Index: src/Makefile.am
===================================================================
--- src/Makefile.am	(revision a10cc029b85f24d56d1c8a1dd7fe5048f9d8f9df)
+++ src/Makefile.am	(revision 7da5cd8f40af510421808552471affe096db4402)
@@ -258,5 +258,5 @@
 libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER} 
 noinst_LIBRARIES = libmenu.a
-bin_PROGRAMS += molecuilder joiner analyzer Controller PoolWorker Server 
+bin_PROGRAMS += molecuilder joiner analyzer PoolWorker Server 
 EXTRA_PROGRAMS = unity
 
@@ -361,25 +361,10 @@
 CONTROLLERSOURCE = \
         controller_MPQCCommandJob.cpp \
-        ControllerCommandRegistry.cpp \
-        ControllerOptions.cpp \
-        ControllerOptions_MPQCCommandJob.cpp \
-        DefaultOptions.cpp
+        ControllerOptions_MPQCCommandJob.cpp
 
 CONTROLLERHEADER = \
-        controller_AddOn.hpp \
         controller_MPQCCommandJob.hpp \
-        ControllerCommand.hpp \
-        ControllerCommandRegistry.hpp \
-        ControllerOptions.hpp \
-        ControllerOptions_MPQCCommandJob.hpp \
-        DefaultOptions.hpp
-
-EXTRA_DIST += \
-	controller_AddOn_SystemCommandJob.cpp \
-        controller_SystemCommandJob.cpp \
-        controller_SystemCommandJob.hpp \
-        ControllerOptions_SystemCommandJob.cpp \
-        ControllerOptions_SystemCommandJob.hpp
-	
+        ControllerOptions_MPQCCommandJob.hpp
+
 
 noinst_LTLIBRARIES += libFragmentationAutomationController.la
@@ -390,78 +375,39 @@
         $(top_builddir)/JobMarket/src/JobMarket/libJobMarket.la
 
-POOLWORKERSOURCE = \
-        DefaultOptions.cpp \
-        SignalHandler.cpp \
-        SignalOptions.cpp \
-        WorkerOptions.cpp
-
-POOLWORKERHEADER = \
-        DefaultOptions.hpp \
-        SignalHandler.hpp \
-        SignalOptions.hpp \
-        WorkerOptions.hpp
-
-lib_LTLIBRARIES += libFragmentationAutomationPoolWorker.la
-libFragmentationAutomationPoolWorker_la_includedir = $(includedir)/MoleCuilder/JobMarket
-nobase_libFragmentationAutomationPoolWorker_la_include_HEADERS = $(POOLWORKERHEADER)
-libFragmentationAutomationPoolWorker_la_SOURCES = $(POOLWORKERSOURCE)
-libFragmentationAutomationPoolWorker_la_LIBADD = \
-        $(top_builddir)/JobMarket/src/JobMarket/libJobMarket.la
-
-SERVERSOURCE = \
-        DefaultOptions.cpp \
-        ServerOptions.cpp \
-        SignalHandler.cpp \
-        SignalOptions.cpp
-
-SERVERHEADER = \
-        DefaultOptions.hpp \
-        ServerOptions.hpp \
-        SignalHandler.hpp \
-        SignalOptions.hpp
-
-noinst_LTLIBRARIES += libFragmentationAutomationServer.la
-libFragmentationAutomationServer_la_includedir = $(includedir)/MoleCuilder/JobMarket
-nobase_libFragmentationAutomationServer_la_include_HEADERS = $(SERVERHEADER)
-libFragmentationAutomationServer_la_SOURCES = $(SERVERSOURCE)
-libFragmentationAutomationServer_la_LIBADD = \
-        $(top_builddir)/JobMarket/src/JobMarket/libJobMarket.la
-
 bin_PROGRAMS += Controller PoolWorker Server
 
-Controller_SOURCES = controller.cpp controller_main.cpp controller_main.hpp controller_AddOn_MPQCCommandJob.cpp
-Controller_LDFLAGS = $(AM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS)
+Controller_SOURCES = controller.cpp controller_AddOn_MPQCCommandJob.cpp
+Controller_LDFLAGS = $(AM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) ${CodePatterns_LDFLAGS}
 Controller_CXXFLAGS = $(AM_CPPFLAGS)
 Controller_LDADD = \
+	libFragmentationAutomationController.la \
         libMolecuilderJobs.la \
-        libFragmentationAutomationController.la \
 	libMolecuilderFragmentation.la \
 	libMolecuilderHelpers.la \
+        $(top_builddir)/JobMarket/src/JobMarket/libJobMarketController.la \
         $(top_builddir)/JobMarket/src/JobMarket/libJobMarket.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
-	${CodePatterns_LIBS} \
-	$(BOOST_PROGRAM_OPTIONS_LIBS)
-
-PoolWorker_SOURCES = poolworker.cpp poolworker_main.cpp poolworker_main.hpp
-PoolWorker_LDFLAGS = $(AM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS)
+	$(BOOST_PROGRAM_OPTIONS_LIBS) \
+	${CodePatterns_LIBS}
+
+PoolWorker_SOURCES = poolworker.cpp 
+PoolWorker_LDFLAGS = $(AM_LDFLAGS) ${CodePatterns_LDFLAGS}
 PoolWorker_CXXFLAGS = $(AM_CPPFLAGS)
 PoolWorker_LDADD = \
         libMolecuilderJobs.la \
-        libFragmentationAutomationPoolWorker.la \
+        $(top_builddir)/JobMarket/src/JobMarket/libJobMarketPoolWorker.la \
         $(top_builddir)/JobMarket/src/JobMarket/libJobMarket.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
-	${CodePatterns_LIBS} \
-	$(BOOST_PROGRAM_OPTIONS_LIBS)
-
-Server_SOURCES = Server.cpp server_main.cpp server_main.hpp
-Server_LDFLAGS = $(AM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS)
+	${CodePatterns_LIBS}
+
+Server_SOURCES = Server.cpp 
+Server_LDFLAGS = $(AM_LDFLAGS) ${CodePatterns_LDFLAGS}
 Server_CXXFLAGS = $(AM_CPPFLAGS)
 Server_LDADD = \
         libMolecuilderJobs.la \
-        libFragmentationAutomationServer.la \
+        $(top_builddir)/JobMarket/src/JobMarket/libJobMarketServer.la \
         $(top_builddir)/JobMarket/src/JobMarket/libJobMarket.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
-	${CodePatterns_LIBS} \
-	$(BOOST_PROGRAM_OPTIONS_LIBS)
+	${CodePatterns_LIBS}
 
 
