Index: lib/Frontend/ModuleDependencyCollector.cpp
===================================================================
--- lib/Frontend/ModuleDependencyCollector.cpp
+++ lib/Frontend/ModuleDependencyCollector.cpp
@@ -156,10 +156,6 @@
   // allows crash reproducer scripts to work across machines.
   VFSWriter.setOverlayDir(VFSDir);
 
-  // Do not ignore non existent contents otherwise we might skip something
-  // that should have been collected here.
-  VFSWriter.setIgnoreNonExistentContents(false);
-
   // Explicitly set case sensitivity for the YAML writer. For that, find out
   // the sensitivity at the path where the headers all collected to.
   VFSWriter.setCaseSensitivity(isCaseSensitivePath(VFSDir));
Index: test/Modules/crash-vfs-headermaps.m
===================================================================
--- test/Modules/crash-vfs-headermaps.m
+++ test/Modules/crash-vfs-headermaps.m
@@ -32,7 +32,6 @@
 // CHECKYAML: 'case-sensitive':
 // CHECKYAML-NEXT: 'use-external-names': 'false',
 // CHECKYAML-NEXT: 'overlay-relative': 'true',
-// CHECKYAML-NEXT: 'ignore-non-existent-contents': 'false'
 // CHECKYAML: 'type': 'directory'
 // CHECKYAML: 'name': "/[[PATH:.*]]/Foo.framework/Headers",
 // CHECKYAML-NEXT: 'contents': [
Index: test/Modules/crash-vfs-include-pch.m
===================================================================
--- test/Modules/crash-vfs-include-pch.m
+++ test/Modules/crash-vfs-include-pch.m
@@ -33,7 +33,6 @@
 // CHECKYAML: 'case-sensitive':
 // CHECKYAML-NEXT: 'use-external-names': 'false',
 // CHECKYAML-NEXT: 'overlay-relative': 'true',
-// CHECKYAML-NEXT: 'ignore-non-existent-contents': 'false'
 // CHECKYAML: 'type': 'directory'
 // CHECKYAML: 'name': "/[[PATH:.*]]/out",
 // CHECKYAML-NEXT: 'contents': [
Index: test/Modules/crash-vfs-ivfsoverlay.m
===================================================================
--- test/Modules/crash-vfs-ivfsoverlay.m
+++ test/Modules/crash-vfs-ivfsoverlay.m
@@ -36,7 +36,6 @@
 // CHECKYAML: 'case-sensitive':
 // CHECKYAML-NEXT: 'use-external-names': 'false',
 // CHECKYAML-NEXT: 'overlay-relative': 'true',
-// CHECKYAML-NEXT: 'ignore-non-existent-contents': 'false'
 // CHECKYAML: 'type': 'directory'
 // CHECKYAML: 'name': "/[[PATH:.*]]/example"
 // CHECKYAML: 'contents': [
Index: test/Modules/crash-vfs-relative-incdir.m
===================================================================
--- test/Modules/crash-vfs-relative-incdir.m
+++ test/Modules/crash-vfs-relative-incdir.m
@@ -36,7 +36,6 @@
 // CHECKYAML: 'case-sensitive':
 // CHECKYAML-NEXT: 'use-external-names': 'false',
 // CHECKYAML-NEXT: 'overlay-relative': 'true',
-// CHECKYAML-NEXT: 'ignore-non-existent-contents': 'false'
 // CHECKYAML: 'type': 'directory'
 // CHECKYAML: 'name': "/[[PATH:.*]]/Inputs/crash-recovery/usr/include",
 // CHECKYAML-NEXT: 'contents': [
Index: test/Modules/crash-vfs-run-reproducer.m
===================================================================
--- test/Modules/crash-vfs-run-reproducer.m
+++ test/Modules/crash-vfs-run-reproducer.m
@@ -36,7 +36,6 @@
 // CHECKYAML: 'case-sensitive':
 // CHECKYAML-NEXT: 'use-external-names': 'false',
 // CHECKYAML-NEXT: 'overlay-relative': 'true',
-// CHECKYAML-NEXT: 'ignore-non-existent-contents': 'false'
 // CHECKYAML: 'type': 'directory'
 // CHECKYAML: 'name': "/[[PATH:.*]]/Inputs/crash-recovery/usr/include",
 // CHECKYAML-NEXT: 'contents': [
Index: test/VFS/Inputs/MissingVFS/vfsoverlay.yaml
===================================================================
--- test/VFS/Inputs/MissingVFS/vfsoverlay.yaml
+++ test/VFS/Inputs/MissingVFS/vfsoverlay.yaml
@@ -1,6 +1,5 @@
 {
   'version': 0,
-  'ignore-non-existent-contents': false,
   'roots': [
     { 'name': 'INPUT_DIR', 'type': 'directory',
       'contents': [
Index: test/VFS/Inputs/Nonmodular/nonmodular-headers.yaml
===================================================================
--- test/VFS/Inputs/Nonmodular/nonmodular-headers.yaml
+++ test/VFS/Inputs/Nonmodular/nonmodular-headers.yaml
@@ -1,7 +1,6 @@
 {
   'version': 0,
   'case-sensitive': 'false',
-  'ignore-non-existent-contents': 'true',
   'roots': [
     {
       'type': 'directory',
Index: test/VFS/Inputs/bar-headers.yaml
===================================================================
--- test/VFS/Inputs/bar-headers.yaml
+++ test/VFS/Inputs/bar-headers.yaml
@@ -1,7 +1,6 @@
 {
   'version': 0,
   'case-sensitive': 'false',
-  'ignore-non-existent-contents': 'true',
   'roots': [
     {
       'type': 'directory',
Index: test/VFS/Inputs/vfsoverlay2.yaml
===================================================================
--- test/VFS/Inputs/vfsoverlay2.yaml
+++ test/VFS/Inputs/vfsoverlay2.yaml
@@ -1,6 +1,5 @@
 {
   'version': 0,
-  'ignore-non-existent-contents': false,
   'roots': [
     { 'name': 'OUT_DIR', 'type': 'directory',
       'contents': [