fix 'make dist', works now (besides ParadisEO).

eo/.cvsignore

@@ -6,6 +6,7 @@ Makefile
 Makefile.in
 aclocal.m4
 autom4te.cache
+build*
 confdefs.h
 config.cache
 config.cache

eo/app/Makefile.am

@@ -5,13 +5,3 @@
 ###############################################################################
 
 SUBDIRS = mastermind gpsymreg 
-
-###############################################################################
-
-all:
-	for i in $(SUBDIRS); do cd $$i && $(MAKE) all; cd ..; done
-
-clean:
-	for i in $(SUBDIRS); do cd $$i && $(MAKE) clean; cd ..; done
-
-###############################################################################

eo/app/gpsymreg/Makefile.am

@@ -4,14 +4,17 @@
 #
 ###############################################################################
 
+bin_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
 
-
-bin_PROGRAMS = gpsymreg
-
 AM_CXXFLAGS		= -I$(top_builddir)/src
 DEPS 			= $(LIBEOUTILS) $(LIBEO)
-LIBS 		=  $(top_builddir)/src/utils/libeoutils.a
+LIBS 			= $(LIBEOUTILS) $(LIBEO)
 
-gpsymreg_SOURCES = main.cpp

eo/app/mastermind/Makefile.am

@@ -4,22 +4,15 @@
 #
 ###############################################################################
 
-DEPS = $(top_builddir)/src/libeo.a $(top_builddir)/src/utils/libeoutils.a
-
-###############################################################################
-
-INCLUDES = -I$(top_builddir)/src -I$(top_srcdir)/src
-LDADDS = $(top_builddir)/src/libeo.a $(top_builddir)/src/utils/libeoutils.a
-
-###############################################################################
-
 bin_PROGRAMS 		= mastermind
 
-###############################################################################
-
 mastermind_SOURCES 	= mastermind.cpp
-mastermind_DEPENDENCIES = $(DEPS)
-mastermind_LDFLAGS = -lm
-mastermind_LDADD = $(LDADDS)
 
-###############################################################################
+noinst_HEADERS		= mastermind.h
+
+LIBEO			= $(top_builddir)/src/libeo.a
+LIBEOUTILS		= $(top_builddir)/src/utils/libeoutils.a
+
+AM_CXXFLAGS		= -I$(top_srcdir)/src
+DEPS 			= $(LIBEOUTILS) $(LIBEO)
+LIBS			= $(LIBEOUTILS) $(LIBEO)

eo/contrib/Makefile.am

@@ -4,6 +4,6 @@
 ##
 ###############################################################################
 
-SUBDIRS = 
-
 pkginclude_HEADERS	= eoAged.h eoDrawable.h
+
+EXTRA_DIST		= MGE/VirusOp.h MGE/eoInitVirus.h MGE/eoVirus.h

eo/src/utils/Makefile.am

@@ -6,10 +6,6 @@
 
 lib_LIBRARIES = libeoutils.a
 
-
-AM_CXXFLAGS 		= -I$(top_srcdir)/src
-
-
 libeoutils_a_SOURCES 	= eoParser.cpp \
 			eoRNG.cpp \
 			eoState.cpp \
@@ -19,6 +15,8 @@ libeoutils_a_SOURCES 	= eoParser.cpp \
 			eoRealBounds.cpp \
 			make_help.cpp
 
-libeoincdir 		= $(includedir)/eo/utils
+pkginclude_HEADERS 	= checkpointing $(srcdir)/*.h
 
-libeoinc_HEADERS 	= checkpointing $(srcdir)/*.h
+AM_CXXFLAGS 		= -I$(top_srcdir)/src
+
+EXTRA_DIST		= *.h

eo/src/utils/eoRealBounds.cpp

@@ -3,8 +3,11 @@
 #pragma warning(disable:4786)
 #endif 
 
-#include <ctime>
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
 
+#include <ctime>
 #ifdef HAVE_SSTREAM
 #include <sstream>
 #else

eo/src/utils/eoState.cpp

@@ -1,11 +1,13 @@
-
 #ifdef _MSC_VER
 #pragma warning(disable:4786)
 #endif
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <algorithm>
 #include <fstream>
-
 #ifdef HAVE_SSTREAM
 #include <sstream>
 #else

eo/src/utils/eoUpdater.cpp

@@ -2,6 +2,10 @@
 #pragma warning(disable:4786)
 #endif
 
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #ifdef HAVE_SSTREAM
 #include <sstream>
 #else

eo/test/Makefile.am

@@ -11,11 +11,11 @@ LIBGA		= $(top_builddir)/src/ga/libga.a
 
 AM_CXXFLAGS			= -g -Wall -I$(top_srcdir)/src 
 
-CLEANFILES 	= *~ *.sav *.status monitor.csv t-eoRandom.out
+CLEANFILES 			= monitor.csv t-eoRandom.out
 
 DEPS	 			= $(LIBGA) $(LIBES) $(LIBEO) $(LIBEOUTILS)
 
-LDADD	 	= $(DEPS)
+LIBS	 			= $(DEPS)
 
 
 
@@ -62,3 +62,6 @@ t_eoPBIL_SOURCES = t-eoPBIL.cpp
 t_eoFitnessAssembled_SOURCES 	= t-eoFitnessAssembled.cpp 
 t_eoRoulette_SOURCES 		= t-eoRoulette.cpp
 t_eoSharing_SOURCES 		= t-eoSharing.cpp
+
+# extra flags for specific targets
+t_eoVirus_CXXFLAGS		= -I$(top_srcdir)/contrib

eo/test/t-eoVirus.cpp

@@ -25,9 +25,9 @@
 
 #include <iostream>   // std::cout
 #include <eo>         // general EO
-#include "../contrib/MGE/VirusOp.h"
+#include "MGE/VirusOp.h"
-#include "../contrib/MGE/eoVirus.h"
+#include "MGE/eoVirus.h"
-#include "../contrib/MGE/eoInitVirus.h"
+#include "MGE/eoInitVirus.h"
 #include <utils/eoRndGenerators.h>
 
 #include "binary_value.h"

eo/tutorial/Lesson5/Makefile.am

@@ -16,10 +16,7 @@ noinst_HEADERS		= eoOneMax.h \
 
 extra_DIST		= Makefile.simple
 
-
+AM_CXXFLAGS		= -I$(top_srcdir)/src
 LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
-
 LIBS			=  -lga -leoutils -leo
 
-INCLUDES		= -I$(top_srcdir)/src
-