Switch the nop pnacl x86-64 IRT shim to the real one generated from IDL.

site_scons/site_tools/naclsdk.py

Index: site_scons/site_tools/naclsdk.py
diff --git a/site_scons/site_tools/naclsdk.py b/site_scons/site_tools/naclsdk.py
index 0b559138be646badf6d6179eab0db9ac80a2bd93..a48226c9dcf4f2f9feaf53a5617a11d714127094 100755
--- a/site_scons/site_tools/naclsdk.py
+++ b/site_scons/site_tools/naclsdk.py
@@ -349,6 +349,12 @@ def PNaClGetNNaClEnv(env):
   native_env = env.Clone()
   native_env.ClearBits('bitcode')
   native_env = native_env.Clone(tools = ['naclsdk'])
+  # These are unfortunately clobbered by running Tool.
+  native_env.Replace(EXTRA_CFLAGS=env['EXTRA_CFLAGS'],
+                     EXTRA_CXXFLAGS=env['EXTRA_CXXFLAGS'],
+                     CCFLAGS=env['CCFLAGS'],
+                     CFLAGS=env['CFLAGS'],
+                     CXXFLAGS=env['CXXFLAGS'])
   return native_env