Index: include/llvm/CodeGen/RuntimeLibcalls.h
===================================================================
--- include/llvm/CodeGen/RuntimeLibcalls.h
+++ include/llvm/CodeGen/RuntimeLibcalls.h
@@ -29,7 +29,7 @@
   ///
   enum Libcall {
 #define HANDLE_LIBCALL(code, name) code,
-    #include "RuntimeLibcalls.def"
+    #include "llvm/IR/RuntimeLibcalls.def"
 #undef HANDLE_LIBCALL
   };
 
Index: include/llvm/module.modulemap
===================================================================
--- include/llvm/module.modulemap
+++ include/llvm/module.modulemap
@@ -26,7 +26,6 @@
     // These are intended for (repeated) textual inclusion.
     textual header "CodeGen/CommandFlags.inc"
     textual header "CodeGen/DIEValue.def"
-    textual header "CodeGen/RuntimeLibcalls.def"
   }
 
   module Target {
@@ -222,6 +221,7 @@
   textual header "IR/Instruction.def"
   textual header "IR/Metadata.def"
   textual header "IR/Value.def"
+  textual header "IR/RuntimeLibcalls.def"
 }
 
 module LLVM_IRReader { requires cplusplus umbrella "IRReader" module * { export * } }
Index: lib/CodeGen/TargetLoweringBase.cpp
===================================================================
--- lib/CodeGen/TargetLoweringBase.cpp
+++ lib/CodeGen/TargetLoweringBase.cpp
@@ -118,7 +118,7 @@
 void TargetLoweringBase::InitLibcalls(const Triple &TT) {
 #define HANDLE_LIBCALL(code, name) \
   setLibcallName(RTLIB::code, name);
-#include "llvm/CodeGen/RuntimeLibcalls.def"
+#include "llvm/IR/RuntimeLibcalls.def"
 #undef HANDLE_LIBCALL
   // Initialize calling conventions to their default.
   for (int LC = 0; LC < RTLIB::UNKNOWN_LIBCALL; ++LC)
Index: lib/Object/IRSymtab.cpp
===================================================================
--- lib/Object/IRSymtab.cpp
+++ lib/Object/IRSymtab.cpp
@@ -42,6 +42,12 @@
 using namespace llvm;
 using namespace irsymtab;
 
+static const char *LibcallRoutineNames[] = {
+#define HANDLE_LIBCALL(code, name) name,
+#include "llvm/IR/RuntimeLibcalls.def"
+#undef HANDLE_LIBCALL
+};
+
 namespace {
 
 const char *getExpectedProducerName() {
@@ -226,7 +232,17 @@
 
   setStr(Sym.IRName, GV->getName());
 
-  if (Used.count(GV))
+  bool isBuiltinFunc = false;
+
+  // FIXME:  This fixes the issue with builtin functions being
+  // internalized (and later dead-code-eliminated) in the new LTO
+  // implementation.  However this does not fix the old LTO implementaion,
+  // which still internalizes the function definitions.
+  for (const char *libcall_name : LibcallRoutineNames)
+    if (GV->getName() == libcall_name)
+      isBuiltinFunc = true;
+
+  if (Used.count(GV) || isBuiltinFunc)
     Sym.Flags |= 1 << storage::Symbol::FB_used;
   if (GV->isThreadLocal())
     Sym.Flags |= 1 << storage::Symbol::FB_tls;
Index: test/ThinLTO/X86/Inputs/builtin-nostrip.ll
===================================================================
--- test/ThinLTO/X86/Inputs/builtin-nostrip.ll
+++ test/ThinLTO/X86/Inputs/builtin-nostrip.ll
@@ -0,0 +1,9 @@
+target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128"
+target triple = "x86_64-unknown-linux-gnu"
+
+
+; Called via llvm.global_ctors, should be detected as live via the
+; marking of llvm.global_ctors as a live root in the index.
+define void @boo() {
+  ret void
+}
Index: test/ThinLTO/X86/builtin-nostrip.ll
===================================================================
--- test/ThinLTO/X86/builtin-nostrip.ll
+++ test/ThinLTO/X86/builtin-nostrip.ll
@@ -0,0 +1,101 @@
+; REQUIRES: x86-registered-target
+; Compile with thinlto indices, to enable thinlto.
+; RUN: opt -module-summary %s -o %t1.bc
+; RUN: opt -module-summary %p/Inputs/builtin-nostrip.ll -o %t2.bc
+
+; Test old lto interface with thinlto (currently known to be broken, so
+; the FileCheck line is commented out).
+; RUN: llvm-lto -exported-symbol=main -thinlto-action=run %t1.bc %t2.bc
+;;; RUN llvm-nm %t1.bc.thinlto.o | FileCheck %s --check-prefix=CHECK-NM
+
+; Test new lto interface with thinlto.
+; RUN: llvm-lto2 run %t1.bc %t2.bc -o %t.out -save-temps \
+; RUN:   -r %t1.bc,main,plx \
+; RUN:   -r %t1.bc,bar,pl \
+; RUN:   -r %t1.bc,boo,l \
+; RUN:   -r %t1.bc,live_available_externally_func,l \
+; RUN:   -r %t1.bc,__stack_chk_fail,pl \
+; RUN:   -r %t1.bc,memmove,pl \
+; RUN:   -r %t1.bc,memcpy,pl \
+; RUN:   -r %t2.bc,boo,pl
+; RUN: llvm-nm %t.out.1 | FileCheck %s --check-prefix=CHECK-NM
+;
+
+; Re-compile, this time without the thinlto indices.
+; RUN: opt %s -o %t4.bc
+; RUN: opt %p/Inputs/builtin-nostrip.ll -o %t3.bc
+
+; Test the new lto interface without thinlto.
+; RUN: llvm-lto2 run %t4.bc %t3.bc -o %t5.out -save-temps \
+; RUN:   -r %t4.bc,main,plx \
+; RUN:   -r %t4.bc,bar,pl \
+; RUN:   -r %t4.bc,boo,l \
+; RUN:   -r %t4.bc,live_available_externally_func,l \
+; RUN:   -r %t4.bc,__stack_chk_fail,pl \
+; RUN:   -r %t4.bc,memmove,pl \
+; RUN:   -r %t4.bc,memcpy,pl \
+; RUN:   -r %t3.bc,boo,pl 
+; RUN: llvm-nm %t5.out.0 | FileCheck %s --check-prefix=CHECK-NM
+
+; Test the old lto interface without thinlto.  For now we need to
+; use a different nm check, because currently the old lto interface
+; internalizes these symbols.  Once the old lto interface gets
+; fixed, we should be able to use the same CHECK-NM tests as the
+; other FileChecks.
+; RUN: llvm-lto -exported-symbol=main %t3.bc %t4.bc -o %t6
+; RUN: llvm-nm %t6 | FileCheck %s --check-prefix=CHECK-NM2
+
+; The final binary should not contain any of the dead functions;
+; make sure memmove and memcpy are there.
+; CHECK-NM-NOT: bar
+; CHECK-NM-DAG: T __stack_chk_fail
+; CHECK-NM-DAG: T memcpy
+; CHECK-NM-DAG: T memmove
+; CHECK-NM-NOT: bar
+
+; Test case for old lto without thinlto.  Hopefully these can be
+; eliminated once the old lto interface is fixed.
+; CHECK-NM2-DAG: t memcpy
+; CHECK-NM2-DAG: t memmove
+; CHECK-NM2-DAG: t __stack_chk_fail
+
+target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128"
+target triple = "x86_64-unknown-linux-gnu"
+
+
+@llvm.global_ctors = appending global [1 x { i32, void ()* }] [{ i32, void ()* } { i32 65535, void ()* @_GLOBAL__I_a }]
+
+declare void @boo()
+
+define internal void @_GLOBAL__I_a() #1 section "__TEXT,__StaticInit,regular,pure_instructions" {
+entry:
+    call void @boo()
+    ret void
+}
+
+define void @bar() {
+    ret void
+}
+
+
+define void @__stack_chk_fail() {
+    ret void
+}
+
+define void @memmove() {
+    ret void
+}
+
+define void @memcpy() {
+    ret void
+}
+
+define available_externally void @live_available_externally_func() {
+    ret void
+}
+
+define void @main() {
+    call void @bar()
+    call void @live_available_externally_func()
+    ret void
+}