diff --git a/eo/autogen.sh b/eo/autogen.sh
index e0eae074..22b83ab3 100755
--- a/eo/autogen.sh
+++ b/eo/autogen.sh
@@ -39,23 +39,9 @@ autoconf
 # we want doc to be recompiled - and it keeps saying it's up to date!!!
 touch doc/eo.cfg
 
-
-# if test -z "$*"; then
-#     echo "I am going to run ./configure with no arguments - if you wish"
-#     echo "to pass any to it, please specify them on the $0 command line."
-# fi
-#
-# ./configure "$@"
-
 echo
 echo "Now run 'configure' and 'make' to build $PROG."
 echo "You can check the libraries by running 'make check'"
 echo
 echo "If you have Doxygen installed, type 'make doc' to generate $PROG documentation."
 echo
-
-#echo "WARNING: Compiling all test programs can take some time."
-#echo "But you don't have to: you can simply type"
-#echo "                    'make lib'"
-#echo "and then go in your application dir (or in the tutorial dir)"
-#echo "and there type 'make'"
diff --git a/eo/src/es/Makefile.am b/eo/src/es/Makefile.am
index 2957f371..e8648910 100644
--- a/eo/src/es/Makefile.am
+++ b/eo/src/es/Makefile.am
@@ -4,44 +4,46 @@
 ##
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src -I$(top_srcdir)/src
-lib_LIBRARIES = libes.a
-libes_a_SOURCES = make_algo_scalar_es.cpp \
-    make_algo_scalar_real.cpp \
-    make_checkpoint_es.cpp \
-    make_checkpoint_real.cpp \
-    make_continue_es.cpp \
-    make_continue_real.cpp \
-    make_genotype_es.cpp \
-    make_genotype_real.cpp \
-    make_op_es.cpp \
-    make_op_real.cpp \
-    make_pop_es.cpp \
-    make_pop_real.cpp \
-    make_run_es.cpp \
-    make_run_real.cpp
+AM_CXXFLAGS		= -I$(top_srcdir)/src
 
-CPPFLAGS = -Wall
-CXXFLAGS = 
-libeoincdir = $(includedir)/eo/es
-libeoinc_HEADERS = eoEsChromInit.h \
-    eoEsFull.h \
-    eoEsGlobalXover.h \
-    eoEsMutate.h \
-    eoEsMutationInit.h \
-    eoEsSimple.h \
-    eoEsStandardXover.h \
-    eoEsStdev.h \
-    eoNormalMutation.h \
-    eoRealAtomXover.h \
-    eoReal.h \
-    eoRealInitBounded.h \
-    eoRealOp.h \
-    eoSBXcross.h \
-    make_es.h \
-    make_genotype_real.h \
-    make_op_es.h \
-    make_op.h \
-    make_op_real.h \
-    make_real.h
+
+lib_LIBRARIES 		= libes.a
+
+libes_a_SOURCES 	= make_algo_scalar_es.cpp \
+			make_algo_scalar_real.cpp \
+			make_checkpoint_es.cpp \
+			make_checkpoint_real.cpp \
+			make_continue_es.cpp \
+			make_continue_real.cpp \
+			make_genotype_es.cpp \
+			make_genotype_real.cpp \
+			make_op_es.cpp \
+			make_op_real.cpp \
+			make_pop_es.cpp \
+			make_pop_real.cpp \
+			make_run_es.cpp \
+			make_run_real.cpp
+
+libeoincdir 		= $(includedir)/eo/es
+
+libeoinc_HEADERS 	= eoEsChromInit.h \
+			eoEsFull.h \
+			eoEsGlobalXover.h \
+			eoEsMutate.h \
+			eoEsMutationInit.h \
+			eoEsSimple.h \
+			eoEsStandardXover.h \
+			eoEsStdev.h \
+			eoNormalMutation.h \
+			eoRealAtomXover.h \
+			eoReal.h \
+			eoRealInitBounded.h \
+			eoRealOp.h \
+			eoSBXcross.h \
+			make_es.h \
+			make_genotype_real.h \
+			make_op_es.h \
+			make_op.h \
+			make_op_real.h \
+			make_real.h
 
diff --git a/eo/src/ga/Makefile.am b/eo/src/ga/Makefile.am
index bd4ba013..1c6959c0 100644
--- a/eo/src/ga/Makefile.am
+++ b/eo/src/ga/Makefile.am
@@ -4,28 +4,29 @@
 ##
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src  -I$(top_srcdir)/src
-lib_LIBRARIES = libga.a
-libga_a_SOURCES = make_algo_scalar_ga.cpp \
-    make_checkpoint_ga.cpp \
-    make_continue_ga.cpp \
-    make_genotype_ga.cpp \
-    make_op_ga.cpp \
-    make_pop_ga.cpp \
-    make_run_ga.cpp
+AM_CXXFLAGS		= -I$(top_builddir)/src  -I$(top_srcdir)/src
 
-CPPFLAGS = -Wall
-CXXFLAGS = 
-libeoincdir = $(includedir)/eo/ga
-libeoinc_HEADERS = eoBit.h \
-    eoBitOpFactory.h \
-    eoBitOp.h \
-    eoBoolFlip.h \
-    eoPBILAdditive.h \
-    eoPBILDistrib.h \
-    eoPBILOrg.h \
-    make_ga.h \
-    make_genotype_ga.h \
-    make_op.h \
-    make_PBILdistrib.h \
-    make_PBILupdate.h
+lib_LIBRARIES 		= libga.a
+
+libga_a_SOURCES 	= make_algo_scalar_ga.cpp \
+			make_checkpoint_ga.cpp \
+			make_continue_ga.cpp \
+			make_genotype_ga.cpp \
+			make_op_ga.cpp \
+			make_pop_ga.cpp \
+			make_run_ga.cpp
+
+libeoincdir 		= $(includedir)/eo/ga
+
+libeoinc_HEADERS 	= eoBit.h \
+			eoBitOpFactory.h \
+			eoBitOp.h \
+			eoBoolFlip.h \
+			eoPBILAdditive.h \
+			eoPBILDistrib.h \
+			eoPBILOrg.h \
+			make_ga.h \
+			make_genotype_ga.h \
+			make_op.h \
+			make_PBILdistrib.h \
+			make_PBILupdate.h
diff --git a/eo/src/utils/Makefile.am b/eo/src/utils/Makefile.am
index 9076455d..7222246b 100644
--- a/eo/src/utils/Makefile.am
+++ b/eo/src/utils/Makefile.am
@@ -4,14 +4,21 @@
 ##
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src  -I$(top_srcdir)/src
-CPPFLAGS = -O2 -Wall
 lib_LIBRARIES = libeoutils.a
-libeoutils_a_SOURCES = eoParser.cpp eoRNG.cpp eoState.cpp eoUpdater.cpp eoFileMonitor.cpp eoStdoutMonitor.cpp eoRealBounds.cpp make_help.cpp
-
-libeoincdir = $(includedir)/eo/utils
-libeoinc_HEADERS = checkpointing $(srcdir)/*.h
-#compatibility.h eoCheckPoint.h eoData.h eoDistance.h eoFDCStat.h eoFileMonitor.h eoGnuplot1DMonitor.h eoGnuplot1DSnapshot.h eoHowMany.h eoMonitor.h eoParam.h eoParser.h eoRNG.h eoStat.h eoScalarFitnessStat.h eoState.h eoStdoutMonitor.h eoUpdatable.h eoUpdater.h rnd_generators.h eoRndGenerators.h selectors.h
 
 
+AM_CXXFLAGS 		= -I$(top_srcdir)/src
 
+
+libeoutils_a_SOURCES 	= eoParser.cpp \
+			eoRNG.cpp \
+			eoState.cpp \
+			eoUpdater.cpp \
+			eoFileMonitor.cpp \
+			eoStdoutMonitor.cpp \
+			eoRealBounds.cpp \
+			make_help.cpp
+
+libeoincdir 		= $(includedir)/eo/utils
+
+libeoinc_HEADERS 	= checkpointing $(srcdir)/*.h