diff --git a/configure b/configure
index 7e64c1ec6..b3817bd49 100755
--- a/configure
+++ b/configure
@@ -1179,7 +1179,7 @@ done
 
 ac_given_srcdir=$srcdir
 
-trap 'rm -fr `echo "Source/InitialConfigureFlags.cmake Source/bootstrap/Makefile Source/cmConfigure.h" | sed "s/:[^ ]*//g"` conftest*; exit 1' 1 2 15
+trap 'rm -fr `echo "Source/InitialConfigureFlags.cmake Makefile Source/Makefile Source/cmConfigure.h" | sed "s/:[^ ]*//g"` conftest*; exit 1' 1 2 15
 EOF
 cat >> $CONFIG_STATUS <<EOF
 
@@ -1259,7 +1259,7 @@ EOF
 
 cat >> $CONFIG_STATUS <<EOF
 
-CONFIG_FILES=\${CONFIG_FILES-"Source/InitialConfigureFlags.cmake Source/bootstrap/Makefile"}
+CONFIG_FILES=\${CONFIG_FILES-"Source/InitialConfigureFlags.cmake Makefile Source/Makefile"}
 EOF
 cat >> $CONFIG_STATUS <<\EOF
 for ac_file in .. $CONFIG_FILES; do if test "x$ac_file" != x..; then
@@ -1433,8 +1433,8 @@ rm -fr confdefs* $ac_clean_files
 test "$no_create" = yes || ${CONFIG_SHELL-/bin/sh} $CONFIG_STATUS || exit 1
 
 # build cmake
-(cd Source/bootstrap; $RUNMAKE)
+$RUNMAKE 
 # run cmake 
-./Source/bootstrap/cmake $fullSrcDir
+./Source/cmake $fullSrcDir
 # run cmake depends
 $RUNMAKE depend
diff --git a/configure.in b/configure.in
index 16fcbd567..8478af242 100644
--- a/configure.in
+++ b/configure.in
@@ -143,10 +143,10 @@ fi
 # find make to use to build cmake, prefer gmake
 AC_PATH_PROGS(RUNMAKE, gmake make)
 
-AC_OUTPUT(Source/InitialConfigureFlags.cmake Source/bootstrap/Makefile)
+AC_OUTPUT(Source/InitialConfigureFlags.cmake Makefile Source/Makefile)
 # build cmake
-(cd Source/bootstrap; $RUNMAKE)
+$RUNMAKE 
 # run cmake 
-./Source/bootstrap/cmake $fullSrcDir
+./Source/cmake $fullSrcDir
 # run cmake depends
 $RUNMAKE depend