diff --git a/apps/commander/.context b/apps/commander/.context
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/makefiles/config_px4fmu_default.mk b/makefiles/config_px4fmu_default.mk
index 1302d15821..6c43377e39 100644
--- a/makefiles/config_px4fmu_default.mk
+++ b/makefiles/config_px4fmu_default.mk
@@ -17,6 +17,11 @@ MODULES		+= drivers/l3gd20
 MODULES		+= drivers/ardrone_interface
 MODULES		+= systemcmds/eeprom
 
+#
+# General system control
+#
+MODULES		+= modules/commander
+
 #
 # Estimation modules (EKF / other filters)
 #
@@ -41,7 +46,6 @@ BUILTIN_COMMANDS := \
 	$(call _B, blinkm,                 ,                          2048,  blinkm_main                ) \
 	$(call _B, bma180,                 ,                          2048,  bma180_main                ) \
 	$(call _B, boardinfo,              ,                          2048,  boardinfo_main             ) \
-	$(call _B, commander,              SCHED_PRIORITY_MAX-30,     2048,  commander_main             ) \
 	$(call _B, control_demo,           ,                          2048,  control_demo_main          ) \
 	$(call _B, delay_test,             ,                          2048,  delay_test_main            ) \
 	$(call _B, fixedwing_att_control,  SCHED_PRIORITY_MAX-30,     2048,  fixedwing_att_control_main ) \
diff --git a/makefiles/config_px4fmuv2_default.mk b/makefiles/config_px4fmuv2_default.mk
index 659b9c95be..fd69baa29a 100644
--- a/makefiles/config_px4fmuv2_default.mk
+++ b/makefiles/config_px4fmuv2_default.mk
@@ -17,6 +17,11 @@ MODULES		+= drivers/px4fmu
 MODULES		+= drivers/rgbled
 MODULES		+= systemcmds/ramtron
 
+#
+# General system control
+#
+MODULES		+= modules/commander
+
 #
 # Estimation modules (EKF / other filters)
 #
diff --git a/apps/commander/calibration_routines.c b/src/modules/commander/calibration_routines.c
similarity index 100%
rename from apps/commander/calibration_routines.c
rename to src/modules/commander/calibration_routines.c
diff --git a/apps/commander/calibration_routines.h b/src/modules/commander/calibration_routines.h
similarity index 100%
rename from apps/commander/calibration_routines.h
rename to src/modules/commander/calibration_routines.h
diff --git a/apps/commander/commander.c b/src/modules/commander/commander.c
similarity index 100%
rename from apps/commander/commander.c
rename to src/modules/commander/commander.c
diff --git a/apps/commander/commander.h b/src/modules/commander/commander.h
similarity index 100%
rename from apps/commander/commander.h
rename to src/modules/commander/commander.h
diff --git a/apps/commander/Makefile b/src/modules/commander/module.mk
similarity index 86%
rename from apps/commander/Makefile
rename to src/modules/commander/module.mk
index d12697274b..b90da8289f 100644
--- a/apps/commander/Makefile
+++ b/src/modules/commander/module.mk
@@ -1,6 +1,6 @@
 ############################################################################
 #
-#   Copyright (C) 2012 PX4 Development Team. All rights reserved.
+#   Copyright (C) 2012-2013 PX4 Development Team. All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
 # modification, are permitted provided that the following conditions
@@ -32,14 +32,10 @@
 ############################################################################
 
 #
-# Commander application
+# Main system state machine
 #
 
-APPNAME		 = commander
-PRIORITY	 = SCHED_PRIORITY_MAX - 30
-STACKSIZE	 = 2048
-
-INCLUDES	= $(TOPDIR)/../mavlink/include/mavlink
-
-include $(APPDIR)/mk/app.mk
-
+MODULE_COMMAND	 = commander
+SRCS		 = commander.c \
+			   state_machine_helper.c \
+			   calibration_routines.c
diff --git a/apps/commander/state_machine_helper.c b/src/modules/commander/state_machine_helper.c
similarity index 100%
rename from apps/commander/state_machine_helper.c
rename to src/modules/commander/state_machine_helper.c
diff --git a/apps/commander/state_machine_helper.h b/src/modules/commander/state_machine_helper.h
similarity index 100%
rename from apps/commander/state_machine_helper.h
rename to src/modules/commander/state_machine_helper.h