diff --git a/clang/lib/Serialization/ASTWriter.cpp b/clang/lib/Serialization/ASTWriter.cpp
--- a/clang/lib/Serialization/ASTWriter.cpp
+++ b/clang/lib/Serialization/ASTWriter.cpp
@@ -1544,7 +1544,6 @@
       continue;
 
     if (isModuleMap(File.getFileCharacteristic()) &&
-        !isSystem(File.getFileCharacteristic()) &&
         !AffectingModuleMaps.empty() &&
         AffectingModuleMaps.find(Cache->OrigEntry) ==
             AffectingModuleMaps.end()) {
diff --git a/clang/test/ClangScanDeps/modules-implicit-dot-private.m b/clang/test/ClangScanDeps/modules-implicit-dot-private.m
--- a/clang/test/ClangScanDeps/modules-implicit-dot-private.m
+++ b/clang/test/ClangScanDeps/modules-implicit-dot-private.m
@@ -15,7 +15,7 @@
 [{
   "file": "DIR/tu.m",
   "directory": "DIR",
-  "command": "clang -fmodules -fmodules-cache-path=DIR/cache -iframework DIR/frameworks -c DIR/tu.m -o DIR/tu.o"
+  "command": "clang -fmodules -fmodules-cache-path=DIR/cache -F DIR/frameworks -c DIR/tu.m -o DIR/tu.o"
 }]
 //--- tu.m
 @import FW.Private;
@@ -33,8 +33,7 @@
 // CHECK-NEXT:       "context-hash": "{{.*}}",
 // CHECK:            "file-deps": [
 // CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Headers/FW.h",
-// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
-// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap"
+// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap"
 // CHECK-NEXT:       ],
 // CHECK-NEXT:       "name": "FW"
 // CHECK:          },
@@ -45,7 +44,6 @@
 // CHECK:            ],
 // CHECK-NEXT:       "context-hash": "{{.*}}",
 // CHECK:            "file-deps": [
-// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
 // CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap",
 // CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/PrivateHeaders/FW_Private.h"
 // CHECK-NEXT:       ],
diff --git a/clang/test/ClangScanDeps/modules-incomplete-umbrella.c b/clang/test/ClangScanDeps/modules-incomplete-umbrella.c
--- a/clang/test/ClangScanDeps/modules-incomplete-umbrella.c
+++ b/clang/test/ClangScanDeps/modules-incomplete-umbrella.c
@@ -45,8 +45,7 @@
 // CHECK_TU-NEXT:       "context-hash": "{{.*}}",
 // CHECK_TU-NEXT:       "file-deps": [
 // CHECK_TU-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Headers/FW.h",
-// CHECK_TU-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
-// CHECK_TU-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap"
+// CHECK_TU-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap"
 // CHECK_TU-NEXT:       ],
 // CHECK_TU-NEXT:       "name": "FW"
 // CHECK_TU-NEXT:     },
@@ -57,7 +56,6 @@
 // CHECK_TU:            ],
 // CHECK_TU-NEXT:       "context-hash": "{{.*}}",
 // CHECK_TU-NEXT:       "file-deps": [
-// CHECK_TU-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
 // CHECK_TU-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap",
 // CHECK_TU-NEXT:         "[[PREFIX]]/frameworks/FW.framework/PrivateHeaders/FW_Private.h",
 // CHECK_TU-NEXT:         "[[PREFIX]]/frameworks/FW.framework/PrivateHeaders/One.h"
@@ -102,7 +100,7 @@
 [{
   "file": "DIR/from_module.m",
   "directory": "DIR",
-  "command": "clang -fmodules -fmodules-cache-path=DIR/cache -iframework DIR/frameworks -c DIR/from_module.m -o DIR/from_module.o"
+  "command": "clang -fmodules -fmodules-cache-path=DIR/cache -F DIR/frameworks -c DIR/from_module.m -o DIR/from_module.o"
 }]
 //--- module.modulemap
 module Mod { header "Mod.h" }
@@ -125,8 +123,7 @@
 // CHECK_MODULE-NEXT:       "context-hash": "{{.*}}",
 // CHECK_MODULE-NEXT:       "file-deps": [
 // CHECK_MODULE-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Headers/FW.h",
-// CHECK_MODULE-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
-// CHECK_MODULE-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap"
+// CHECK_MODULE-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap"
 // CHECK_MODULE-NEXT:       ],
 // CHECK_MODULE-NEXT:       "name": "FW"
 // CHECK_MODULE-NEXT:     },
@@ -137,7 +134,6 @@
 // CHECK_MODULE:            ],
 // CHECK_MODULE-NEXT:       "context-hash": "{{.*}}",
 // CHECK_MODULE-NEXT:       "file-deps": [
-// CHECK_MODULE-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
 // CHECK_MODULE-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap",
 // CHECK_MODULE-NEXT:         "[[PREFIX]]/frameworks/FW.framework/PrivateHeaders/FW_Private.h",
 // CHECK_MODULE-NEXT:         "[[PREFIX]]/frameworks/FW.framework/PrivateHeaders/One.h"
diff --git a/clang/test/ClangScanDeps/modules-redefinition.m b/clang/test/ClangScanDeps/modules-redefinition.m
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/modules-redefinition.m
@@ -0,0 +1,37 @@
+// This test checks that we don't report (potentially) duplicate module maps
+// implicit build picked up from a system search directory.
+
+// RUN: rm -rf %t
+// RUN: split-file %s %t
+
+//--- tu.m
+@import first; // this doesn't repro with "@import third;"
+
+//--- zeroth/module.modulemap
+module X {} // module name must match "-fmodule-name=" value
+
+//--- first/module.modulemap
+module first { header "first.h" }
+//--- first/first.h
+@import third;
+//--- second/module.modulemap
+module X {}
+//--- third/module.modulemap
+module third {}
+
+//--- cdb.json.template
+[{
+  "file": "DIR/tu.m",
+  "directory": "DIR",
+  "command": "clang -fmodules -fmodules-cache-path=DIR/cache -fmodule-name=X -fmodule-map-file=DIR/zeroth/module.modulemap -isystem DIR/first -isystem DIR/second -isystem DIR/third -c DIR/tu.m -o DIR/tu.o"
+}]
+
+// RUN: %clang -fmodules -fmodules-cache-path=%t/cache -fmodule-name=X -fmodule-map-file=%t/zeroth/module.modulemap -isystem %t/first -isystem %t/second -isystem %t/third -c %t/tu.m -o %t/tu.o
+
+// 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 > %t/result.json
+// RUN: %deps-to-rsp %t/result.json --module-name=third > %t/third.cc1.rsp
+// RUN: %deps-to-rsp %t/result.json --module-name=first > %t/first.cc1.rsp
+// RUN: %clang @%t/third.cc1.rsp
+// RUN: %clang @%t/first.cc1.rsp