Fix file extensions

CMakeLists.txt

@@ -24,7 +24,7 @@ SET(LIBRARY_OUTPUT_PATH
   "Built libraries are placed here before installation."
 )
 
-INCLUDE_DIRECTORIES(../Empirical/source)
+INCLUDE_DIRECTORIES(../Empirical/include/emp)
 
 ADD_SUBDIRECTORY(libs/apto)
 if(NOT WIN32 AND NOT DEFINED ENV{AVIDA_DISABLE_BACKTRACE})
@@ -34,7 +34,7 @@ IF(NOT WIN32)
   ADD_SUBDIRECTORY(libs/tcmalloc-1.4)
 ENDIF(NOT WIN32)
 ADD_SUBDIRECTORY(avida-core)
-#ADD_SUBDIRECTORY(../Empirical/source/ .)
+# ADD_SUBDIRECTORY(../Empirical/include/emp .)
 
 # Default location for installed software/configs/ docs is the build directory.
 SET(CMAKE_INSTALL_PREFIX

avida-core/source/main/cWorld.h

@@ -33,15 +33,15 @@
 #include "avida/core/InstructionSequence.h"
 #include "avida/core/Genome.h"
 
-#include "Evolve/Systematics.h"
-#include "Evolve/SystematicsAnalysis.h"
-#include "Evolve/OEE.h"
-#include "control/Signal.h"
-#include "control/SignalControl.h"
-#include "tools/memo_function.h"
-#include "base/Ptr.h"
-#include "base/vector.h"
-#include "data/DataFile.h"
+#include "Evolve/Systematics.hpp"
+#include "Evolve/SystematicsAnalysis.hpp"
+#include "Evolve/OEE.hpp"
+#include "control/Signal.hpp"
+#include "control/SignalControl.hpp"
+#include "functional/memo_function.hpp"
+#include "base/Ptr.hpp"
+#include "base/vector.hpp"
+#include "data/DataFile.hpp"
 
 #include <array>
 #include <cassert>