Maarten was right

eo/src/eoAtomCreep.h

@@ -25,7 +25,7 @@
 #ifndef _EOATOMCREEP_H
 #define _EOATOMCREEP_H
 
-#include <eoRNG.h>
+#include <utils/eoRNG.h>
 #include <eoAtomMutator.h>
 
 /** With uniform probability, decrements or increments by one the value.

eo/src/eoAtomMutation.h

@@ -30,7 +30,7 @@
 // EO includes
 #include <eoOp.h>
 #include <eoUniform.h>
-#include <eoRNG.h>
+#include <utils/eoRNG.h>
 #include <eoAtomMutator.h>
 
 /** Atomic mutation of an EO. Acts on containers, and applies a mutation

eo/src/eoGOpSelector.h

@@ -34,7 +34,7 @@
 #include <list>
 #include "eoOpSelector.h"
 #include "eoWrappedOps.h" // for eoCombinedOp
-#include "eoRNG.h"
+#include <utils/eoRNG.h>
 
 using namespace std;
 

eo/src/eoWrappedOps.h

@@ -32,7 +32,7 @@
 //-----------------------------------------------------------------------------
 
 #include <eoOp.h>          // eoOp, eoMonOp, eoBinOp
-#include "eoRNG.h"
+#include <utils/eoRNG.h>
 
 using namespace std;
 

eo/src/es/eoESFullChrom.h

@@ -34,7 +34,7 @@
 
 // EO includes
 #include <eoVector.h>
-#include <eoRNG.h>
+#include <utils/eoRNG.h>
 /**@name Chromosomes for evolution strategies
 Each chromosome in an evolution strategies is composed of a vector of floating point
 values plus a vector of sigmas, that are added to them during mutation and a vector of correlations
@@ -84,7 +84,7 @@ class eoESFullChrom  : public eoVector<double, fitT> {
   /* And now the useful constructor: from a parser (should be in the
      factory, if such a thing exists one day for eoESFullChrom 
    */
-  eoESFullChrom(Parser & parser) : StdDev(0), CorCff(0) {
+  eoESFullChrom(eoParser & parser) : StdDev(0), CorCff(0) {
     parser.AddTitle("Description of ES individuals");
     int num_genes, num_sigma;
     bool correlated_mutations;

eo/src/es/eoESFullMut.h

@@ -29,11 +29,11 @@
 #ifndef _EOESMUT_H
 #define _EOESMUT_H
 
-#include <eoParser.h>
+#include <utils/eoParser.h>
-#include <eoRNG.h>
+#include <utils/eoRNG.h>
 #include <cmath>		// for exp
 
-#include <eoESFullChrom.h>
+#include <es/eoESFullChrom.h>
 #include <eoOp.h>
 
 #ifndef M_PI

eo/test/Makefile.am

@@ -9,7 +9,7 @@ EXTRA_DIST = LICENSE
 
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src -I$(top_builddir)/src/es -I$(top_builddir)/src/ga -I$(top_builddir)/src/gp -I$(top_builddir)/src/obsolete -I$(top_builddir)/src/utils
+INCLUDES = -I$(top_builddir)/src
 LDADDS = $(top_builddir)/src/libeo.a $(top_builddir)/src/obsolete/libeoobsolete.a $(top_builddir)/src/utils/libeoutils.a
 
 ###############################################################################
@@ -18,7 +18,7 @@ noinst_PROGRAMS = t-eobreeder t-eoinclusion t-eoinsertion t-eo t-eofitness \
 	t-eoproblem t-eobin t-eolottery t-eo2dVector t-eogeneration t-eoEasyEA\
 	t-eoNonUniform t-eoUniform t-eoRandom t-parser t-eoESFull t-eoESOps\
 	t-eoAtomOps t-selectOne t-eoaltbreeder t-eoGeneralOps t-eoGOpSel \
-	t-eoVector
+	t-eoVector t-eoCheckpointing
 
 ###############################################################################
 
@@ -177,3 +177,10 @@ t_parser_LDFLAGS = -lm
 t_parser_LDADD = $(LDADDS) 
 
 ###############################################################################
+
+t_eoCheckpointing_SOURCES = t-eoCheckpointing.cpp
+t_eoCheckpointing_DEPENDENCIES = $(DEPS) 
+t_eoCheckpointing_LDFLAGS = -lm 
+t_eoCheckpointing_LDADD = $(LDADDS) 
+
+###############################################################################

eo/test/real_value.h

@@ -1,4 +1,4 @@
-#include <eoESFullChrom.h>
+#include <es/eoESFullChrom.h>
 
 //-----------------------------------------------------------------------------
 

eo/test/t-eoAtomOps.cpp

@@ -42,7 +42,7 @@ using namespace std;
 #include <eoAtomMutation.h>
 
 // Several EOs
-#include <eoString.h>
+#include <other/eoString.h>
 
 // RNGs
 #include <eoNegExp.h>

eo/test/t-eoESFull.cpp

@@ -32,7 +32,7 @@ main(int argc, char *argv[]) {
 //  bool comma;
 
   // Create the command-line parser
-  Parser parser( argc, argv, "Basic EA for vector<float> with adaptive mutations");
+  eoParser parser( argc, argv, "Basic EA for vector<float> with adaptive mutations");
 
   // Define Parameters and load them
   eoValueParam<uint32>& seed        = parser.createParam(time(0), "seed", "Random number seed");

eo/test/t-eoESOps.cpp

@@ -11,16 +11,16 @@
 using namespace std;
 
 // general
-#include <eoParser.h>            // though contained in all others!
+#include <utils/eoParser.h>            // though contained in all others!
 // evolution specific
 #include <eoEvalFuncPtr.h>
 //#include <eoSequentialOpHolder.h>
 //#include <eoFullEA.h>
 // representation specific
 
-#include <eoESFullChrom.h>            // though contained in following
+#include <es/eoESFullChrom.h>            // though contained in following
 //#include <eoESReco.h>
-#include <eoESFullMut.h>
+#include <es/eoESFullMut.h>
 //#include <eoESRandomize.h>
 // this fitness
 #include "real_value.h"		// the sphere fitness

eo/test/t-eoGOpSel.cpp

@@ -28,9 +28,9 @@
 // to avoid long name warnings
 #pragma warning(disable:4786)
 
-#include "eoBin.h"  // eoBin, eoPop, eoBreeder
+#include <ga/eoBin.h>  // eoBin, eoPop, eoBreeder
 #include <eoPop.h>
-#include <eoBitOp.h>
+#include <ga/eoBitOp.h>
 #include <eoProportionalGOpSel.h>
 //#include <eoAltBreeder.h>
 

eo/test/t-eoGeneralOps.cpp

@@ -43,7 +43,7 @@ using namespace std;
 #include <eoAtomMutation.h>
 
 // Several EOs
-#include <eoString.h>
+#include <other/eoString.h>
 
 // generalOp we are testing
 #include <eoGeneralOp.h>

eo/test/t-eobreeder.cpp

@@ -27,9 +27,9 @@
 // to avoid long name warnings
 #pragma warning(disable:4786)
 
-#include <eoBin.h>  // eoBin, eoPop, eoBreeder
+#include <ga/eoBin.h>  // eoBin, eoPop, eoBreeder
 #include <eoPop.h>
-#include <eoBitOp.h>
+#include <ga/eoBitOp.h>
 #include <eoProportionalOpSel.h>
 #include <eoBreeder.h>
 

eo/test/t-eoinclusion.cpp

@@ -2,7 +2,7 @@
 // t-eoinclusion.cpp
 //-----------------------------------------------------------------------------
 
-#include <eoBin.h>
+#include <ga/eoBin.h>
 #include <eoPop.h>
 #include <eoInclusion.h>
 

eo/test/t-parser.cpp

@@ -7,11 +7,11 @@
  (c) geneura team, 1999
 -----------------------------------------------------------------------------*/
 
-#include <eoParser.h>
+#include <utils/eoParser.h>
-#include <eoRNG.h>
+#include <utils/eoRNG.h>
 #include <sys/time.h>
 
-void GetOutputParam(Parser & parser, 
+void GetOutputParam(eoParser & parser, 
 		    string & _string) {
 
   try {

eo/test/t-selectOne.cpp

@@ -27,9 +27,9 @@
 // to avoid long name warnings
 #pragma warning(disable:4786)
 
-#include <eoBin.h>  // eoBin, eoPop, eoBreeder
+#include <ga/eoBin.h>  // eoBin, eoPop, eoBreeder
 #include <eoPop.h>
-#include <eoBitOp.h>
+#include <ga/eoBitOp.h>
 
 #include <eoUniformSelect.h>
 #include <eoStochTournament.h>