diff --git a/apps/mk/app.mk b/apps/mk/app.mk
deleted file mode 100644
index fa4a12cab6..0000000000
--- a/apps/mk/app.mk
+++ /dev/null
@@ -1,237 +0,0 @@
-############################################################################
-#
-#   Copyright (C) 2012 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
-# are met:
-#
-# 1. Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-# 2. Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in
-#    the documentation and/or other materials provided with the
-#    distribution.
-# 3. Neither the name PX4 nor the names of its contributors may be
-#    used to endorse or promote products derived from this software
-#    without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
-# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
-# COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-# OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
-# AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
-# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#
-############################################################################
-
-#
-# Common Makefile for nsh command modules and utility libraries; should be 
-# included by the module-specific Makefile.
-#
-# To build an app that appears as an nsh external command, the caller 
-# must define:
-#
-# APPNAME	- the name of the application, defaults to the name
-#		  of the parent directory.
-#
-# If APPNAME is not defined, a utility library is built instead. The library
-# name is normally automatically determined, but it can be overridden by
-# setting:
-#
-# LIBNAME	- the name of the library, defaults to the name of the
-#		  directory
-#
-# The calling makefile may also set:
-#
-# ASRCS		- list of assembly source files, defaults to all .S 
-#		  files in the directory
-#
-# CSRCS		- list of C source files, defaults to all .c files
-#		  in the directory
-#
-# CXXSRCS	- list of C++ source files, defaults to all .cpp
-#		  files in the directory
-#
-# INCLUDES	- list of directories to be added to the include
-#		  search path
-#
-# PRIORITY	- thread priority for the command (defaults to 
-#		  SCHED_PRIORITY_DEFAULT)
-#
-# STACKSIZE	- stack size for the command (defaults to 
-#		  CONFIG_PTHREAD_STACK_DEFAULT)
-#
-# Symbols in the module are private to the module unless deliberately exported
-# using the __EXPORT tag, or DEFAULT_VISIBILITY is set
-#
-
-############################################################################
-# No user-serviceable parts below
-############################################################################
-
-
-############################################################################
-# Work out who included us so we can report decent errors
-#
-THIS_MAKEFILE	:= $(lastword $(MAKEFILE_LIST))
-ifeq ($(APP_MAKEFILE),)
-APP_MAKEFILE	:= $(lastword $(filter-out $(THIS_MAKEFILE),$(MAKEFILE_LIST)))
-endif
-
-############################################################################
-# Get configuration
-#
--include $(TOPDIR)/.config
--include $(TOPDIR)/Make.defs
-include $(APPDIR)/Make.defs
-
-############################################################################
-# Sanity-check the information we've been given and set any defaults
-#
-SRCDIR		?= $(dir $(APP_MAKEFILE))
-PRIORITY	?= SCHED_PRIORITY_DEFAULT
-STACKSIZE	?= CONFIG_PTHREAD_STACK_DEFAULT
-
-INCLUDES	+= $(APPDIR)
-
-ASRCS		?= $(wildcard $(SRCDIR)/*.S)
-CSRCS		?= $(wildcard $(SRCDIR)/*.c)
-CHDRS		?= $(wildcard $(SRCDIR)/*.h)
-CXXSRCS		?= $(wildcard $(SRCDIR)/*.cpp)
-CXXHDRS		?= $(wildcard $(SRCDIR)/*.hpp)
-
-# if APPNAME is not set, this is a library
-ifeq ($(APPNAME),)
-LIBNAME		?= $(lastword $(subst /, ,$(realpath $(SRCDIR))))
-endif
-
-# there has to be a source file
-ifeq ($(ASRCS)$(CSRCS)$(CXXSRCS),)
-$(error $(realpath $(APP_MAKEFILE)): at least one of ASRCS, CSRCS or CXXSRCS must be set)
-endif
-
-# check that C++ is configured if we have C++ source files and we are building
-ifneq ($(CXXSRCS),)
-ifneq ($(CONFIG_HAVE_CXX),y)
-ifeq ($(MAKECMDGOALS),build)
-$(error $(realpath $(APP_MAKEFILE)): cannot set CXXSRCS if CONFIG_HAVE_CXX not set in configuration)
-endif
-endif
-endif
-
-############################################################################
-# Adjust compilation flags to implement EXPORT
-#
-
-ifeq ($(DEFAULT_VISIBILITY),)
-DEFAULT_VISIBILITY = hidden
-else
-DEFAULT_VISIBILITY = default
-endif
-
-CFLAGS		+= -fvisibility=$(DEFAULT_VISIBILITY) -include $(APPDIR)/systemlib/visibility.h
-CXXFLAGS	+= -fvisibility=$(DEFAULT_VISIBILITY) -include $(APPDIR)/systemlib/visibility.h
-
-############################################################################
-# Add extra include directories
-#
-CFLAGS		+= $(addprefix -I,$(INCLUDES))
-CXXFLAGS	+= $(addprefix -I,$(INCLUDES))
-
-############################################################################
-# Things we are going to build
-#
-
-SRCS		 = $(ASRCS) $(CSRCS) $(CXXSRCS)
-AOBJS		 = $(patsubst %.S,%.o,$(ASRCS))
-COBJS		 = $(patsubst %.c,%.o,$(CSRCS))
-CXXOBJS		 = $(patsubst %.cpp,%.o,$(CXXSRCS))
-OBJS		 = $(AOBJS) $(COBJS) $(CXXOBJS)
-
-# Automatic depdendency generation
-DEPS		 = $(OBJS:$(OBJEXT)=.d)
-CFLAGS		+= -MD
-CXXFLAGS	+= -MD
-
-# The prelinked object that we are ultimately going to build
-ifneq ($(APPNAME),)
-PRELINKOBJ	 = $(APPNAME).pre.o
-else
-PRELINKOBJ	 = $(LIBNAME).pre.o
-endif
-
-# The archive the prelinked object will be linked into
-# XXX does WINTOOL ever get set?
-ifeq ($(WINTOOL),y)
-  INCDIROPT	= -w
-  BIN		 = "$(shell cygpath -w  $(APPDIR)/libapps$(LIBEXT))"
-else
-  BIN		 = "$(APPDIR)/libapps$(LIBEXT)"
-endif
-
-############################################################################
-# Rules for building things
-#
-
-all:		.built
-.PHONY:		clean depend distclean
-
-#
-# Top-level build; add prelinked object to the apps archive
-#
-.built:		$(PRELINKOBJ)
-	@$(call ARCHIVE, $(BIN), $(PRELINKOBJ))
-	@touch $@
-
-#
-# Source dependencies
-#
-depend:
-	@exit 0
-
-ifneq ($(APPNAME),)
-#
-# App registration
-#
-context:	.context
-.context:	$(MAKEFILE_LIST)
-	$(call REGISTER,$(APPNAME),$(PRIORITY),$(STACKSIZE),$(APPNAME)_main)
-	@touch $@
-else
-context:
-	@exit 0
-endif
-
-#
-# Object files
-#
-$(PRELINKOBJ):	$(OBJS)
-	$(call PRELINK, $@, $(OBJS))
-
-$(AOBJS): %.o : %.S $(MAKEFILE_LIST)
-	$(call ASSEMBLE, $<, $@)
-
-$(COBJS): %.o : %.c $(MAKEFILE_LIST)
-	$(call COMPILE, $<, $@)
-
-$(CXXOBJS): %.o : %.cpp $(MAKEFILE_LIST)
-	$(call COMPILEXX, $<, $@)
-
-#
-# Tidying up
-#
-clean:
-	@rm -f $(OBJS) $(DEPS) $(PRELINKOBJ) .built
-	$(call CLEAN)
-
-distclean:	clean
-	@rm -f Make.dep .depend
-
--include $(DEPS)
diff --git a/makefiles/config_px4fmu_default.mk b/makefiles/config_px4fmu_default.mk
index bc3031cd67..52b7e7e48c 100644
--- a/makefiles/config_px4fmu_default.mk
+++ b/makefiles/config_px4fmu_default.mk
@@ -89,6 +89,17 @@ MODULES		+= modules/uORB
 # Demo apps
 #
 MODULES		+= examples/math_demo
+# Tutorial code from
+# https://pixhawk.ethz.ch/px4/dev/hello_sky
+MODULES		+= examples/px4_simple_app
+
+# Tutorial code from
+# https://pixhawk.ethz.ch/px4/dev/daemon
+MODULES		+= examples/px4_daemon_app
+
+# Tutorial code from
+# https://pixhawk.ethz.ch/px4/dev/debug_values
+MODULES		+= examples/px4_mavlink_debug
 
 #
 # Transitional support - add commands from the NuttX export archive.
diff --git a/nuttx/configs/px4fmu/nsh/appconfig b/nuttx/configs/px4fmu/nsh/appconfig
index 6e91f3d1a3..0e18aa8ef1 100644
--- a/nuttx/configs/px4fmu/nsh/appconfig
+++ b/nuttx/configs/px4fmu/nsh/appconfig
@@ -41,93 +41,6 @@ CONFIGURED_APPS	+= examples/nsh
 CONFIGURED_APPS += nshlib
 CONFIGURED_APPS += system/readline
 
-# System library - utility functions
-CONFIGURED_APPS += systemlib
-CONFIGURED_APPS += systemlib/mixer
-
-# Math library
-ifneq ($(CONFIG_APM),y)
-CONFIGURED_APPS += mathlib
-CONFIGURED_APPS += mathlib/CMSIS
-CONFIGURED_APPS += examples/math_demo
-endif
-
-# Control library
-ifneq ($(CONFIG_APM),y)
-CONFIGURED_APPS	+= controllib
-CONFIGURED_APPS += examples/control_demo
-CONFIGURED_APPS += examples/kalman_demo
-endif
-
-# System utility commands
-CONFIGURED_APPS += systemcmds/reboot
-CONFIGURED_APPS += systemcmds/perf
-CONFIGURED_APPS += systemcmds/top
-CONFIGURED_APPS += systemcmds/boardinfo
-CONFIGURED_APPS += systemcmds/mixer
-CONFIGURED_APPS += systemcmds/param
-CONFIGURED_APPS += systemcmds/pwm
-CONFIGURED_APPS += systemcmds/bl_update
-CONFIGURED_APPS += systemcmds/preflight_check
-CONFIGURED_APPS += systemcmds/delay_test
-
-# Tutorial code from
-# https://pixhawk.ethz.ch/px4/dev/hello_sky
-# CONFIGURED_APPS += examples/px4_simple_app
-
-# Tutorial code from
-# https://pixhawk.ethz.ch/px4/dev/deamon
-# CONFIGURED_APPS += examples/px4_deamon_app
-
-# Tutorial code from
-# https://pixhawk.ethz.ch/px4/dev/debug_values
-# CONFIGURED_APPS += examples/px4_mavlink_debug
-
-# Shared object broker; required by many parts of the system.
-CONFIGURED_APPS += uORB
-
-CONFIGURED_APPS += mavlink
-CONFIGURED_APPS += mavlink_onboard
-CONFIGURED_APPS += commander
-CONFIGURED_APPS += sdlog
-CONFIGURED_APPS += sensors
-
-ifneq ($(CONFIG_APM),y)
-CONFIGURED_APPS += ardrone_interface
-CONFIGURED_APPS += multirotor_att_control
-CONFIGURED_APPS += multirotor_pos_control
-CONFIGURED_APPS += position_estimator_mc
-CONFIGURED_APPS += fixedwing_att_control
-CONFIGURED_APPS += fixedwing_pos_control
-CONFIGURED_APPS += position_estimator
-CONFIGURED_APPS += attitude_estimator_ekf
-CONFIGURED_APPS += hott_telemetry
-endif
-
-# Hacking tools
-#CONFIGURED_APPS += system/i2c
-CONFIGURED_APPS += systemcmds/i2c
-
-# Communication and Drivers
-#CONFIGURED_APPS += drivers/boards/px4fmu
-CONFIGURED_APPS	+= drivers/device
-CONFIGURED_APPS += drivers/ms5611
-CONFIGURED_APPS += drivers/hmc5883
-CONFIGURED_APPS += drivers/mpu6000
-CONFIGURED_APPS += drivers/bma180
-CONFIGURED_APPS	+= drivers/px4io
-CONFIGURED_APPS += drivers/stm32
-#CONFIGURED_APPS += drivers/led
-CONFIGURED_APPS += drivers/blinkm
-CONFIGURED_APPS += drivers/stm32/tone_alarm
-CONFIGURED_APPS += drivers/stm32/adc
-CONFIGURED_APPS += drivers/hil
-CONFIGURED_APPS += drivers/gps
-CONFIGURED_APPS += drivers/mb12xx
-
-# Testing stuff
-CONFIGURED_APPS += px4/sensors_bringup
-
 ifeq ($(CONFIG_CAN),y)
 #CONFIGURED_APPS += examples/can
 endif
diff --git a/apps/examples/px4_mavlink_debug/Makefile b/src/examples/px4_daemon_app/module.mk
similarity index 88%
rename from apps/examples/px4_mavlink_debug/Makefile
rename to src/examples/px4_daemon_app/module.mk
index f59aef16fb..d23c19b75d 100644
--- a/apps/examples/px4_mavlink_debug/Makefile
+++ b/src/examples/px4_daemon_app/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
@@ -32,11 +32,9 @@
 ############################################################################
 
 #
-# Basic example application
+# Daemon application
 #
 
-APPNAME		 = px4_mavlink_debug
-PRIORITY	 = SCHED_PRIORITY_DEFAULT
-STACKSIZE	 = 2048
+MODULE_COMMAND		= px4_daemon_app
 
-include $(APPDIR)/mk/app.mk
+SRCS				= px4_daemon_app.c
diff --git a/apps/examples/px4_deamon_app/px4_deamon_app.c b/src/examples/px4_daemon_app/px4_daemon_app.c
similarity index 100%
rename from apps/examples/px4_deamon_app/px4_deamon_app.c
rename to src/examples/px4_daemon_app/px4_daemon_app.c
diff --git a/apps/examples/px4_deamon_app/Makefile b/src/examples/px4_mavlink_debug/module.mk
similarity index 90%
rename from apps/examples/px4_deamon_app/Makefile
rename to src/examples/px4_mavlink_debug/module.mk
index e4c169872b..3d400fdbfc 100644
--- a/apps/examples/px4_deamon_app/Makefile
+++ b/src/examples/px4_mavlink_debug/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
@@ -35,8 +35,6 @@
 # Basic example application
 #
 
-APPNAME		 = px4_deamon_app
-PRIORITY	 = SCHED_PRIORITY_DEFAULT
-STACKSIZE	 = 2048
+MODULE_COMMAND		= px4_mavlink_debug
 
-include $(APPDIR)/mk/app.mk
+SRCS				= px4_mavlink_debug.c
\ No newline at end of file
diff --git a/apps/examples/px4_mavlink_debug/px4_mavlink_debug.c b/src/examples/px4_mavlink_debug/px4_mavlink_debug.c
similarity index 100%
rename from apps/examples/px4_mavlink_debug/px4_mavlink_debug.c
rename to src/examples/px4_mavlink_debug/px4_mavlink_debug.c
diff --git a/apps/examples/px4_simple_app/Makefile b/src/examples/px4_simple_app/module.mk
similarity index 90%
rename from apps/examples/px4_simple_app/Makefile
rename to src/examples/px4_simple_app/module.mk
index 102f51fd48..2c102fa500 100644
--- a/apps/examples/px4_simple_app/Makefile
+++ b/src/examples/px4_simple_app/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
@@ -35,8 +35,6 @@
 # Basic example application
 #
 
-APPNAME		 = px4_simple_app
-PRIORITY	 = SCHED_PRIORITY_DEFAULT
-STACKSIZE	 = 2048
+MODULE_COMMAND		= px4_simple_app
 
-include $(APPDIR)/mk/app.mk
+SRCS				= px4_simple_app.c
diff --git a/apps/examples/px4_simple_app/px4_simple_app.c b/src/examples/px4_simple_app/px4_simple_app.c
similarity index 100%
rename from apps/examples/px4_simple_app/px4_simple_app.c
rename to src/examples/px4_simple_app/px4_simple_app.c