diff --git a/cmake/extract_includes.bat.in b/cmake/extract_includes.bat.in
index b2e9444da1e19..0661ac4c476eb 100644
--- a/cmake/extract_includes.bat.in
+++ b/cmake/extract_includes.bat.in
@@ -88,6 +88,7 @@ copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\stubs\common.h include
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\stubs\fastmem.h include\google\protobuf\stubs\fastmem.h
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\stubs\hash.h include\google\protobuf\stubs\hash.h
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\stubs\once.h include\google\protobuf\stubs\once.h
+copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\stubs\pbconfig.h include\google\protobuf\stubs\pbconfig.h
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\stubs\platform_macros.h include\google\protobuf\stubs\platform_macros.h
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\stubs\shared_ptr.h include\google\protobuf\stubs\shared_ptr.h
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\stubs\singleton.h include\google\protobuf\stubs\singleton.h
@@ -102,4 +103,3 @@ copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\wire_format.h include\
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\wire_format_lite.h include\google\protobuf\wire_format_lite.h
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\wire_format_lite_inl.h include\google\protobuf\wire_format_lite_inl.h
 copy ${PROTOBUF_SOURCE_WIN32_PATH}\..\src\google\protobuf\wrappers.pb.h include\google\protobuf\wrappers.pb.h
-copy ${PROTOBUF_BINARY_WIN32_PATH}\google\protobuf\stubs\pbconfig.h include\google\protobuf\stubs\pbconfig.h
diff --git a/cmake/update_file_lists.sh b/update_file_lists.sh
similarity index 93%
rename from cmake/update_file_lists.sh
rename to update_file_lists.sh
index 4466c0211a374..7202650f6069a 100755
--- a/cmake/update_file_lists.sh
+++ b/update_file_lists.sh
@@ -61,9 +61,9 @@ sort_files() {
   done | LC_ALL=C sort | uniq
 }
 
-MAKEFILE=../src/Makefile.am
-CMAKE_DIR=.
-EXTRACT_INCLUDES_BAT=extract_includes.bat.in
+MAKEFILE=src/Makefile.am
+CMAKE_DIR=cmake
+EXTRACT_INCLUDES_BAT=cmake/extract_includes.bat.in
 
 [ -f "$MAKEFILE" ] || {
   echo "Cannot find: $MAKEFILE"
@@ -117,5 +117,3 @@ for HEADER in $PUBLIC_HEADERS; do
   WINPATH=$(echo $HEADER | sed 's;/;\\;g')
   echo "copy \${PROTOBUF_SOURCE_WIN32_PATH}\\..\\src\\$WINPATH include\\$WINPATH" >> $EXTRACT_INCLUDES_BAT
 done
-# Add pbconfig.h.
-echo "copy \${PROTOBUF_BINARY_WIN32_PATH}\\google\\protobuf\\stubs\\pbconfig.h include\\google\\protobuf\\stubs\\pbconfig.h" >> $EXTRACT_INCLUDES_BAT