Address review comments

* Assign the CompilerInstance's PrefixMapper during the ActionController's
for compiler caching
* Add PCH test

clang/lib/Tooling/DependencyScanning/CASFSActionController.cpp

@@ -56,6 +56,7 @@ Error CASFSActionController::initialize(CompilerInstance &ScanInstance,
   // Setup prefix mapping.
   Mapper.emplace(&CacheFS);
   DepscanPrefixMapping::configurePrefixMapper(NewInvocation, *Mapper);
+  ScanInstance.setPrefixMapper(*Mapper);
 
   const PreprocessorOptions &PPOpts = ScanInstance.getPreprocessorOpts();
   if (!PPOpts.Includes.empty() || !PPOpts.ImplicitPCHInclude.empty())

clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp

@@ -586,10 +586,14 @@ class DependencyScanningAction : public tooling::ToolAction {
     auto *FileMgr = ScanInstance.createFileManager(FS);
     ScanInstance.createSourceManager(*FileMgr);
 
-    // Initialize PrefixMapper incase mappings exist.
-    DepscanPrefixMapping::configurePrefixMapper(
-        ScanInstance.getFrontendOpts().PathPrefixMappings,
-        ScanInstance.getPrefixMapper());
+    auto reportError = [&ScanInstance](Error &&E) -> bool {
+      ScanInstance.getDiagnostics().Report(diag::err_cas_depscan_failed)
+          << std::move(E);
+      return false;
+    };
+
+    if (Error E = Controller.initialize(ScanInstance, OriginalInvocation))
+      return reportError(std::move(E));
 
     // Create a collection of stable directories derived from the ScanInstance
     // for determining whether module dependencies would fully resolve from
@@ -649,12 +653,6 @@ class DependencyScanningAction : public tooling::ToolAction {
       Opts->IncludeSystemHeaders = true;
     }
 
-    auto reportError = [&ScanInstance](Error &&E) -> bool {
-      ScanInstance.getDiagnostics().Report(diag::err_cas_depscan_failed)
-          << std::move(E);
-      return false;
-    };
-
     // FIXME: The caller APIs in \p DependencyScanningTool expect a specific
     // DependencyCollector to get attached to the preprocessor in order to
     // function properly (e.g. \p FullDependencyConsumer needs \p
@@ -724,9 +722,6 @@ class DependencyScanningAction : public tooling::ToolAction {
     if (ScanInstance.getFrontendOpts().ProgramAction == frontend::GeneratePCH)
       ScanInstance.getLangOpts().CompilingPCH = true;
 
-    if (Error E = Controller.initialize(ScanInstance, OriginalInvocation))
-      return reportError(std::move(E));
-
     if (ScanInstance.getDiagnostics().hasErrorOccurred())
       return false;
 

clang/lib/Tooling/DependencyScanning/IncludeTreeActionController.cpp

@@ -299,6 +299,7 @@ Expected<cas::IncludeTreeRoot> IncludeTreeActionController::getIncludeTree() {
 Error IncludeTreeActionController::initialize(
     CompilerInstance &ScanInstance, CompilerInvocation &NewInvocation) {
   DepscanPrefixMapping::configurePrefixMapper(NewInvocation, PrefixMapper);
+  ScanInstance.setPrefixMapper(PrefixMapper);
 
   auto ensurePathRemapping = [&]() {
     if (PrefixMapper.empty())

clang/test/ClangScanDeps/prebuilt-modules-in-stable-dirs-with-prefix-mapping.c

@@ -0,0 +1,139 @@
+/// This test validates that modules that depend on prebuilt modules 
+///   resolve `is-in-stable-directories` correctly. 
+
+// REQUIRES: shell,ondisk_cas
+
+/// The steps are: 
+/// 1. Scan dependencies to build the PCH. One of the module's depend on header 
+///   that is seemingly from the sysroot. However, it depends on a local header.
+/// 2. Build the PCH & dependency PCMs.
+/// 3. Scan a source file that transitively depends on the same modules as the pcm.
+
+// REQUIRES: shell
+// RUN: rm -rf %t
+// RUN: split-file %s %t
+// RUN: sed -e "s|DIR|%/t|g" %t/compile-pch.json.in > %t/compile-pch.json
+// RUN: sed -e "s|DIR|%/t|g" %t/compile-commands.json.in > %t/compile-commands.json
+
+// == Scan PCH
+// RUN: clang-scan-deps -compilation-database %t/compile-pch.json -format experimental-full \
+// RUN:    -cas-path %t/cas -module-files-dir %t/modules \
+// RUN:    -prefix-map=%t/modules=/^modules -prefix-map=%t=/^src -prefix-map-sdk=/^sdk -prefix-map-toolchain=/^tc \
+// RUN:  > %t/deps_pch.db
+
+// == Build Deps & PCH
+// RUN: %deps-to-rsp %t/deps_pch.db --module-name=A > %t/A.cc1.rsp
+// RUN: %deps-to-rsp %t/deps_pch.db --module-name=B > %t/B.cc1.rsp
+// RUN: %deps-to-rsp %t/deps_pch.db --module-name=B_transitive > %t/B_transitive.cc1.rsp
+// RUN: %deps-to-rsp %t/deps_pch.db --module-name=C > %t/C.cc1.rsp
+// RUN: %deps-to-rsp %t/deps_pch.db --tu-index 0 > %t/pch.cc1.rsp
+// RUN: %clang @%t/A.cc1.rsp
+// RUN: %clang @%t/B.cc1.rsp
+// RUN: %clang @%t/B_transitive.cc1.rsp
+// RUN: %clang @%t/C.cc1.rsp
+// Ensure we load pcms from action cache
+// RUN: rm -rf %t/modules
+// RUN: %clang @%t/pch.cc1.rsp
+
+// == Scan TU
+// RUN: clang-scan-deps -compilation-database %t/compile-commands.json -format experimental-full \
+// RUN:    -cas-path %t/cas -module-files-dir %t/modules \
+// RUN:    -prefix-map=%t/modules=/^modules -prefix-map=%t=/^src -prefix-map-sdk=/^sdk -prefix-map-toolchain=/^tc \
+// RUN:  > %t/deps.db
+
+// == Check Deps 
+// RUN: cat %t/deps_pch.db | sed 's:\\\\\?:/:g' | FileCheck %s -DPREFIX=%/t --check-prefix PCH_DEP
+// RUN: cat %t/deps.db | sed 's:\\\\\?:/:g' | FileCheck %s -DPREFIX=%/t  --check-prefix CLIENT
+
+// PCH_DEP: "is-in-stable-directories": true
+// PCH_DEP: "name": "A"
+
+// PCH_DEP-NOT: "is-in-stable-directories": true
+
+// Verify is-in-stable-directories is only assigned to the module that only depends on A.
+// CLIENT-NOT: "is-in-stable-directories": true
+
+// CLIENT: "name": "D"
+// CLIENT: "is-in-stable-directories": true
+// CLIENT: "name": "sys"
+
+// CLIENT-NOT: "is-in-stable-directories": true
+
+//--- compile-pch.json.in
+[
+{
+    "directory": "DIR",
+    "command": "clang -x c-header -c DIR/prebuild.h -isysroot DIR/MacOSX.sdk -IDIR/BuildDir -IDIR/MacOSX.sdk/usr/include -fmodules -fmodules-cache-path=DIR/module-cache -fimplicit-module-maps -o DIR/prebuild.pch",
+    "file": "DIR/prebuild.h"
+}
+]
+
+//--- compile-commands.json.in
+[
+{
+    "directory": "DIR",
+    "command": "clang -c DIR/client.c -isysroot DIR/MacOSX.sdk -IDIR/BuildDir -IDIR/MacOSX.sdk/usr/include -fmodules -fmodules-cache-path=DIR/module-cache -fimplicit-module-maps -include-pch DIR/prebuild.pch",
+    "file": "DIR/client.c"
+}
+]
+
+//--- MacOSX.sdk/usr/include/A/module.modulemap
+module A [system] {
+  umbrella "."
+}
+
+//--- MacOSX.sdk/usr/include/A/A.h
+typedef int A_type;
+
+//--- MacOSX.sdk/usr/include/B/module.modulemap
+module B [system] {
+  umbrella "."
+}
+
+//--- MacOSX.sdk/usr/include/B/B.h
+#include <Local/Local.h>
+
+//--- BuildDir/Local/Local.h
+typedef int local_t;
+
+//--- MacOSX.sdk/usr/include/sys/sys.h
+#include <A/A.h>
+typedef int sys_t_m;
+
+//--- MacOSX.sdk/usr/include/sys/module.modulemap
+module sys [system] {
+  umbrella "."
+}
+
+//--- MacOSX.sdk/usr/include/B_transitive/B.h
+#include <B/B.h>
+
+//--- MacOSX.sdk/usr/include/B_transitive/module.modulemap
+module B_transitive [system] {
+  umbrella "."
+}
+
+//--- MacOSX.sdk/usr/include/C/module.modulemap
+module C [system] {
+  umbrella "."
+}
+
+//--- MacOSX.sdk/usr/include/C/C.h
+#include <B_transitive/B.h>
+
+
+//--- MacOSX.sdk/usr/include/D/module.modulemap
+module D [system] {
+  umbrella "."
+}
+
+//--- MacOSX.sdk/usr/include/D/D.h
+#include <C/C.h>
+
+//--- prebuild.h
+#include <A/A.h>
+#include <C/C.h> // This dependency transitively depends on a local header.
+
+//--- client.c
+#include <sys/sys.h>
+#include <D/D.h> // This dependency transitively depends on a local header.