<FileManager>(FSOpts, FinalFS);
+  auto FileMgr =
+      llvm::makeIntrusiveRefCnt<FileManager>(FileSystemOptions{}, FinalFS);
 
   std::vector<const char *> FinalCCommandLine(FinalCommandLine.size(), nullptr);
   llvm::transform(FinalCommandLine, FinalCCommandLine.begin(),

clang/test/ClangScanDeps/working-directory-option.c

@@ -0,0 +1,30 @@
+// Test that -working-directory works even when it differs from the working
+// directory of the filesystem.
+
+// RUN: rm -rf %t
+// RUN: mkdir -p %t/other
+// RUN: split-file %s %t
+// RUN: sed -e "s|DIR|%/t|g" %t/cdb.json.template > %t/cdb.json
+
+// RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full \
+// RUN:   > %t/deps.json
+
+// RUN: cat %t/deps.json | sed 's:\\\\\?:/:g' | FileCheck %s -DPREFIX=%/t
+
+// CHECK:      "file-deps": [
+// CHECK-NEXT:   "[[PREFIX]]/cwd/t.c"
+// CHECK-NEXT:   "[[PREFIX]]/cwd/relative/h1.h"
+// CHECK-NEXT: ]
+// CHECK-NEXT: "input-file": "[[PREFIX]]/cwd/t.c"
+
+//--- cdb.json.template
+[{
+  "directory": "DIR/other",
+  "command": "clang -c t.c -I relative -working-directory DIR/cwd",
+  "file": "DIR/cwd/t.c"
+}]
+
+//--- cwd/relative/h1.h
+
+//--- cwd/t.c
+#include "h1.h"