Index: clang/include/clang/Lex/ModuleMap.h
===================================================================
--- clang/include/clang/Lex/ModuleMap.h
+++ clang/include/clang/Lex/ModuleMap.h
@@ -60,14 +60,21 @@
   /// Called when a header is added during module map parsing.
   ///
   /// \param Filename The header file itself.
-  virtual void moduleMapAddHeader(StringRef Filename) {}
+  /// \param IsSystem Whether this header is from a system include path.
+  /// \param Imported if this header was imported from an AST file.
+  virtual void moduleMapAddHeader(StringRef Filename, bool IsSystem,
+                                  bool Imported = false) {}
 
   /// Called when an umbrella header is added during module map parsing.
   ///
   /// \param FileMgr FileManager instance
   /// \param Header The umbrella header to collect.
+  /// \param IsSystem Whether this header is from a system include path.
+  /// \param Imported if this header was imported from an AST file.
   virtual void moduleMapAddUmbrellaHeader(FileManager *FileMgr,
-                                          const FileEntry *Header) {}
+                                          const FileEntry *Header,
+                                          bool IsSystem,
+                                          bool Imported = false) {}
 };
 
 class ModuleMap {
@@ -641,6 +648,7 @@
 
   /// Adds this header to the given module.
   /// \param Role The role of the header wrt the module.
+  /// \param Imported If this header was found in an AST file.
   void addHeader(Module *Mod, Module::Header Header,
                  ModuleHeaderRole Role, bool Imported = false);
 
Index: clang/lib/Frontend/DependencyFile.cpp
===================================================================
--- clang/lib/Frontend/DependencyFile.cpp
+++ clang/lib/Frontend/DependencyFile.cpp
@@ -89,6 +89,24 @@
                                     /*IsModuleFile*/false,
                                     /*IsMissing*/false);
   }
+
+  void moduleMapAddHeader(StringRef HeaderPath, bool IsSystem,
+                          bool Imported) override {
+    // If this file name was found embedded in an AST file, then don't track it
+    // here. This is to avoid including -fmodule-file= dependencies.
+    if (Imported)
+      return;
+
+    DepCollector.maybeAddDependency(HeaderPath, /*FromModule=*/false, IsSystem,
+                                    /*IsModuleFile*/ false,
+                                    /*IsMissing=*/false);
+  }
+
+  void moduleMapAddUmbrellaHeader(FileManager *FileMgr, const FileEntry *Header,
+                                  bool IsSystem, bool Imported) override {
+    DepCollectorMMCallbacks::moduleMapAddHeader(Header->getName(), IsSystem,
+                                                Imported);
+  }
 };
 
 struct DepCollectorASTListener : public ASTReaderListener {
@@ -215,12 +233,32 @@
 
 class DFGMMCallback : public ModuleMapCallbacks {
   DFGImpl &Parent;
+
+  void addFile(StringRef Path, bool IsSystem) {
+    if (!IsSystem || Parent.includeSystemHeaders())
+      Parent.AddFilename(Path);
+  }
+
 public:
   DFGMMCallback(DFGImpl &Parent) : Parent(Parent) {}
+
   void moduleMapFileRead(SourceLocation Loc, const FileEntry &Entry,
                          bool IsSystem) override {
-    if (!IsSystem || Parent.includeSystemHeaders())
-      Parent.AddFilename(Entry.getName());
+    addFile(Entry.getName(), IsSystem);
+  }
+
+  void moduleMapAddHeader(StringRef HeaderPath, bool IsSystem,
+                          bool Imported) override {
+    // If this file name was found embedded in an AST file, then don't track it
+    // here. This is to avoid including -fmodule-file= dependencies.
+    if (Imported)
+      return;
+    addFile(HeaderPath, IsSystem);
+  }
+
+  void moduleMapAddUmbrellaHeader(FileManager *FileMgr, const FileEntry *Header,
+                                  bool IsSystem, bool Imported) override {
+    DFGMMCallback::moduleMapAddHeader(Header->getName(), IsSystem, Imported);
   }
 };
 
Index: clang/lib/Frontend/ModuleDependencyCollector.cpp
===================================================================
--- clang/lib/Frontend/ModuleDependencyCollector.cpp
+++ clang/lib/Frontend/ModuleDependencyCollector.cpp
@@ -63,14 +63,17 @@
   ModuleDependencyMMCallbacks(ModuleDependencyCollector &Collector)
       : Collector(Collector) {}
 
-  void moduleMapAddHeader(StringRef HeaderPath) override {
+  void moduleMapAddHeader(StringRef HeaderPath, bool IsSystem,
+                          bool Imported) override {
     if (llvm::sys::path::is_absolute(HeaderPath))
       Collector.addFile(HeaderPath);
   }
   void moduleMapAddUmbrellaHeader(FileManager *FileMgr,
-                                  const FileEntry *Header) override {
+                                  const FileEntry *Header,
+                                  bool IsSystem,
+                                  bool Imported) override {
     StringRef HeaderFilename = Header->getName();
-    moduleMapAddHeader(HeaderFilename);
+    moduleMapAddHeader(HeaderFilename, IsSystem, Imported);
     // The FileManager can find and cache the symbolic link for a framework
     // header before its real path, this means a module can have some of its
     // headers to use other paths. Although this is usually not a problem, it's
@@ -92,7 +95,7 @@
       llvm::sys::path::append(AltHeaderFilename, UmbrellaDir,
                               llvm::sys::path::filename(HeaderFilename));
       if (FileMgr->getFile(AltHeaderFilename))
-        moduleMapAddHeader(AltHeaderFilename);
+        moduleMapAddHeader(AltHeaderFilename, IsSystem, Imported);
     }
   }
 };
Index: clang/lib/Lex/ModuleMap.cpp
===================================================================
--- clang/lib/Lex/ModuleMap.cpp
+++ clang/lib/Lex/ModuleMap.cpp
@@ -1090,7 +1090,8 @@
 
   // Notify callbacks that we just added a new header.
   for (const auto &Cb : Callbacks)
-    Cb->moduleMapAddUmbrellaHeader(&SourceMgr.getFileManager(), UmbrellaHeader);
+    Cb->moduleMapAddUmbrellaHeader(&SourceMgr.getFileManager(), UmbrellaHeader,
+                                   Mod->IsSystem);
 }
 
 void ModuleMap::setUmbrellaDir(Module *Mod, const DirectoryEntry *UmbrellaDir,
@@ -1185,9 +1186,22 @@
                                     isCompilingModuleHeader);
   }
 
-  // Notify callbacks that we just added a new header.
-  for (const auto &Cb : Callbacks)
-    Cb->moduleMapAddHeader(Header.Entry->getName());
+  SmallString<128> FullPathAsWritten;
+  if (Mod->Directory) {
+    FullPathAsWritten = Mod->Directory->getName();
+    llvm::sys::path::append(FullPathAsWritten, Header.NameAsWritten);
+  }
+
+  for (const auto &Cb : Callbacks) {
+    Cb->moduleMapAddHeader(Header.Entry->getName(), Mod->IsSystem, Imported);
+
+    // If the header in the module map refers to a symlink, Header.Entry
+    // refers to the actual file. The callback should be notified of both.
+    if (!FullPathAsWritten.empty() &&
+        !FullPathAsWritten.equals(Header.Entry->getName())) {
+      Cb->moduleMapAddHeader(FullPathAsWritten, Mod->IsSystem, Imported);
+    }
+  }
 }
 
 void ModuleMap::excludeHeader(Module *Mod, Module::Header Header) {
Index: clang/test/Modules/Inputs/dfg-symlinks.modulemap
===================================================================
--- /dev/null
+++ clang/test/Modules/Inputs/dfg-symlinks.modulemap
@@ -0,0 +1,4 @@
+module my_module {
+  header "link.h" export *
+  header "misc.h" export *
+}
Index: clang/test/Modules/dependency-file-symlinks.c
===================================================================
--- /dev/null
+++ clang/test/Modules/dependency-file-symlinks.c
@@ -0,0 +1,55 @@
+// REQUIRES: shell
+
+// RUN: rm -rf %t
+// RUN: mkdir -p %t/cache
+
+// Set up %t as follows:
+//  * misc.h #includes target.h
+//  * target.h is empty
+//  * link.h is a symlink to target.h
+
+// RUN: cp %S/Inputs/dfg-symlinks.modulemap %t/module.modulemap
+// RUN: echo "int foo();" > %t/target.h
+// RUN: ln -s %t/target.h %t/link.h
+// RUN: echo '#include "target.h"' >> %t/misc.h
+// RUN: echo 'int foo();'          >> %t/misc.h
+
+// RUN: %clang_cc1 -fmodules -fimplicit-module-maps -fmodules-cache-path=%t/cache %s \
+// RUN:   -I %t -MT dependency-file-symlinks.o -dependency-file - | FileCheck --check-prefix=CHECK_IMP %s
+
+// Run clang again, to make sure that we get identical output with the cached
+// modules.
+
+// RUN: %clang_cc1 -fmodules -fimplicit-module-maps -fmodules-cache-path=%t/cache %s \
+// RUN:   -I %t -MT dependency-file-symlinks.o -dependency-file - | FileCheck --check-prefix=CHECK_IMP %s
+
+// Verify that the an explicit use of a module via -fmodule-file doesn't include
+// any headers from that files's modulemap.
+
+// RUN: %clang_cc1 -fmodules -fmodule-name="my_module" -emit-module \
+// RUN:   -o %t/my_module.pcm %t/module.modulemap
+
+// RUN: %clang_cc1 -fmodules -fmodule-file=%t/my_module.pcm %s -MT  \
+// RUN:   dependency-file-symlinks.o -I %t -dependency-file - | \
+// RUN:   FileCheck --check-prefix CHECK_EXP %s
+
+#include "misc.h"
+
+int main() {
+  void *p = foo;
+}
+
+// CHECK_IMP:      dependency-file-symlinks.o:
+// CHECK_IMP-NEXT:   {{.*}}dependency-file-symlinks.c
+// CHECK_IMP-NEXT:   {{.*}}link.h
+// CHECK_IMP-NEXT:   {{.*}}misc.h
+// CHECK_IMP-NEXT:   {{.*}}module.modulemap
+// CHECK_IMP-NEXT:   {{.*}}target.h
+
+// CHECK_EXP:       dependency-file-symlinks.o:
+// CHECK_EXP-NEXT:    {{.*}}my_module.pcm
+// CHECK_EXP-NEXT:    {{.*}}dependency-file-symlinks.c
+
+// CHECK_EXP-NOT:     misc.h
+// CHECK_EXP-NOT:     link.h
+// CHECK_EXP-NOT:     target.h
Index: clang/test/Modules/dependency-gen-pch.m
===================================================================
--- clang/test/Modules/dependency-gen-pch.m
+++ clang/test/Modules/dependency-gen-pch.m
@@ -5,9 +5,9 @@
 // RUN: %clang_cc1 -isysroot %S/Inputs/System -triple x86_64-apple-darwin10 -module-file-deps -dependency-file %t.d -MT %s.o -I %S/Inputs -fmodules -fimplicit-module-maps -fdisable-module-hash -fmodules-cache-path=%t-mcp -emit-pch -o %t.pch %s
 // RUN: FileCheck %s < %t.d
 // CHECK: dependency-gen-pch.m.o
-// CHECK-NEXT: dependency-gen-pch.m
-// CHECK-NEXT: Inputs{{.}}module.map
-// CHECK-NEXT: diamond_top.pcm
-// CHECK-NEXT: Inputs{{.}}diamond_top.h
+// CHECK: dependency-gen-pch.m
+// CHECK: Inputs{{.}}diamond_top.h
+// CHECK: Inputs{{.}}module.map
+// CHECK: diamond_top.pcm
 
 #import "diamond_top.h"
Index: clang/test/Modules/dependency-gen.m
===================================================================
--- clang/test/Modules/dependency-gen.m
+++ clang/test/Modules/dependency-gen.m
@@ -4,8 +4,8 @@
 // RUN: %clang_cc1 -x objective-c -isystem %S/Inputs/System/usr/include -dependency-file %t.d.1 -MT %s.o -I %S/Inputs -fsyntax-only -fmodules -fimplicit-module-maps -fmodules-cache-path=%t-mcp %s
 // RUN: FileCheck %s < %t.d.1
 // CHECK: dependency-gen.m
-// CHECK: Inputs{{.}}module.map
 // CHECK: Inputs{{.}}diamond_top.h
+// CHECK: Inputs{{.}}module.map
 // CHECK-NOT: usr{{.}}include{{.}}module.map
 // CHECK-NOT: stdint.h
 
@@ -13,10 +13,10 @@
 // RUN: %clang_cc1 -x objective-c -isystem %S/Inputs/System/usr/include -dependency-file %t.d.2 -MT %s.o -I %S/Inputs -sys-header-deps -fsyntax-only -fmodules -fimplicit-module-maps -fmodules-cache-path=%t-mcp %s
 // RUN: FileCheck %s -check-prefix=CHECK-SYS < %t.d.2
 // CHECK-SYS: dependency-gen.m
-// CHECK-SYS: Inputs{{.}}module.map
 // CHECK-SYS: Inputs{{.}}diamond_top.h
-// CHECK-SYS: usr{{.}}include{{.}}module.map
+// CHECK-SYS: Inputs{{.}}module.map
 // CHECK-SYS: stdint.h
+// CHECK-SYS: usr{{.}}include{{.}}module.map
 
 #import "diamond_top.h"
 #import "stdint.h" // inside sysroot
Index: clang/test/Modules/relative-dep-gen.cpp
===================================================================
--- clang/test/Modules/relative-dep-gen.cpp
+++ clang/test/Modules/relative-dep-gen.cpp
@@ -29,10 +29,8 @@
 
 #include "Inputs/relative-dep-gen-1.h"
 
-// CHECK-BUILD: mod.pcm:
+// CHECK-BUILD: mod.pcm: {{.*}}Inputs{{[/\\]}}relative-dep-gen-1.h {{.*}}Inputs{{[/\\]}}relative-dep-gen-2.h
 // CHECK-BUILD:   {{[ \t]}}Inputs{{[/\\]}}relative-dep-gen{{(-cwd)?}}.modulemap
-// CHECK-BUILD:   {{[ \t]}}Inputs{{[/\\]}}relative-dep-gen-1.h
-// CHECK-BUILD:   {{[ \t]}}Inputs{{[/\\]}}relative-dep-gen-2.h
 // CHECK-USE: use.o:
 // CHECK-USE-DAG:   {{[ \t]}}relative-dep-gen.cpp
 // CHECK-EXPLICIT-DAG:   mod.pcm