diff --git a/eo/Makefile.am b/eo/Makefile.am
deleted file mode 100644
index e9b7e7aa..00000000
--- a/eo/Makefile.am
+++ /dev/null
@@ -1,30 +0,0 @@
-## Makefile.am for eo
-
-if USE_APPLICATIONS
-SUBDIRS_APP		= app
-endif
-
-if USE_TUTORIAL
-SUBDIRS_TUT		= tutorial
-endif
-
-SUBDIRS			= src doc contrib $(SUBDIRS_APP) $(SUBDIRS_TUT) test
-
-
-# Directory for documents
-DOCDIR 			= ~/public_html/eodocs
-
-# Directory for indices -- not useful for the user
-IDXDIR 			= ~/index
-
-
-# Add documentation to distribution
-dist-hook:
-			$(MAKE) documentation
-			$(INSTALL_DATA) -d $(srcdir)/doc/html $(srcdir)/doc/latex $(srcdir)/doc/man $(distdir)/doc/
-
-# Prepare documentation
-documentation:
-			cd doc && $(MAKE) doc && cd ..
-# convinience-target
-doc: 			documentation
diff --git a/eo/acinclude.m4 b/eo/acinclude.m4
deleted file mode 100644
index f9e35376..00000000
--- a/eo/acinclude.m4
+++ /dev/null
@@ -1,84 +0,0 @@
-# AC_APPLICATIONS()
-#
-# Compile applications unless user requests not to do it.
-AC_DEFUN([AC_APPLICATIONS],[dnl
-  AC_ARG_ENABLE([applications],
-    AC_HELP_STRING([--enable-applications], [build applications (default=yes)]),
-    [ case "${enableval}" in
-      yes) applications=true ;;
-      no) applications=false ;;
-      *) AC_MSG_ERROR(bad value ${enableval} for applications option) ;;
-    esac],
-    [applications=true])
-  if test "$applications" = "true"; then
-    AM_CONDITIONAL([USE_APPLICATIONS], true)
-  else
-    AM_CONDITIONAL([USE_APPLICATIONS], false)
-  fi
-])
-
-
-
-# AC_DEBUG()
-#
-# Check for commandline options requesting DEBUG feature.
-# Might define DEBUG, NODEBUG, or NDEBUG, depending on flags given.
-AC_DEFUN([AC_DEBUG],[dnl
-  AC_ARG_ENABLE([debug], 
-    AC_HELP_STRING([--enable-debug], [include debugging code (default=no)]),
-    [ case "${enableval}" in
-      yes) debug=true ;;
-      no) debug=false ;;
-      *) AC_MSG_ERROR(bad value ${enableval} for debug option) ;;
-    esac],
-    [debug=false])
-  if test "$debug" = true; then
-    AC_DEFINE([DEBUG], true, [Debugging flag])
-  else
-    AC_DEFINE([NDEBUG], true, [no debugging])
-    AC_DEFINE([NODEBUG], true, [no debugging])
-  fi
-])
-
-
-
-# AC_GNUPLOT()
-#
-# Compile applications unless user requests not to do it.
-AC_DEFUN([AC_GNUPLOT], [dnl
-    AC_ARG_ENABLE([gnuplot],
-                  AC_HELP_STRING([--enable-gnuplot], [use gnuplot for graphical display (default=yes)]),
-                  [ac_cv_use_gnuplot=$enableval],
-                  [ac_cv_use_gnuplot=yes])
-    AC_CACHE_CHECK([use gnuplot for graphical display],
-                   [ac_cv_use_gnuplot],
-                   [ac_cv_use_gnuplot=no])
-    if test "$ac_cv_use_gnuplot" = "yes"; then
-        AC_ARG_VAR([GNUPLOT], [gnuplot executable used for graphical display])
-        AC_CHECK_PROG([GNUPLOT], [gnuplot], [gnuplot], [true])
-        AC_DEFINE([HAVE_GNUPLOT], [1], [gnuplot graphical display])
-    else
-        AC_DEFINE([NO_GNUPLOT], [1], [no gnuplot graphical display -- deprecated, will be reomoved!])
-    fi
-])
-
-
-
-# AC_TUTORIAL()
-#
-# Compile tutorial unless user requests not to do it.
-AC_DEFUN([AC_TUTORIAL],[dnl
-  AC_ARG_ENABLE([tutorial],
-    AC_HELP_STRING([--enable-tutorial], [build tutorial (default=yes)]),
-    [ case "${enableval}" in
-      yes) tutorial=true ;;
-      no) tutorial=false ;;
-      *) AC_MSG_ERROR(bad value ${enableval} for tutorial option) ;;
-    esac],
-    [tutorial=true])
-  if test "$tutorial" = "true"; then
-    AM_CONDITIONAL([USE_TUTORIAL], true)
-  else
-    AM_CONDITIONAL([USE_TUTORIAL], false)
-  fi
-])
diff --git a/eo/app/Makefile.am b/eo/app/Makefile.am
deleted file mode 100644
index 66224802..00000000
--- a/eo/app/Makefile.am
+++ /dev/null
@@ -1,3 +0,0 @@
-## Makefile.am for app dir in eo
-
-SUBDIRS = mastermind gprop gpsymreg 
diff --git a/eo/app/gprop/Makefile.am b/eo/app/gprop/Makefile.am
deleted file mode 100644
index b1515ce5..00000000
--- a/eo/app/gprop/Makefile.am
+++ /dev/null
@@ -1,22 +0,0 @@
-# Makefile.am for app/gprop
-
-noinst_PROGRAMS 	= gprop
-
-
-gprop_SOURCES 		= gprop.cpp
-
-noinst_HEADERS		= gprop.h \
-			l2.h \
-			mlp.h \
-			mse.h \
-			qp.h \
-			vecop.h
-
-
-AM_CXXFLAGS		= -I$(top_srcdir)/src
-
-LIBEO			= $(top_builddir)/src/libeo.a
-LIBEOUTILS		= $(top_builddir)/src/utils/libeoutils.a
-
-DEPS 			= $(LIBEO) $(LIBEOUTILS)
-LIBS 			= $(LIBEO) $(LIBEOUTILS)
diff --git a/eo/app/gpsymreg/Makefile.am b/eo/app/gpsymreg/Makefile.am
deleted file mode 100644
index 0ada4ba5..00000000
--- a/eo/app/gpsymreg/Makefile.am
+++ /dev/null
@@ -1,15 +0,0 @@
-# Makefile.am for app/gpsymreg
-
-noinst_PROGRAMS 	= gpsymreg
-
-gpsymreg_SOURCES 	= main.cpp
-
-noinst_HEADERS		= fitness.h node.h parameters.h
-
-
-LIBEO			= $(top_builddir)/src/libeo.a
-LIBEOUTILS		= $(top_builddir)/src/utils/libeoutils.a
-
-AM_CXXFLAGS		= -I$(top_srcdir)/src
-DEPS 			= $(LIBEO) $(LIBEOUTILS)
-LIBS 			= $(LIBEO) $(LIBEOUTILS)
diff --git a/eo/app/mastermind/Makefile.am b/eo/app/mastermind/Makefile.am
deleted file mode 100644
index 91caec05..00000000
--- a/eo/app/mastermind/Makefile.am
+++ /dev/null
@@ -1,14 +0,0 @@
-# Makefile.am for app/mastermind
-
-noinst_PROGRAMS 	= mastermind
-
-mastermind_SOURCES 	= mastermind.cpp
-
-noinst_HEADERS		= mastermind.h
-
-LIBEO			= $(top_builddir)/src/libeo.a
-LIBEOUTILS		= $(top_builddir)/src/utils/libeoutils.a
-
-AM_CXXFLAGS		= -I$(top_srcdir)/src
-DEPS 			= $(LIBEO) $(LIBEOUTILS)
-LIBS			= $(LIBEO) $(LIBEOUTILS)
diff --git a/eo/autogen.sh b/eo/autogen.sh
deleted file mode 100755
index 7825332c..00000000
--- a/eo/autogen.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/bin/sh
-
-DIE=0
-PROG=eo
-
-(autoconf --version) < /dev/null > /dev/null 2>&1 ||
-{
-    echo
-    echo "You must have autoconf installed to compile $PROG."
-    DIE=1
-}
-
-(automake --version) < /dev/null > /dev/null 2>&1 ||
-{
-    echo
-    echo "You must have automake installed to compile $PROG."
-    DIE=1
-}
-
-if test "$DIE" -eq 1; then
-    exit 1
-fi
-
-set aclocalinclude="$ACLOCAL_FLAGS"
-aclocal $aclocalinclude
-unset $aclocalinclude
-autoheader
-automake -a -c
-autoconf
-
-# we want doc to be recompiled - and it keeps saying it's up to date!!!
-# touch doc/eo.cfg
-
-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 $PROG documentation."
-echo
diff --git a/eo/configure.in b/eo/configure.in
deleted file mode 100644
index 50c25794..00000000
--- a/eo/configure.in
+++ /dev/null
@@ -1,88 +0,0 @@
-dnl Process this file with autoconf to produce a configure script.
-dnl
-dnl Change the version number here
-AC_INIT([Evolving Objects], [1.0.1], [eodev-help@sourceforge.net], [eo])
-AC_PREREQ(2.53)
-
-dnl make sure we are compiling from the correct sources
-AC_CONFIG_SRCDIR(src/eoOp.h)
-
-dnl define host, build, and target machine
-AC_CANONICAL_BUILD
-AC_CANONICAL_HOST
-AC_CANONICAL_TARGET
-
-dnl automake initialization
-AM_INIT_AUTOMAKE([gnu dist-bzip2 dist-zip])
-AM_CONFIG_HEADER(config.h)
-
-dnl Checks for programs.
-AC_PROG_CC
-AC_PROG_CXX
-AC_PROG_INSTALL
-AC_PROG_LN_S
-AC_PROG_MAKE_SET
-AC_PROG_RANLIB
-AC_PATH_PROG([AR], [ar], [false], [$PATH:/usr/ccs/bin]) # solaris-x86 needs extra path
-AC_ARG_VAR([DOXYGEN], [automatic documentation generation])
-AC_CHECK_PROGS([DOXYGEN], [doxygen], [true])
-
-dnl Checks for header files.
-AC_LANG(C++)
-AC_HEADER_STDC
-
-dnl Checks for typedefs, structures, and compiler characteristics.
-AC_CHECK_TYPES(uint32_t, [], AC_MSG_WARN([Need uint32_t from C99 standard.]))
-AC_TYPE_SIZE_T
-
-dnl Checks for libraries and library functions.
-AC_CHECK_LIB(m, cos)
-
-
-dnl Check for C++ library yaml-cpp (AC_CHEC_LIB only supports checking for C libraries)
-AC_MSG_CHECKING('libyaml-cpp available')
-AC_LANG(C++)
-SAVED_LDFLAGS=$LDFLAGS
-LDFLAGS="$LDFLAGS -lyaml-cpp"
-AC_LINK_IFELSE(
-    [AC_LANG_PROGRAM([#include <yaml-cpp/yaml.h>], [YAML::Emitter  dummy])],
-        [ AC_MSG_RESULT([yes])
-          SAVED_LDFLAGS="$SAVED_LDFLAGS -lyaml-cpp"
-          AC_DEFINE(HAVE_LIBYAML_CPP,1,[Define to 1 if you have libyaml-cpp installed]) ],
-        [AC_MSG_RESULT([no])])
-LDFLAGS=$SAVED_LDFLAGS
-
-
-
-dnl user-switches
-AC_APPLICATIONS
-AC_DEBUG
-AC_GNUPLOT
-AC_TUTORIAL
-
-dnl create makefiles
-AC_OUTPUT(Makefile \
-          app/Makefile \
-          app/mastermind/Makefile \
-          app/gprop/Makefile \
-          app/gpsymreg/Makefile \
-          contrib/Makefile \
-          doc/Makefile \
-          src/Makefile \
-          src/do/Makefile \
-          src/es/Makefile \
-          src/gp/Makefile \
-          src/ga/Makefile \
-          src/other/Makefile \
-          src/utils/Makefile \
-          src/moo/Makefile \
-          test/Makefile \
-          tutorial/Makefile \
-          tutorial/html/Makefile \
-          tutorial/Lesson1/Makefile \
-          tutorial/Lesson2/Makefile \
-          tutorial/Lesson3/Makefile \
-          tutorial/Lesson4/Makefile \
-          tutorial/Lesson5/Makefile \
-          tutorial/Templates/Makefile \
-          tutorial/pdf/Makefile)
diff --git a/eo/contrib/Makefile.am b/eo/contrib/Makefile.am
deleted file mode 100644
index e0137720..00000000
--- a/eo/contrib/Makefile.am
+++ /dev/null
@@ -1,9 +0,0 @@
-###############################################################################
-##
-## Makefile.am for eo/src
-##
-###############################################################################
-
-pkginclude_HEADERS	= eoAged.h eoDrawable.h
-
-EXTRA_DIST		= MGE/VirusOp.h MGE/eoInitVirus.h MGE/eoVirus.h
diff --git a/eo/doc/Makefile.am b/eo/doc/Makefile.am
deleted file mode 100644
index 885cfdb7..00000000
--- a/eo/doc/Makefile.am
+++ /dev/null
@@ -1,11 +0,0 @@
-## Makefile.am for eo/doc
-
-
-EXTRA_DIST 		= EO_EA2001.pdf LeCreusot.pdf eo.cfg index.h \
-			mainpage.html publications.html sflogo-hammer1.jpg
-
-doc:
-			cd $(srcdir) && $(DOXYGEN) eo.cfg
-
-clean-local:
-			cd $(srcdir) && rm -rf html latex man
diff --git a/eo/src/Makefile.am b/eo/src/Makefile.am
deleted file mode 100644
index 37817996..00000000
--- a/eo/src/Makefile.am
+++ /dev/null
@@ -1,146 +0,0 @@
-# Makefile.am for eo/src
-
-SUBDIRS 		= es ga gp do utils other moo
-
-lib_LIBRARIES 		= libeo.a
-
-libeo_a_SOURCES 	= eoFunctorStore.cpp \
-			eoPersistent.cpp \
-			eoPrintable.cpp \
-			eoCtrlCContinue.cpp \
-			eoParetoFitness.cpp \
-			eoScalarFitnessAssembled.cpp  
-
-
-pkginclude_HEADERS 	= eo \
-			EO.h \
-			apply.h \
-			eoAlgo.h \
-			eoBinaryFlight.h \
-			eoBitParticle.h \
-			eoBreed.h \
-			eoCellularEasyEA.h \
-			eoCloneOps.h \
-			eoCombinedContinue.h \
-			eoCombinedInit.h \
-			eoConstrictedVariableWeightVelocity.h \
-			eoConstrictedVelocity.h \
-			eoContinue.h \
-			eoCounter.h \
-			eoCtrlCContinue.h \
-			eoDetSelect.h \
-			eoDetTournamentSelect.h \
-			eoDistribUpdater.h \
-			eoDistribution.h \
-			eoDominanceMap.h \
-			eoEDA.h \
-			eoEasyEA.h \
-			eoEasyPSO.h \
-			eoEvalContinue.h \
-			eoEvalFunc.h \
-			eoEvalFuncCounter.h \
-			eoEvalFuncPtr.h \
-			eoFactory.h \
-			eoFitContinue.h \
-			eoFitnessScalingSelect.h \
-			eoFixedInertiaWeightedVelocity.h \
-			eoFlight.h \
-			eoFlOrBinOp.h \
-			eoFlOrMonOp.h \
-			eoFlOrQuadOp.h \
-			eoFunctor.h \
-			eoFunctorStore.h \
-			eoG3Replacement.h \
-			eoGaussRealWeightUp.h \
-			eoGenContinue.h \
-			eoGenOp.h \
-			eoGeneralBreeder.h \
-			eoInit.h \
-			eoInvalidateOps.h \
-			eoLinearDecreasingWeightUp.h  \
-			eoLinearFitScaling.h \
-			eoLinearTopology.h \
-			eoMGGReplacement.h \
-			eoMerge.h \
-			eoMergeReduce.h \
-			eoNDSorting.h \
-			eoNeighborhood.h \
-			eoObject.h \
-			eoOneToOneBreeder.h \
-			eoOp.h \
-			eoOpContainer.h \
-			eoOpSelMason.h \
-			eoParetoConstraintFitness.h \
-			eoParetoFitness.h \
-			eoParetoRanking.h \
-			eoParticleBestInit.h \
-			eoPerf2Worth.h \
-			eoPeriodicContinue.h \
-			eoPersistent.h \
-			eoPop.h \
-			eoPopAlgo.h \
-			eoPopEvalFunc.h \
-			eoPopulator.h \
-			eoPrintable.h \
-			eoPropGAGenOp.h \
-			eoProportionalCombinedOp.h \
-			eoProportionalSelect.h \
-			eoPSO.h \
-			eoRandomRealWeightUp.h \
-			eoRandomSelect.h \
-			eoRanking.h \
-			eoRankingSelect.h \
-			eoRealBoundModifier.h \
-			eoRealParticle.h \
-			eoReduce.h \
-			eoReduceMerge.h \
-			eoReduceMergeReduce.h \
-			eoReduceSplit.h \
-			eoReplacement.h \
-			eoSGA.h \
-			eoSGAGenOp.h \
-			eoSGATransform.h \
-			eoSTLFunctor.h \
-			eoScalarFitness.h \
-			eoScalarFitnessAssembled.cpp \
-			eoScalarFitnessAssembled.h \
-			eoSelect.h \
-			eoSelectFactory.h \
-			eoSelectFromWorth.h \
-			eoSelectMany.h \
-			eoSelectNumber.h \
-			eoSelectOne.h \
-			eoSelectPerc.h \
-			eoSequentialSelect.h \
-			eoSharing.h \
-			eoSharingSelect.h \
-			eoSigBinaryFlight.h \
-			eoSimpleEDA.h \
-			eoSocialNeighborhood.h \
-			eoStandardFlight.h \
-			eoStandardVelocity.h \
-			eoStarTopology.h \
-			eoSteadyFitContinue.h \
-			eoStochTournamentSelect.h \
-			eoStochasticUniversalSelect.h \
-			eoSurviveAndDie.h \
-			eoSyncEasyPSO.h \
-			eoTopology.h \
-			eoTransform.h \
-			eoTruncSelect.h \
-			eoTruncatedSelectMany.h \
-			eoTruncatedSelectOne.h \
-			eoVariableInertiaWeightedVelocity.h \
-			eoVariableLengthCrossover.h \
-			eoVariableLengthMutation.h \
-			eoVector.h \
-			eoVectorParticle.h \
-			eoVelocity.h \
-			eoVelocityInit.h \
-			eoWeightUpdater.h \
-			es.h \
-			ga.h \
-			PO.h \
-			eoTimeContinue.h
-
-AM_CXXFLAGS		= -I$(top_srcdir)/src
diff --git a/eo/src/do/Makefile.am b/eo/src/do/Makefile.am
deleted file mode 100644
index 3ec74729..00000000
--- a/eo/src/do/Makefile.am
+++ /dev/null
@@ -1,15 +0,0 @@
-pkginclude_HEADERS	= make_algo_easea.h \
-			make_algo_pareto.h \
-			make_algo_scalar.h \
-			make_checkpoint.h \
-			make_checkpoint_FDC.h \
-			make_checkpoint_assembled.h \
-			make_checkpoint_pareto.h \
-			make_continue.h \
-			make_continue_pareto.h \
-			make_general_replacement.h \
-			make_pop.h \
-			make_run.h
-
-
-EXTRA_DIST		= Readme
diff --git a/eo/src/eoDetTournamentSelect.h b/eo/src/eoDetTournamentSelect.h
old mode 100755
new mode 100644
diff --git a/eo/src/eoProportionalSelect.h b/eo/src/eoProportionalSelect.h
old mode 100755
new mode 100644
diff --git a/eo/src/eoSteadyFitContinue.h b/eo/src/eoSteadyFitContinue.h
old mode 100755
new mode 100644
diff --git a/eo/src/eoStochTournamentSelect.h b/eo/src/eoStochTournamentSelect.h
old mode 100755
new mode 100644
diff --git a/eo/src/eoStochasticUniversalSelect.h b/eo/src/eoStochasticUniversalSelect.h
old mode 100755
new mode 100644
diff --git a/eo/src/es/Makefile.am b/eo/src/es/Makefile.am
deleted file mode 100644
index d9c280df..00000000
--- a/eo/src/es/Makefile.am
+++ /dev/null
@@ -1,56 +0,0 @@
-## Makefile.am for eo/src/es
-
-lib_LIBRARIES 		= libes.a libcma.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
-
-esincludedir		= $(pkgincludedir)/es
-
-esinclude_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
-
-libcma_a_SOURCES	= eig.cpp \
-			CMAState.cpp \
-			CMAParams.cpp
-
-cmaincludedir		= $(pkgincludedir)/es
-
-cmainclude_HEADERS	=  CMAParams.h \
-			CMAState.h \
-			eig.h \
-			eoCMAInit.h \
-			eoCMABreed.h \
-			matrices.h 
-
-AM_CXXFLAGS		= -I$(top_srcdir)/src
diff --git a/eo/src/ga/Makefile.am b/eo/src/ga/Makefile.am
deleted file mode 100644
index 6429011e..00000000
--- a/eo/src/ga/Makefile.am
+++ /dev/null
@@ -1,32 +0,0 @@
-###############################################################################
-##
-## Makefile.am for eo/src/ga
-##
-###############################################################################
-
-AM_CXXFLAGS		= -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
-
-gaincludedir 		= $(pkgincludedir)/ga
-
-gainclude_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/gp/Makefile.am b/eo/src/gp/Makefile.am
deleted file mode 100644
index 9ebcdd23..00000000
--- a/eo/src/gp/Makefile.am
+++ /dev/null
@@ -1,11 +0,0 @@
-## Makefile.am for eo/src/gp
-
-gpincludedir 		= $(pkgincludedir)/gp
-
-gpinclude_HEADERS	= eoParseTreeDepthInit.h \
-			eoParseTree.h \
-			eoParseTreeOp.h \
-			eoStParseTreeDepthInit.h \
-			eoStParseTreeOp.h \
-			node_pool.h \
-			parse_tree.h
diff --git a/eo/src/moo/Makefile.am b/eo/src/moo/Makefile.am
deleted file mode 100644
index e829bd1f..00000000
--- a/eo/src/moo/Makefile.am
+++ /dev/null
@@ -1,18 +0,0 @@
-
-lib_LIBRARIES 		= libeomoo.a
-
-libeomoo_a_SOURCES 	= 	eoFrontSorter.cpp \
-				eoNSGA_IIa_Eval.cpp \
-				eoNSGA_II_Eval.cpp
-
-pkginclude_HEADERS 	=\
-eoEpsilonArchive.h\
-eoEpsMOEA.h\
-eoFrontSorter.h\
-eoMOEval.h\
-eoMOFitness.h\
-eoNSGA_I_Eval.h\
-eoNSGA_IIa_Eval.h\
-eoNSGA_II_Eval.h
-
-AM_CXXFLAGS		= -I$(top_srcdir)/src
diff --git a/eo/src/obsolete/Makefile.am b/eo/src/obsolete/Makefile.am
deleted file mode 100644
index 1a94e144..00000000
--- a/eo/src/obsolete/Makefile.am
+++ /dev/null
@@ -1,14 +0,0 @@
-###############################################################################
-##
-## Makefile.am for eo/src/obsolete
-##
-###############################################################################
-
-INCLUDES = -I$(top_builddir)/src
-
-lib_LIBRARIES = libeoobsolete.a
-libeoobsolete_a_SOURCES = eoParserUtils.cpp
-
-libeoobsoleteincdir = $(includedir)/eo/obsolete
-libeoobsoleteinc_HEADERS = eo1d.h eo1dWDistance.h eo2d.h eo2dVector.h eoAtomBitFlip.h eoAtomCreep.h eoAtomMutation.h eoAtomMutator.h eoAtomRandom.h eoBin.h eoBreeder.h eoCopyElite.h eoDetTournament.h eoDetTournamentIndiSelector.h eoDistance.h eoDup.h eoES.h eoESChrom.h eoESFullChrom.h eoESFullMut.h eoEsObjectiveBounds.h eoEvalFuncPtrCnt.h eoFitTerm.h eoFitness.h eoGenTerm.h eoGeneration.h eoID.h eoInclusion.h eoInsertion.h eoKill.h eoLottery.h eoMutation.h eoNegExp.h eoNonUniform.h eoNormal.h eoParser.h eoParserUtils.h eoPopOps.h eoProblem.h eoProportional.h eoRandomBreed.h eoRandomIndiSelector.h eoRandomSelect.h eoRank.h eoRnd.h eoScheme.h eoSelectRandom.h eoStochTournament.h eoStringMutation.h eoTerm.h eoTournament.h eoTranspose.h eoUniform.h eoUniformXOver.h eoVector.h eoXOver2.h  
-
diff --git a/eo/src/other/Makefile.am b/eo/src/other/Makefile.am
deleted file mode 100644
index 074966a3..00000000
--- a/eo/src/other/Makefile.am
+++ /dev/null
@@ -1,11 +0,0 @@
-## Makefile.am for eo/src/other
-
-
-AM_CXXFLAGS 		= -I$(top_builddir)/src
-
-otherincludedir 	= $(pkgincludedir)/other
-
-otherinclude_HEADERS 	= eoExternalEO.h \
-			eoString.h \
-			external_eo \
-			eoExternalOpFunctions.h
diff --git a/eo/src/utils/Makefile.am b/eo/src/utils/Makefile.am
deleted file mode 100644
index fc807253..00000000
--- a/eo/src/utils/Makefile.am
+++ /dev/null
@@ -1,58 +0,0 @@
-## Makefile.am for eo/src/utils
-
-lib_LIBRARIES 		= libeoutils.a
-
-libeoutils_a_SOURCES 	= eoData.cpp \
-			eoFileMonitor.cpp \
-			eoGnuplot.cpp \
-			eoGnuplot1DMonitor.cpp \
-			eoGnuplot1DSnapshot.cpp \
-			eoIntBounds.cpp \
-			eoParser.cpp \
-			eoRealBounds.cpp \
-			eoRNG.cpp \
-			eoState.cpp \
-			eoStdoutMonitor.cpp \
-			eoUpdater.cpp \
-			make_help.cpp \
-			pipecom.cpp
-
-utilsincludedir		= $(pkgincludedir)/utils
-
-utilsinclude_HEADERS 	= checkpointing \
-			compatibility.h \
-			eoAssembledFitnessStat.h \
-			eoCheckPoint.h \
-			eoData.h \
-			eoDistance.h \
-			eoFDCStat.h \
-			eoFileMonitor.h \
-			eoFileSnapshot.h \
-			eoGnuplot.h \
-			eoGnuplot1DMonitor.h \
-			eoGnuplot1DSnapshot.h \
-			eoHowMany.h \
-			eoMOFitnessStat.h \
-			eoMonitor.h \
-			eoParam.h \
-			eoParser.h \
-			eoPopStat.h \
-			eoRNG.h \
-			eoRealBounds.h \
-			eoIntBounds.h \
-			eoRealVectorBounds.h \
-			eoRndGenerators.h \
-			eoScalarFitnessStat.h \
-			eoStat.h \
-			eoState.h \
-			eoStdoutMonitor.h \
-			eoTimeCounter.h \
-			eoTimedMonitor.h \
-			eoUniformInit.h \
-			eoUpdatable.h \
-			eoUpdater.h \
-			pipecom.h \
-			rnd_generators.h \
-			selectors.h
-
-AM_CXXFLAGS 		= -I$(top_srcdir)/src -DGNUPLOT_PROGRAM=\"@GNUPLOT@\"
diff --git a/eo/stamp-h1 b/eo/stamp-h1
deleted file mode 100644
index 4547fe1b..00000000
--- a/eo/stamp-h1
+++ /dev/null
@@ -1 +0,0 @@
-timestamp for config.h
diff --git a/eo/test/Makefile.am b/eo/test/Makefile.am
deleted file mode 100644
index 80b87bde..00000000
--- a/eo/test/Makefile.am
+++ /dev/null
@@ -1,118 +0,0 @@
-###############################################################################
-##
-## Makefile.am for eo/test
-##
-###############################################################################
-LIBEO				= $(top_builddir)/src/libeo.a
-LIBEOUTILS			= $(top_builddir)/src/utils/libeoutils.a
-LIBES				= $(top_builddir)/src/es/libes.a
-LIBGA				= $(top_builddir)/src/ga/libga.a
-LIBCMA				= $(top_builddir)/src/es/libcma.a
-LIBMOO				= $(top_builddir)/src/moo/libeomoo.a
-
-# PLEASE don't break the line (see create_batch.sh)
-check_PROGRAMS 			= t-eoParetoFitness \
-				t-eoPareto \
-				t-eofitness \
-				t-eoRandom \
-				t-eobin \
-				t-eoVirus \
-				t-MGE \
-				t-MGE1bit \
-				t-MGE-control \
-				t-eoStateAndParser \
-				t-eoCheckpointing \
-				t-eoSSGA \
-				t-eoExternalEO \
-				t-eoSymreg \
-				t-eo \
-				t-eoReplacement \
-				t-eoSelect \
-				t-eoGenOp \
-				t-eoGA \
-				t-eoReal \
-				t-eoVector \
-				t-eoESAll \
-				t-eoPBIL \
-				t-eoFitnessAssembled \
-				t-eoFitnessAssembledEA \
-				t-eoRoulette \
-				t-eoSharing \
-				t-eoCMAES \
-				t-eoSecondsElapsedContinue\
-				t-eoRNG		\
-				t-eoEasyPSO \
-				t-eoNSGA \
-				t-eoFrontSorter \
-				t-eoEpsMOEA \
-				t-eoInt \
-				t-eoInitPermutation \
-				t-eoSwapMutation \
-				t-eoShiftMutation \
-				t-eoTwoOptMutation \
-				t-eoRingTopology	\
-				t-eoSyncEasyPSO
-
-TESTS				= $(check_PROGRAMS) \
-				run_tests # This script can be used to check command-line arguments
-
-noinst_HEADERS			= binary_value.h real_value.h RoyalRoad.h
-
-
-DEPS	 			= $(LIBGA) $(LIBES) $(LIBCMA) $(LIBEOUTILS) $(LIBEO) $(LIBMOO)
-INCLUDES			= -I$(top_srcdir)/src -I$(srcdir)/../src 
-LIBS	 			= $(DEPS)
-
-CLEANFILES 			= monitor.csv t-eoRandom.out
-EXTRA_DIST			= run_tests
-
-# extra flags for specific targets
-t_eoVirus_CXXFLAGS		= $(AM_CXXFLAGS) -I$(top_srcdir)/contrib
-t_MGE_CXXFLAGS 			= -I$(top_srcdir)/contrib/MGE
-t_MGE1bit_CXXFLAGS 		= -I$(top_srcdir)/contrib/MGE
-t_MGE_control_CXXFLAGS 		= -I$(top_srcdir)/contrib/MGE
-
-# Specify source-files,
-# otherwise automake/make looks for C sources
-#
-t_eoRandom_SOURCES 		= t-eoRandom.cpp
-t_eofitness_SOURCES 		= t-eofitness.cpp
-t_eoFitnessAssembledEA_SOURCES 	= t-eoFitnessAssembledEA.cpp
-t_eobin_SOURCES 		= t-eobin.cpp
-t_eoVirus_SOURCES 		= t-eoVirus.cpp
-t_MGE1bit_SOURCES 		= t-MGE1bit.cpp
-t_MGE_SOURCES 			= t-MGE.cpp
-t_MGE_control_SOURCES 		= t-MGE-control.cpp
-t_eoStateAndParser_SOURCES 	= t-eoStateAndParser.cpp
-t_eoCheckpointing_SOURCES 	= t-eoCheckpointing.cpp
-t_eoReplacement_SOURCES 	= t-eoReplacement.cpp
-t_eoSelect_SOURCES 		= t-eoSelect.cpp
-t_eoExternalEO_SOURCES 		= t-eoExternalEO.cpp
-t_eoSymreg_SOURCES 		= t-eoSymreg.cpp
-t_eo_SOURCES 			= t-eo.cpp
-t_eoGenOp_SOURCES 		= t-eoGenOp.cpp
-t_eoVector_SOURCES 		= t-eoVector.cpp
-t_eoGA_SOURCES 			= t-eoGA.cpp
-t_eoReal_SOURCES 		= t-eoReal.cpp
-t_eoESAll_SOURCES 		= t-eoESAll.cpp
-t_eoSSGA_SOURCES 		= t-eoSSGA.cpp
-t_eoPareto_SOURCES 		= t-eoPareto.cpp 
-t_eoParetoFitness_SOURCES 	= t-eoParetoFitness.cpp 
-t_eoPBIL_SOURCES 		= t-eoPBIL.cpp 
-t_eoFitnessAssembled_SOURCES 	= t-eoFitnessAssembled.cpp 
-t_eoRoulette_SOURCES 		= t-eoRoulette.cpp
-t_eoSharing_SOURCES 		= t-eoSharing.cpp
-t_eoCMAES_SOURCES		= t-eoCMAES.cpp
-t_eoRNG_SOURCES 		= t-eoRNG.cpp
-t_eoSecondsElapsedContinue_SOURCES 		= t-eoSecondsElapsedContinue.cpp
-t_eoEasyPSO_SOURCES		= t-eoEasyPSO.cpp
-t_eoNSGA_SOURCES		= t-eoNSGA.cpp
-t_eoFrontSorter_SOURCES		= t-eoFrontSorter.cpp
-t_eoEpsMOEA_SOURCES		= t-eoEpsMOEA.cpp
-t_eoInt_SOURCES			= t-eoInt.cpp
-t_eoInitPermutation_SOURCES	= t-eoInitPermutation.cpp
-t_eoSwapMutation_SOURCES        = t-eoSwapMutation.cpp
-t_eoShiftMutation_SOURCES	= t-eoShiftMutation.cpp
-t_eoTwoOptMutation_SOURCES	= t-eoTwoOptMutation.cpp
-t_eoRingTopology_SOURCES	= t-eoRingTopology.cpp
-t_eoSyncEasyPSO_SOURCES	= t-eoSyncEasyPSO.cpp
diff --git a/eo/tutorial/Lesson1/Makefile.am b/eo/tutorial/Lesson1/Makefile.am
deleted file mode 100644
index d74f0733..00000000
--- a/eo/tutorial/Lesson1/Makefile.am
+++ /dev/null
@@ -1,16 +0,0 @@
-
-noinst_PROGRAMS		= FirstBitGA FirstRealGA exercise1.3
-
-FirstBitGA_SOURCES	= FirstBitGA.cpp
-
-FirstRealGA_SOURCES	= FirstRealGA.cpp
-
-exercise1_3_SOURCES	= exercise1.3.cpp
-
-
-LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
-
-LIBS			=  -lga -leoutils -leo
-
-INCLUDES		= -I$(top_srcdir)/src
-
diff --git a/eo/tutorial/Lesson2/Makefile.am b/eo/tutorial/Lesson2/Makefile.am
deleted file mode 100644
index 44abb144..00000000
--- a/eo/tutorial/Lesson2/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-
-noinst_PROGRAMS		= FirstBitEA FirstRealEA exercise2.3
-
-
-FirstBitEA_SOURCES	= FirstBitEA.cpp
-
-FirstRealEA_SOURCES	= FirstRealEA.cpp
-
-exercise2_3_SOURCES	= exercise2.3.cpp
-
-
-noinst_HEADERS		= binary_value.h \
-			real_value.h
-
-extra_DIST		= Makefile.simple
-
-
-LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
-
-LIBS			=  -lga -leo -leoutils
-
-INCLUDES		= -I$(top_srcdir)/src
-
diff --git a/eo/tutorial/Lesson3/Makefile.am b/eo/tutorial/Lesson3/Makefile.am
deleted file mode 100644
index 50f53cd8..00000000
--- a/eo/tutorial/Lesson3/Makefile.am
+++ /dev/null
@@ -1,22 +0,0 @@
-
-noinst_PROGRAMS		= SecondBitEA SecondRealEA exercise3.1
-
-
-SecondBitEA_SOURCES	= SecondBitEA.cpp
-
-SecondRealEA_SOURCES	= SecondRealEA.cpp
-
-exercise3_1_SOURCES	= exercise3.1.cpp
-
-
-noinst_HEADERS		= binary_value.h \
-			real_value.h
-
-extra_DIST		= Makefile.simple
-
-
-LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
-
-LIBS			=  -lga -leoutils -leo
-
-INCLUDES		= -I$(top_srcdir)/src
diff --git a/eo/tutorial/Lesson4/Makefile.am b/eo/tutorial/Lesson4/Makefile.am
deleted file mode 100644
index 7b1c2dcc..00000000
--- a/eo/tutorial/Lesson4/Makefile.am
+++ /dev/null
@@ -1,26 +0,0 @@
-noinst_PROGRAMS		= BitEA RealEA ESEA
-
-
-BitEA_SOURCES		= BitEA.cpp
-
-RealEA_SOURCES		= RealEA.cpp
-
-ESEA_SOURCES		= ESEA.cpp
-
-
-noinst_HEADERS		= binary_value.h \
-			real_value.h
-
-extra_DIST		= Makefile.simple
-
-
-AM_CXXFLAGS		= -I$(top_srcdir)/src
-
-LIBEO			= $(top_builddir)/src/libeo.a
-LIBES			= $(top_builddir)/src/es/libes.a
-LIBGA			= $(top_builddir)/src/ga/libga.a
-LIBUTILS		= $(top_builddir)/src/utils/libeoutils.a
-
-DEPS			= $(LIBEO) $(LIBUTILS) $(LIBES) $(LIBGA)
-
-LIBS			= $(LIBES) $(LIBGA) $(LIBEO) $(LIBUTILS)
diff --git a/eo/tutorial/Lesson5/Makefile.am b/eo/tutorial/Lesson5/Makefile.am
deleted file mode 100644
index 110cfb08..00000000
--- a/eo/tutorial/Lesson5/Makefile.am
+++ /dev/null
@@ -1,28 +0,0 @@
-
-noinst_PROGRAMS		= OneMaxEA OneMaxLibEA
-
-OneMaxEA_SOURCES	= OneMaxEA.cpp
-
-OneMaxLibEA_SOURCES	= OneMaxLibEA.cpp make_OneMax.cpp
-
-
-noinst_HEADERS		= eoOneMax.h \
-			eoOneMaxEvalFunc.h \
-			eoOneMaxInit.h \
-			eoOneMaxMutation.h \
-			eoOneMaxQuadCrossover.h \
-			make_genotype_OneMax.h \
-			make_op_OneMax.h
-
-extra_DIST		= Makefile.simple
-
-AM_CXXFLAGS		= -I$(top_srcdir)/src
-
-LIBEO			= $(top_builddir)/src/libeo.a
-LIBES			= $(top_builddir)/src/es/libes.a
-LIBGA			= $(top_builddir)/src/ga/libga.a
-LIBUTILS		= $(top_builddir)/src/utils/libeoutils.a
-
-DEPS			= $(LIBEO) $(LIBUTILS) $(LIBES) $(LIBGA)
-
-LIBS			= $(LIBES) $(LIBGA) $(LIBEO) $(LIBUTILS)
diff --git a/eo/tutorial/Lesson6/Makefile.am b/eo/tutorial/Lesson6/Makefile.am
deleted file mode 100644
index 460fae7a..00000000
--- a/eo/tutorial/Lesson6/Makefile.am
+++ /dev/null
@@ -1,19 +0,0 @@
-
-noinst_PROGRAMS		= BinaryPSO RealPSO
-
-
-SecondBitEA_SOURCES	= BinaryPSO.cpp
-
-SecondRealEA_SOURCES	= RealPSO.cpp
-
-
-noinst_HEADERS		= 
-
-extra_DIST		= Makefile.simple
-
-
-LDADD			= -L$(top_builddir)/src 
-
-LIBS			=  -leoutils -leo
-
-INCLUDES		= -I$(top_srcdir)/src
diff --git a/eo/tutorial/Makefile.am b/eo/tutorial/Makefile.am
deleted file mode 100644
index 41f6058d..00000000
--- a/eo/tutorial/Makefile.am
+++ /dev/null
@@ -1,2 +0,0 @@
-SUBDIRS = html Lesson1 Lesson2 Lesson3 Lesson4 Lesson5 pdf Templates
-
diff --git a/eo/tutorial/Templates/Makefile.am b/eo/tutorial/Templates/Makefile.am
deleted file mode 100644
index c7c30ced..00000000
--- a/eo/tutorial/Templates/Makefile.am
+++ /dev/null
@@ -1,15 +0,0 @@
-EXTRA_DIST	= EO.tpl \
-		eoMyStruct.tmpl \
-		evalFunc.tmpl \
-		init.tmpl \
-		mutation.tmpl \
-		quadCrossover.tmpl \
-		MyStructSEA.cpp \
-		stat.tmpl \
-		README \
-		README.manual \
-		README.tmpl \
-		configure.ac.tmpl \
-		Makefile.am.top-tmpl \
-		Makefile.am.src-tmpl \
-		createEOproject.sh
diff --git a/eo/tutorial/html/Makefile.am b/eo/tutorial/html/Makefile.am
deleted file mode 100644
index 0191bbef..00000000
--- a/eo/tutorial/html/Makefile.am
+++ /dev/null
@@ -1,44 +0,0 @@
-EXTRA_DIST 	= BitEA.html \
-		EA_tutorial.jpg \
-		FirstBitEA.html \
-		FirstBitGA.html \
-		FirstRealEA.html \
-		FirstRealGA.html \
-		Firstmerge.html \
-		NoWay.html \
-		OneMaxEA.html \
-		SecondBitEA.html \
-		SecondRealEA.html \
-		beige009.jpg \
-		binary_value.html \
-		debut.html \
-		eoBottomUp.html \
-		eoCheckPoint.html \
-		eoEngine.html \
-		eoEval.html \
-		eoGeneration.html \
-		eoInit.html \
-		eoIo.html \
-		eoLesson1.html \
-		eoLesson2.html \
-		eoLesson3.html \
-		eoLesson4.html \
-		eoLesson5.html \
-		eoOneMax.html \
-		eoOneMaxEvalFunc.html \
-		eoOneMaxInit.html \
-		eoOneMaxMutation.html \
-		eoOneMaxQuadCrossover.html \
-		eoOneMax_complete.html \
-		eoOperators.html \
-		eoOutput.html \
-		eoProgramming.html \
-		eoRepresentation.html \
-		eoSGA.html \
-		eoSelect.html \
-		eoStop.html \
-		eoTopDown.html \
-		eoTutorial.html \
-		make_genotype_OneMax.html \
-		make_op_OneMax.html \
-		real_value.html
diff --git a/eo/tutorial/pdf/Makefile.am b/eo/tutorial/pdf/Makefile.am
deleted file mode 100644
index 363f857f..00000000
--- a/eo/tutorial/pdf/Makefile.am
+++ /dev/null
@@ -1 +0,0 @@
-EXTRA_DIST 	= 
diff --git a/eo/win/Makefile.am b/eo/win/Makefile.am
deleted file mode 100644
index fdb0ff6c..00000000
--- a/eo/win/Makefile.am
+++ /dev/null
@@ -1,7 +0,0 @@
-EXTRA_DIST		= eo.sln \
-			EO/eo.vcproj \
-			ES/es.vcproj \
-			GA/ga.vcproj \
-			UTILS/utils.vcproj \
-			README \
-			lib/Readme