diff --git a/eo/Makefile.am b/eo/Makefile.am
index ae03e3c9..9e6eb03a 100644
--- a/eo/Makefile.am
+++ b/eo/Makefile.am
@@ -4,7 +4,8 @@
 ##
 ###############################################################################
 
-SUBDIRS = src test app tutorial
+SUBDIRS = src test doc app tutorial contrib win
+
 
 #Directory for documents
 DOCDIR = ~/public_html/eodocs
@@ -12,9 +13,6 @@ DOCDIR = ~/public_html/eodocs
 #Directory for indices -- not useful for the user
 IDXDIR = ~/index
 
-# EXTRA_DIST=LICENSE 
-
-
 
 # special targets
 app:
@@ -24,10 +22,6 @@ app:
 doc:    doc/eo.cfg
 	cd doc; $(MAKE) doc; touch eo.cfg; cd ..
 
-tutorial:
-	cd $(srcdir)/tutorial; $(MAKE) all; cd ..
-
-
 
 
 
@@ -35,12 +29,3 @@ tutorial:
 
 #lib:	
 #	cd src; $(MAKE) all; cd ..
-
-
-#all:
-#	for i in $(SUBDIRS); do cd $$i && $(MAKE) all; cd ..; done
-
-#clean:
-#	for i in $(SUBDIRS); do cd $$i && $(MAKE) clean; cd ..; done
-
-###############################################################################
diff --git a/eo/configure.in b/eo/configure.in
index d705abf9..8af929c9 100644
--- a/eo/configure.in
+++ b/eo/configure.in
@@ -39,6 +39,11 @@ AC_CHECK_FUNCS(select)
 
 dnl create makefiles
 AC_OUTPUT(Makefile \
+          app/Makefile \
+          app/mastermind/Makefile \
+          app/gpsymreg/Makefile \
+          contrib/Makefile \
+          doc/Makefile \
           src/Makefile \
           src/do/Makefile \
           src/es/Makefile \
@@ -46,9 +51,6 @@ AC_OUTPUT(Makefile \
           src/ga/Makefile \
           src/other/Makefile \
           src/utils/Makefile \
-          contrib/Makefile \
-          doc/Makefile \
-          win/Makefile \
           test/Makefile \
           tutorial/Makefile \
           tutorial/Lesson1/Makefile \
@@ -56,6 +58,4 @@ AC_OUTPUT(Makefile \
           tutorial/Lesson3/Makefile \
           tutorial/Lesson4/Makefile \
           tutorial/Lesson5/Makefile \
-          app/Makefile \
-          app/mastermind/Makefile \
-          app/gpsymreg/Makefile)
+          win/Makefile)
diff --git a/eo/contrib/Makefile.am b/eo/contrib/Makefile.am
index d9268a84..f0faf747 100644
--- a/eo/contrib/Makefile.am
+++ b/eo/contrib/Makefile.am
@@ -6,8 +6,4 @@
 
 SUBDIRS = 
 
-#lib_LIBRARIES = 
-#libeo_a_SOURCES =
-
-libeoincdir = $(includedir)/eo
-libeoinc_HEADERS=eoAged.h eoDraw.h
+pkginclude_HEADERS	= eoAged.h eoDrawable.h
diff --git a/eo/doc/Makefile.am b/eo/doc/Makefile.am
index 64f03e40..c3140794 100644
--- a/eo/doc/Makefile.am
+++ b/eo/doc/Makefile.am
@@ -4,12 +4,11 @@
 ##
 ###############################################################################
 
-###############################################################################
 
-EXTRA_DIST = eo.cfg foot.html html/* latex/*
+# EXTRA_DIST = eo.cfg foot.html html/* latex/*
 
-doc:	eo.cfg
-	doxygen eo.cfg
+doc:			eo.cfg
+			doxygen eo.cfg
 
-clean:
-	rm -rf html latex man
+clean-local:
+			rm -rf html latex man
diff --git a/eo/src/Makefile.am b/eo/src/Makefile.am
index f6f9280e..42772c24 100644
--- a/eo/src/Makefile.am
+++ b/eo/src/Makefile.am
@@ -4,20 +4,19 @@
 ##
 ###############################################################################
 
-SUBDIRS 	= es ga gp utils other do
+SUBDIRS 		= es ga gp utils other do
 
-AM_CXXFLAGS	= -I$(top_srcdir)/src
 
-lib_LIBRARIES = libeo.a
+lib_LIBRARIES 		= libeo.a
 
-libeo_a_SOURCES = eoFunctorStore.cpp \
-		eoPersistent.cpp
-		eoPrintable.cpp \
-		eoCtrlCContinue.cpp \
-		eoParetoFitness.cpp \
-		eoScalarFitnessAssembled.cpp  
+libeo_a_SOURCES 	= eoFunctorStore.cpp \
+			eoPersistent.cpp \
+			eoPrintable.cpp \
+			eoCtrlCContinue.cpp \
+			eoParetoFitness.cpp \
+			eoScalarFitnessAssembled.cpp  
 
-libeoincdir = $(includedir)/eo
+pkginclude_HEADERS 	= eo *.h do/*.h 
 
-libeoinc_HEADERS = $(srcdir)/*.h $(srcdir)/eo $(srcdir)/do/*.h 
 
+AM_CXXFLAGS		= -I$(top_srcdir)/src
diff --git a/eo/src/es/Makefile.am b/eo/src/es/Makefile.am
index e8648910..ae6d7d0f 100644
--- a/eo/src/es/Makefile.am
+++ b/eo/src/es/Makefile.am
@@ -4,9 +4,6 @@
 ##
 ###############################################################################
 
-AM_CXXFLAGS		= -I$(top_srcdir)/src
-
-
 lib_LIBRARIES 		= libes.a
 
 libes_a_SOURCES 	= make_algo_scalar_es.cpp \
@@ -24,9 +21,7 @@ libes_a_SOURCES 	= make_algo_scalar_es.cpp \
 			make_run_es.cpp \
 			make_run_real.cpp
 
-libeoincdir 		= $(includedir)/eo/es
-
-libeoinc_HEADERS 	= eoEsChromInit.h \
+pkginclude_HEADERS 	= eoEsChromInit.h \
 			eoEsFull.h \
 			eoEsGlobalXover.h \
 			eoEsMutate.h \
diff --git a/eo/win/Makefile.am b/eo/win/Makefile.am
index 13426269..88b4fcc2 100644
--- a/eo/win/Makefile.am
+++ b/eo/win/Makefile.am
@@ -1,4 +1 @@
-
-EXTRA_DIST=eo.dsw eo.dsp
-
-
+EXTRA_DIST		= eo.dsw eo.dsp