diff --git a/conf/airframes/examples/disco_energy.xml b/conf/airframes/examples/disco_energy.xml
index 9e2ed1f97c..3b132f1f21 100644
--- a/conf/airframes/examples/disco_energy.xml
+++ b/conf/airframes/examples/disco_energy.xml
@@ -66,7 +66,7 @@
     
     
     <!-- Navigation -->    
-    <define name="USE_GPS_UBX_RTCM" value="TRUE"/> <!--  required so that RTCM messages are decoded in /subsystems/gps/gps_ubx.c -->
+    <define name="USE_GPS_UBX_RTCM" value="TRUE"/> <!--  required so that RTCM messages are decoded in /modules/gps/gps_ubx.c -->
     <define name="GPS_UBX_UCENTER_RATE" value="0x00FA"/> <!-- Ucenter rate for RTCM messsage.. In milliseconds. 0x00FA = 250ms = 4Hz-->
     <module name="gps" type="ublox"/>
     <module name="gps" type="ubx_ucenter"/>
diff --git a/conf/firmwares/subsystems/shared/actuators_pwm.makefile b/conf/firmwares/actuators_pwm.makefile
similarity index 100%
rename from conf/firmwares/subsystems/shared/actuators_pwm.makefile
rename to conf/firmwares/actuators_pwm.makefile
diff --git a/conf/firmwares/subsystems/shared/baro_board.makefile b/conf/firmwares/baro_board.makefile
similarity index 100%
rename from conf/firmwares/subsystems/shared/baro_board.makefile
rename to conf/firmwares/baro_board.makefile
diff --git a/conf/firmwares/demo.makefile b/conf/firmwares/demo.makefile
index dbd60907fc..3fd254e7af 100644
--- a/conf/firmwares/demo.makefile
+++ b/conf/firmwares/demo.makefile
@@ -30,10 +30,9 @@
 
 SRC_ARCH=arch/$(ARCH)
 SRC_BOARD=boards/$(BOARD)
-SRC_SUBSYSTEMS=subsystems
 SRC_MODULES=modules
 
-CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/shared
+CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares
 
 VPATH += $(PAPARAZZI_HOME)/var/share
 
@@ -77,7 +76,7 @@ endif
 #
 # Demo AHRS and actuators
 #
-# required subsystems:
+# required:
 #   - telemetry
 #   - imu
 #   - ahrs
@@ -92,8 +91,8 @@ demo_ahrs_actuators.ARCHDIR = $(ARCH)
 demo_ahrs_actuators.CFLAGS += $(COMMON_DEMO_CFLAGS)
 demo_ahrs_actuators.srcs   += $(COMMON_DEMO_SRCS)
 demo_ahrs_actuators.srcs   += mcu_periph/i2c.c $(SRC_ARCH)/mcu_periph/i2c_arch.c
-demo_ahrs_actuators.srcs   += subsystems/settings.c $(SRC_ARCH)/subsystems/settings_arch.c
-demo_ahrs_actuators.srcs   += subsystems/commands.c modules/actuators/actuators.c
+demo_ahrs_actuators.srcs   += modules/core/settings.c $(SRC_ARCH)/modules/core/settings_arch.c
+demo_ahrs_actuators.srcs   += modules/core/commands.c modules/actuators/actuators.c
 demo_ahrs_actuators.srcs   += state.c
 demo_ahrs_actuators.srcs   += math/pprz_geodetic_int.c math/pprz_geodetic_float.c math/pprz_geodetic_double.c math/pprz_trig_int.c math/pprz_orientation_conversion.c math/pprz_algebra_int.c math/pprz_algebra_float.c math/pprz_algebra_double.c
 demo_ahrs_actuators.srcs   += firmwares/demo/demo_ahrs_actuators.c
diff --git a/conf/firmwares/fixedwing.makefile b/conf/firmwares/fixedwing.makefile
index 4decaa8da9..d4c81aca92 100644
--- a/conf/firmwares/fixedwing.makefile
+++ b/conf/firmwares/fixedwing.makefile
@@ -5,12 +5,7 @@
 #
 
 
-CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/shared
-CFG_FIXEDWING=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/fixedwing
-
-
-# Standard Fixed Wing Code
-include $(CFG_FIXEDWING)/autopilot.makefile
+CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares
 
 # automatically include correct actuators for the ap target
 ACTUATOR_TARGET = ap
diff --git a/conf/firmwares/rotorcraft.makefile b/conf/firmwares/rotorcraft.makefile
index 47a99d737c..9702219caf 100644
--- a/conf/firmwares/rotorcraft.makefile
+++ b/conf/firmwares/rotorcraft.makefile
@@ -21,7 +21,6 @@
 #
 #
 
-CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/shared
-CFG_ROTORCRAFT=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/rotorcraft
+CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares
 
 
diff --git a/conf/firmwares/rover.makefile b/conf/firmwares/rover.makefile
index 484289175d..515202fd74 100644
--- a/conf/firmwares/rover.makefile
+++ b/conf/firmwares/rover.makefile
@@ -21,5 +21,5 @@
 #
 #
 
-CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/shared
+CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares
 
diff --git a/conf/firmwares/setup.makefile b/conf/firmwares/setup.makefile
index dd721ce7e1..fba26d1888 100644
--- a/conf/firmwares/setup.makefile
+++ b/conf/firmwares/setup.makefile
@@ -5,10 +5,9 @@
 
 SRC_ARCH=arch/$(ARCH)
 SRC_BOARD=boards/$(BOARD)
-SRC_SUBSYSTEMS=subsystems
 SRC_MODULES=modules
 
-CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/shared
+CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares
 
 SRC_FIRMWARE=firmwares/setup
 
diff --git a/conf/firmwares/subsystems/shared/spi_master.makefile b/conf/firmwares/spi_master.makefile
similarity index 100%
rename from conf/firmwares/subsystems/shared/spi_master.makefile
rename to conf/firmwares/spi_master.makefile
diff --git a/conf/firmwares/subsystems/fixedwing/autopilot.makefile b/conf/firmwares/subsystems/fixedwing/autopilot.makefile
deleted file mode 100644
index c596d902c8..0000000000
--- a/conf/firmwares/subsystems/fixedwing/autopilot.makefile
+++ /dev/null
@@ -1,23 +0,0 @@
-# Hey Emacs, this is a -*- makefile -*-
-#
-# Copyright (C) 2008 Antoine Drouin
-#
-# This file is part of paparazzi.
-#tin
-# paparazzi is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-#
-# paparazzi is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with paparazzi; see the file COPYING.  If not, write to
-# the Free Software Foundation, 59 Temple Place - Suite 330,
-# Boston, MA 02111-1307, USA.
-#
-#
-
diff --git a/conf/firmwares/test_chibios.makefile b/conf/firmwares/test_chibios.makefile
index 1a2e24f4a9..caaa1b1580 100644
--- a/conf/firmwares/test_chibios.makefile
+++ b/conf/firmwares/test_chibios.makefile
@@ -35,10 +35,9 @@
 ################################################################################
 SRC_ARCH=arch/$(ARCH)
 SRC_BOARD=boards/$(BOARD)
-SRC_SUBSYSTEMS=subsystems
 SRC_MODULES=modules
 
-CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/shared
+CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares
 
 # Enable debug mode by default for test programs
 RTOS_DEBUG ?= 1
diff --git a/conf/firmwares/test_progs.makefile b/conf/firmwares/test_progs.makefile
index fc733faa6a..e2363d6df1 100644
--- a/conf/firmwares/test_progs.makefile
+++ b/conf/firmwares/test_progs.makefile
@@ -30,10 +30,9 @@
 
 SRC_ARCH=arch/$(ARCH)
 SRC_BOARD=boards/$(BOARD)
-SRC_SUBSYSTEMS=subsystems
 SRC_MODULES=modules
 
-CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares/subsystems/shared
+CFG_SHARED=$(PAPARAZZI_SRC)/conf/firmwares
 
 VPATH += $(PAPARAZZI_HOME)/var/share
 
@@ -338,7 +337,7 @@ test_actuators_pwm.srcs   += $(COMMON_TELEMETRY_SRCS)
 test_actuators_pwm.srcs   += test/test_actuators_pwm.c
 test_actuators_pwm.srcs   += $(SRC_ARCH)/modules/actuators/actuators_pwm_arch.c $(SRC_ARCH)/modules/actuators/actuators_shared_arch.c
 # only add this so it doesn't fail to build if you also have setup_actuators.xml settings file loaded
-# remove me again when we have auto loading of settings according to subsystem/module/target...
+# remove me again when we have auto loading of settings according to module/target...
 test_actuators_pwm.srcs   += modules/actuators/actuators.c
 
 
@@ -354,7 +353,7 @@ test_actuators_pwm_sin.srcs   += $(SRC_ARCH)/modules/actuators/actuators_pwm_arc
 
 #
 # Test manual : a simple test with rc and servos
-# add the desired actuators and radio_control subsystem to this target
+# add the desired actuators and radio_control modules to this target
 #
 test_manual.ARCHDIR = $(ARCH)
 test_manual.CFLAGS += $(COMMON_TEST_CFLAGS)
@@ -362,7 +361,7 @@ test_manual.srcs   += $(COMMON_TEST_SRCS)
 test_manual.CFLAGS += $(COMMON_TELEMETRY_CFLAGS)
 test_manual.srcs   += $(COMMON_TELEMETRY_SRCS)
 
-test_manual.srcs   += subsystems/commands.c
+test_manual.srcs   += modules/core/commands.c
 test_manual.srcs   += modules/actuators/actuators.c
 test_manual.srcs   += test/test_manual.c
 
@@ -420,7 +419,7 @@ test_adc.srcs   += test/mcu_periph/test_adc.c
 #
 # test_imu
 #
-# add imu subsystem to test_imu target!
+# add imu module to test_imu target!
 #
 # configuration
 #   SYS_TIME_LED
@@ -434,14 +433,14 @@ test_imu.CFLAGS += $(COMMON_TELEMETRY_CFLAGS)
 test_imu.srcs   += $(COMMON_TELEMETRY_SRCS)
 test_imu.srcs   += mcu_periph/i2c.c $(SRC_ARCH)/mcu_periph/i2c_arch.c
 test_imu.srcs   += state.c
-test_imu.srcs   += test/subsystems/test_imu.c
+test_imu.srcs   += test/modules/test_imu.c
 test_imu.srcs   += math/pprz_geodetic_int.c math/pprz_geodetic_float.c math/pprz_geodetic_double.c math/pprz_trig_int.c math/pprz_orientation_conversion.c math/pprz_algebra_int.c math/pprz_algebra_float.c math/pprz_algebra_double.c
 
 
 #
 # test_ahrs
 #
-# add imu and ahrs subsystems to test_ahrs target!
+# add imu and ahrs modules to test_ahrs target!
 #
 # configuration
 #   SYS_TIME_LED
@@ -456,7 +455,7 @@ test_ahrs.srcs   += $(COMMON_TELEMETRY_SRCS)
 test_ahrs.srcs   += modules/datalink/telemetry.c
 test_ahrs.CFLAGS += -DPERIODIC_TELEMETRY
 test_ahrs.srcs   += mcu_periph/i2c.c $(SRC_ARCH)/mcu_periph/i2c_arch.c
-test_ahrs.srcs   += test/subsystems/test_ahrs.c
+test_ahrs.srcs   += test/modules/test_ahrs.c
 test_ahrs.srcs   += state.c
 test_ahrs.srcs   += math/pprz_geodetic_int.c math/pprz_geodetic_float.c math/pprz_geodetic_double.c math/pprz_trig_int.c math/pprz_orientation_conversion.c math/pprz_algebra_int.c math/pprz_algebra_float.c math/pprz_algebra_double.c
 
@@ -471,7 +470,7 @@ test_radio_control.CFLAGS += $(COMMON_TEST_CFLAGS)
 test_radio_control.srcs   += $(COMMON_TEST_SRCS)
 test_radio_control.CFLAGS += $(COMMON_TELEMETRY_CFLAGS)
 test_radio_control.srcs   += $(COMMON_TELEMETRY_SRCS)
-test_radio_control.srcs   += test/subsystems/test_radio_control.c
+test_radio_control.srcs   += test/modules/test_radio_control.c
 
 
 #
@@ -486,9 +485,9 @@ test_settings.CFLAGS += $(COMMON_TEST_CFLAGS)
 test_settings.srcs   += $(COMMON_TEST_SRCS)
 test_settings.CFLAGS += $(COMMON_TELEMETRY_CFLAGS)
 test_settings.srcs   += $(COMMON_TELEMETRY_SRCS)
-test_settings.srcs   += subsystems/settings.c
-test_settings.srcs   += $(SRC_ARCH)/subsystems/settings_arch.c
-test_settings.srcs   += test/subsystems/test_settings.c
+test_settings.srcs   += modules/core/settings.c
+test_settings.srcs   += $(SRC_ARCH)/modules/core/settings_arch.c
+test_settings.srcs   += test/modules/test_settings.c
 test_settings.CFLAGS += -DUSE_PERSISTENT_SETTINGS
 
 
diff --git a/conf/firmwares/subsystems/shared/uart.makefile b/conf/firmwares/uart.makefile
similarity index 100%
rename from conf/firmwares/subsystems/shared/uart.makefile
rename to conf/firmwares/uart.makefile
diff --git a/conf/firmwares/subsystems/shared/udp.makefile b/conf/firmwares/udp.makefile
similarity index 100%
rename from conf/firmwares/subsystems/shared/udp.makefile
rename to conf/firmwares/udp.makefile
diff --git a/conf/flight_plans/OPENUAS/include_obc2014_mission.xml b/conf/flight_plans/OPENUAS/include_obc2014_mission.xml
index f64cae2413..d226a43002 100644
--- a/conf/flight_plans/OPENUAS/include_obc2014_mission.xml
+++ b/conf/flight_plans/OPENUAS/include_obc2014_mission.xml
@@ -53,9 +53,9 @@ TESTS:
 //Set Generic options
     #include "autopilot.h"
 //Enable AHRS Health test functions
-    #include "subsystems/ahrs/ahrs_aligner.h"
+    #include "modules/ahrs/ahrs_aligner.h"
 //Enable advanced electrical power functions
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
 //Enable datalink tests
     #include "modules/datalink/datalink.h"
 //For interaction with the Flight termination Device (FTD)
diff --git a/conf/flight_plans/OPENUAS/openuas_rotorcraft_simple.xml b/conf/flight_plans/OPENUAS/openuas_rotorcraft_simple.xml
index e783a12c41..0fe01a8858 100644
--- a/conf/flight_plans/OPENUAS/openuas_rotorcraft_simple.xml
+++ b/conf/flight_plans/OPENUAS/openuas_rotorcraft_simple.xml
@@ -14,9 +14,9 @@ Your safe aircraft operation is *your* responsibility
 //Set Generic options
     #include "autopilot.h"
 //Enable AHRS Health test functions
-    #include "subsystems/ahrs/ahrs_aligner.h"
+    #include "modules/ahrs/ahrs_aligner.h"
 //Enable advanced electrical power functions
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
 //Enable datalink tests
     #include "modules/datalink/datalink.h"
 #include "firmwares/rotorcraft/guidance/guidance_v.h"
diff --git a/conf/flight_plans/OPENUAS/openuas_versatile_unified.xml b/conf/flight_plans/OPENUAS/openuas_versatile_unified.xml
index 07c7f85ad3..d8fdc307c0 100644
--- a/conf/flight_plans/OPENUAS/openuas_versatile_unified.xml
+++ b/conf/flight_plans/OPENUAS/openuas_versatile_unified.xml
@@ -19,9 +19,9 @@ Should be unified for Hybrid, FW and rotorcraft
 //Set Generic options
     #include "autopilot.h"
 //Enable AHRS Health test functions
-    #include "subsystems/ahrs/ahrs_aligner.h"
+    #include "modules/ahrs/ahrs_aligner.h"
 //Enable advanced electrical power functions
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
 //Enable datalink tests
     #include "modules/datalink/datalink.h"
 
diff --git a/conf/flight_plans/quadshot_delft.xml b/conf/flight_plans/quadshot_delft.xml
index dbcafa2fe0..9c41200fb2 100644
--- a/conf/flight_plans/quadshot_delft.xml
+++ b/conf/flight_plans/quadshot_delft.xml
@@ -4,7 +4,7 @@
   <header>
     #include "autopilot.h"
     #include "modules/radio_control/radio_control.h"
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
     #include "modules/actuators/actuators.h"
     #include "firmwares/rotorcraft/guidance/guidance_h.h"
     #include "firmwares/rotorcraft/guidance/guidance_hybrid.h"
diff --git a/conf/flight_plans/rotorcraft_basic_superbitrf_from_hand.xml b/conf/flight_plans/rotorcraft_basic_superbitrf_from_hand.xml
index 6ffcd5d551..2ad80a7777 100644
--- a/conf/flight_plans/rotorcraft_basic_superbitrf_from_hand.xml
+++ b/conf/flight_plans/rotorcraft_basic_superbitrf_from_hand.xml
@@ -6,8 +6,8 @@ The goal of this flightplan is to have a safe, simple no-brainer flightplan for
   <header>
 
 #include "autopilot.h"
-#include "subsystems/ahrs.h"
-#include "subsystems/electrical.h"
+#include "modules/ahrs/ahrs.h"
+#include "modules/energy/electrical.h"
 #include "modules/datalink/datalink.h"
 
   </header>
diff --git a/conf/flight_plans/rotorcraft_optitrack_stereoavoid.xml b/conf/flight_plans/rotorcraft_optitrack_stereoavoid.xml
index 83a6ffc990..f75dbdca24 100644
--- a/conf/flight_plans/rotorcraft_optitrack_stereoavoid.xml
+++ b/conf/flight_plans/rotorcraft_optitrack_stereoavoid.xml
@@ -3,7 +3,7 @@
 <flight_plan alt="1" ground_alt="0" lat0="51.990634" lon0="4.376789" max_dist_from_home="20" name="Rotorcraft Optitrack (Delft)" security_height="2">
   <header>
 #include "autopilot.h"
-#include "subsystems/electrical.h"
+#include "modules/energy/electrical.h"
 #include "modules/stereocam/nav_line_avoid/avoid_navigation.h"
 </header>
   <waypoints>
diff --git a/conf/flight_plans/tudelft/course_orangeavoid_cyberzoo.xml b/conf/flight_plans/tudelft/course_orangeavoid_cyberzoo.xml
index 7eda68f916..b70b95e5ca 100644
--- a/conf/flight_plans/tudelft/course_orangeavoid_cyberzoo.xml
+++ b/conf/flight_plans/tudelft/course_orangeavoid_cyberzoo.xml
@@ -3,9 +3,9 @@
 <flight_plan alt="1.0" ground_alt="0" lat0="51.990634" lon0="4.376789" max_dist_from_home="60" name="Bebop avoid orange TU Delft Cyberzoo" security_height="0.4">
   <header>
     #include "modules/datalink/datalink.h"
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
     #include "modules/radio_control/radio_control.h"
-    #include "subsystems/ahrs.h"
+    #include "modules/ahrs/ahrs.h"
     #define NPS_GAZEBO_WORLD "cyberzoo_orange_poles.world"
 </header>
   <waypoints>
diff --git a/conf/flight_plans/tudelft/course_orangeavoid_cyberzoo_guided.xml b/conf/flight_plans/tudelft/course_orangeavoid_cyberzoo_guided.xml
index dc392e4c47..48758f834a 100644
--- a/conf/flight_plans/tudelft/course_orangeavoid_cyberzoo_guided.xml
+++ b/conf/flight_plans/tudelft/course_orangeavoid_cyberzoo_guided.xml
@@ -3,9 +3,9 @@
 <flight_plan alt="1.0" ground_alt="0" lat0="51.990634" lon0="4.376789" max_dist_from_home="60" name="Bebop avoid orange TU Delft Cyberzoo" security_height="0.4">
   <header>
     #include "modules/datalink/datalink.h"
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
     #include "modules/radio_control/radio_control.h"
-    #include "subsystems/ahrs.h"
+    #include "modules/ahrs/ahrs.h"
     #define NPS_GAZEBO_WORLD "cyberzoo_orange_poles.world"
 #include "autopilot.h"
 inline void setNav(void){
diff --git a/conf/flight_plans/tudelft/delft_basic.xml b/conf/flight_plans/tudelft/delft_basic.xml
index 19d260eb55..834a59a291 100644
--- a/conf/flight_plans/tudelft/delft_basic.xml
+++ b/conf/flight_plans/tudelft/delft_basic.xml
@@ -4,7 +4,7 @@
   <header>
     #include "autopilot.h"
     #include "modules/datalink/datalink.h"
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
     #include "modules/radio_control/radio_control.h"
   </header>
   <waypoints>
diff --git a/conf/flight_plans/tudelft/delft_bebop.xml b/conf/flight_plans/tudelft/delft_bebop.xml
index fc5f856855..08b61869e3 100644
--- a/conf/flight_plans/tudelft/delft_bebop.xml
+++ b/conf/flight_plans/tudelft/delft_bebop.xml
@@ -4,7 +4,7 @@
   <header>
     #include "autopilot.h"
     #include "modules/datalink/datalink.h"
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
     #include "modules/radio_control/radio_control.h"
 </header>
   <waypoints>
diff --git a/conf/flight_plans/tudelft/include_rotorcraft_survey_mission.xml b/conf/flight_plans/tudelft/include_rotorcraft_survey_mission.xml
index 71f7f887ca..3f54209ac6 100644
--- a/conf/flight_plans/tudelft/include_rotorcraft_survey_mission.xml
+++ b/conf/flight_plans/tudelft/include_rotorcraft_survey_mission.xml
@@ -4,7 +4,7 @@
 
   <header>
 #include "autopilot.h"
-#include "subsystems/electrical.h"
+#include "modules/energy/electrical.h"
 #ifdef dc_Survey
 #define LINE_START_FUNCTION dc_Survey(dc_distance_interval);
 #define LINE_STOP_FUNCTION {dc_autoshoot = DC_AUTOSHOOT_STOP;}
diff --git a/conf/flight_plans/tudelft/nederdrone_cyberzoo.xml b/conf/flight_plans/tudelft/nederdrone_cyberzoo.xml
index a524adb105..0545dc7a32 100644
--- a/conf/flight_plans/tudelft/nederdrone_cyberzoo.xml
+++ b/conf/flight_plans/tudelft/nederdrone_cyberzoo.xml
@@ -3,9 +3,9 @@
 <flight_plan alt="1.0" ground_alt="0" lat0="51.990634" lon0="4.376789" max_dist_from_home="60" name="Nederdrone Cyberzoo" security_height="0.4">
   <header>
     #include "modules/datalink/datalink.h"
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
     #include "modules/radio_control/radio_control.h"
-    #include "subsystems/ahrs.h"
+    #include "modules/ahrs/ahrs.h"
     #include "firmwares/rotorcraft/guidance/guidance_indi_hybrid.h"
     #include "firmwares/rotorcraft/navigation.h"
 </header>
diff --git a/conf/flight_plans/tudelft/ralphthesis2020_stereo_cyberzoo.xml b/conf/flight_plans/tudelft/ralphthesis2020_stereo_cyberzoo.xml
index 1664006a07..9fb7be9e00 100644
--- a/conf/flight_plans/tudelft/ralphthesis2020_stereo_cyberzoo.xml
+++ b/conf/flight_plans/tudelft/ralphthesis2020_stereo_cyberzoo.xml
@@ -3,9 +3,9 @@
 <flight_plan alt="1.0" ground_alt ="0" lat0="51.990634" lon0="4.376789" max_dist_from_home="20" name="Bebop with stereo cam and Wedgebug TU Delft Cyberzoo" security_height="0.4">
   <header>
     #include "modules/datalink/datalink.h"
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
     #include "modules/radio_control/radio_control.h"
-    #include "subsystems/ahrs.h"
+    #include "modules/ahrs/ahrs.h"
     #define NPS_GAZEBO_WORLD "cyberzoo2019_ralphthesis2020.world" <!-- Current world is based on "cyberzoo2019_orange_poles_panels_mats.world" and replaced the original "cyberzoo_orange_poles.world" that was used here -->
 
 #include "autopilot.h"
diff --git a/conf/flight_plans/tudelft/rotorcraft_optitrack_path.xml b/conf/flight_plans/tudelft/rotorcraft_optitrack_path.xml
index 3cf761485d..05c3715f36 100644
--- a/conf/flight_plans/tudelft/rotorcraft_optitrack_path.xml
+++ b/conf/flight_plans/tudelft/rotorcraft_optitrack_path.xml
@@ -5,8 +5,8 @@
   <header>
     #include "autopilot.h"
     #include "modules/radio_control/radio_control.h"
-    #include "subsystems/ahrs.h"
-    #include "subsystems/electrical.h"
+    #include "modules/ahrs/ahrs.h"
+    #include "modules/energy/electrical.h"
     #include "modules/datalink/datalink.h"
   </header>
   <waypoints>
diff --git a/conf/flight_plans/tudelft/train_safe_zoo.xml b/conf/flight_plans/tudelft/train_safe_zoo.xml
index fc40723325..ccb55d6333 100644
--- a/conf/flight_plans/tudelft/train_safe_zoo.xml
+++ b/conf/flight_plans/tudelft/train_safe_zoo.xml
@@ -3,9 +3,9 @@
 <flight_plan alt="1.0" ground_alt="0" lat0="51.990634" lon0="4.376789" max_dist_from_home="60" name="Safe TU Delft Cyberzoo" security_height="0.4">
   <header>
     #include "modules/datalink/datalink.h"
-    #include "subsystems/electrical.h"
+    #include "modules/energy/electrical.h"
     #include "modules/radio_control/radio_control.h"
-    #include "subsystems/ahrs.h"
+    #include "modules/ahrs/ahrs.h"
 </header>
   <waypoints>
     <waypoint lat="51.990631" lon="4.376796" name="HOME"/>
diff --git a/conf/modules/board_matek_f405_wing.xml b/conf/modules/board_matek_f405_wing.xml
index 5c1f62dffc..4dc4a3fe0a 100644
--- a/conf/modules/board_matek_f405_wing.xml
+++ b/conf/modules/board_matek_f405_wing.xml
@@ -3,7 +3,7 @@
 <module name="board_matek_f405_wing" dir="boards">
   <doc>
     <description>
-      Autoload several onboard sensors and subsystems
+      Autoload several onboard sensors and modules
       for the Matek F405 Wing board with proper configuration.
       IMU MPU6000
       Baro (BMP280)
diff --git a/conf/modules/board_matek_f765_wing.xml b/conf/modules/board_matek_f765_wing.xml
index 606ed11909..d14f3675ed 100644
--- a/conf/modules/board_matek_f765_wing.xml
+++ b/conf/modules/board_matek_f765_wing.xml
@@ -3,7 +3,7 @@
 <module name="board_matek_f765_wing" dir="boards">
   <doc>
     <description>
-      Autoload several onboard sensors and subsystems
+      Autoload several onboard sensors and modules
       for the Matek F765 Wing board with proper configuration.
       IMU ICM20602 (auto-detected from MPU6000 driver)
       Baro (BMP280)
diff --git a/conf/modules/system_core.xml b/conf/modules/system_core.xml
index bd5be8644c..558f463223 100644
--- a/conf/modules/system_core.xml
+++ b/conf/modules/system_core.xml
@@ -14,7 +14,6 @@
   </dep>
   <makefile>
     <configure name="SRC_BOARD" value="boards/$(BOARD)"/>
-    <configure name="SRC_SUBSYSTEMS" value="subsystems"/>
     <configure name="SRC_MODULES" value="modules"/>
     <configure name="SRC_ARCH" value="arch/$(ARCH)"/>
     <define name="BOARD_CONFIG" value="$(BOARD_CFG)"/>
diff --git a/conf/settings/OPENUAS/openuas_fixedwing_basic_extra.xml b/conf/settings/OPENUAS/openuas_fixedwing_basic_extra.xml
index 7743d62e71..ea57bb92b5 100644
--- a/conf/settings/OPENUAS/openuas_fixedwing_basic_extra.xml
+++ b/conf/settings/OPENUAS/openuas_fixedwing_basic_extra.xml
@@ -7,9 +7,9 @@
     <dl_settings NAME="flight params">
       <dl_setting MAX="1000" MIN="0" STEP="10" VAR="flight_altitude" shortname="altitude"/>
       <dl_setting MAX="360" MIN="0" STEP="1" VAR="nav_course"/>
-      <dl_setting MAX="10" MIN="-10" STEP="5" VAR="nav_shift" module="subsystems/nav" handler="IncreaseShift" shortname="inc. shift"/>
+      <dl_setting MAX="10" MIN="-10" STEP="5" VAR="nav_shift" module="firmwares/fixedwing/nav" handler="IncreaseShift" shortname="inc. shift"/>
       <dl_setting MAX="0" MIN="0" STEP="1" VAR="autopilot.flight_time" shortname="flight time" module="autopilot" handler="ResetFlightTimeAndLaunch"/>
-      <dl_setting MAX="200" MIN="-200" STEP="10" VAR="nav_radius" module="subsystems/nav" handler="SetNavRadius">
+      <dl_setting MAX="200" MIN="-200" STEP="10" VAR="nav_radius" module="firmwares/fixedwing/nav" handler="SetNavRadius">
         <strip_button icon="circle-right.png" name="Circle right" value="1" group="circle"/>
         <strip_button icon="circle-left.png" name="Circle left" value="-1" group="circle"/>
         <key_press key="greater" value="1"/>
diff --git a/conf/settings/OPENUAS/openuas_tuning_basic_ins.xml b/conf/settings/OPENUAS/openuas_tuning_basic_ins.xml
index 2b6568fe68..b8df6fa8bd 100644
--- a/conf/settings/OPENUAS/openuas_tuning_basic_ins.xml
+++ b/conf/settings/OPENUAS/openuas_tuning_basic_ins.xml
@@ -20,7 +20,7 @@
       <dl_setting MAX="2" MIN="0" STEP="1" VAR="telemetry_mode_Ap_DefaultChannel" shortname="tele_AP" module="downlink"/>
       <dl_setting MAX="1" MIN="0" STEP="1" VAR="telemetry_mode_Fbw_DefaultChannel" shortname="tele_FBW" module="downlink"/>
 
-      <dl_setting MAX="200" MIN="-200" STEP="10" VAR="nav_radius" module="subsystems/nav" handler="SetNavRadius">
+      <dl_setting MAX="200" MIN="-200" STEP="10" VAR="nav_radius" module="firmwares/fixedwing/nav" handler="SetNavRadius">
         <strip_button icon="circle-right.png" name="Circle right" value="1"/>
         <strip_button icon="circle-left.png" name="Circle left" value="-1"/>
         <key_press key="greater" value="1"/>
@@ -31,7 +31,7 @@
     <dl_settings NAME="control">
 
       <dl_settings NAME="ins">
-        <dl_setting MAX="0.3" MIN="-0.3" STEP="0.01" VAR="ins_roll_neutral" shortname="roll_neutral" module="subsystems/ahrs" param="INS_ROLL_NEUTRAL_DEFAULT" unit="rad"/>
+        <dl_setting MAX="0.3" MIN="-0.3" STEP="0.01" VAR="ins_roll_neutral" shortname="roll_neutral" module="modules/ahrs/ahrs" param="INS_ROLL_NEUTRAL_DEFAULT" unit="rad"/>
         <dl_setting MAX="0.6" MIN="-0.6" STEP="0.01" VAR="ins_pitch_neutral" shortname="pitch_neutral" param="INS_PITCH_NEUTRAL_DEFAULT" unit="rad"/>
       </dl_settings>
 
@@ -89,7 +89,7 @@
         <dl_setting MAX="2" MIN="1" STEP="1" VAR="nav_mode"/>
         <dl_setting MAX="5" MIN="-5" STEP="0.5" VAR="nav_climb"/>
         <dl_setting MAX="15" MIN="-15" STEP="1" VAR="fp_pitch"/>
-        <dl_setting MAX="50" MIN="-50" STEP="5" VAR="nav_shift" module="subsystems/nav" handler="IncreaseShift" shortname="inc. shift"/>
+        <dl_setting MAX="50" MIN="-50" STEP="5" VAR="nav_shift" module="firmwares/fixedwing/nav" handler="IncreaseShift" shortname="inc. shift"/>
         <dl_setting MAX="50" MIN="5" STEP="0.5" VAR="nav_ground_speed_setpoint" shortname="ground speed"/>
         <dl_setting MAX="0." MIN="-0.2" STEP="0.01" VAR="nav_ground_speed_pgain" shortname="ground speed pgain"/>
         <dl_setting MAX="500" MIN="50" STEP="5" VAR="nav_survey_shift"/>
diff --git a/conf/settings/estimation/ahrs_secondary.xml b/conf/settings/estimation/ahrs_secondary.xml
index 05a5834646..6931506c61 100644
--- a/conf/settings/estimation/ahrs_secondary.xml
+++ b/conf/settings/estimation/ahrs_secondary.xml
@@ -4,7 +4,7 @@
   <dl_settings>
 
     <dl_settings NAME="AHRS">
-       <dl_setting var="ahrs_output_idx" min="0" step="1" max="1" values="PRIMARY|SECONDARY" module="subsystems/ahrs" shortname="ahrs output" handler="switch"/>
+       <dl_setting var="ahrs_output_idx" min="0" step="1" max="1" values="PRIMARY|SECONDARY" module="modules/ahrs/ahrs" shortname="ahrs output" handler="switch"/>
     </dl_settings>
 
   </dl_settings>
diff --git a/conf/settings/estimation/ins_neutrals.xml b/conf/settings/estimation/ins_neutrals.xml
index 1b3964dcb0..b986636823 100644
--- a/conf/settings/estimation/ins_neutrals.xml
+++ b/conf/settings/estimation/ins_neutrals.xml
@@ -3,7 +3,7 @@
 <settings>
   <dl_settings>
     <dl_settings NAME="ins">
-      <dl_setting MAX="15" MIN="-15" STEP="0.5" VAR="ins_roll_neutral" shortname="roll_neutral" module="subsystems/ahrs" param="INS_ROLL_NEUTRAL_DEFAULT" unit="rad" alt_unit="deg" type="float" persistent="true"/>
+      <dl_setting MAX="15" MIN="-15" STEP="0.5" VAR="ins_roll_neutral" shortname="roll_neutral" module="modules/ahrs/ahrs" param="INS_ROLL_NEUTRAL_DEFAULT" unit="rad" alt_unit="deg" type="float" persistent="true"/>
       <dl_setting MAX="15" MIN="-15" STEP="0.5" VAR="ins_pitch_neutral" shortname="pitch_neutral" param="INS_PITCH_NEUTRAL_DEFAULT" unit="rad" alt_unit="deg" type="float" persistent="true"/>
     </dl_settings>
   </dl_settings>
diff --git a/conf/settings/estimation/ins_sonar.xml b/conf/settings/estimation/ins_sonar.xml
index dddf144a52..dba7dffc3e 100644
--- a/conf/settings/estimation/ins_sonar.xml
+++ b/conf/settings/estimation/ins_sonar.xml
@@ -3,7 +3,7 @@
 <settings>
   <dl_settings>
     <dl_settings NAME="sonar">
-      <dl_setting MAX="1" MIN="0" STEP="1" VAR="ins_int.update_on_agl" shortname="use_sonar" values="FALSE|TRUE" module="subsystems/ins/vf_extended_float"/>
+      <dl_setting MAX="1" MIN="0" STEP="1" VAR="ins_int.update_on_agl" shortname="use_sonar" values="FALSE|TRUE" module="modules/ins/vf_extended_float"/>
     </dl_settings>
   </dl_settings>
 </settings>
diff --git a/conf/settings/persistent_settings.xml b/conf/settings/persistent_settings.xml
index d0ea83cdc8..7600ea7230 100644
--- a/conf/settings/persistent_settings.xml
+++ b/conf/settings/persistent_settings.xml
@@ -3,8 +3,8 @@
 <settings>
   <dl_settings>
     <dl_settings NAME="Persistence">
-      <dl_setting var="settings_store_flag" min="1" step="1" max="1" shortname="store" handler="StoreSettings" module="subsystems/settings" values="Stored"/>
-      <dl_setting var="settings_clear_flag" min="1" step="1" max="1" shortname="clear" handler="ClearSettings" module="subsystems/settings" values="Cleared"/>
+      <dl_setting var="settings_store_flag" min="1" step="1" max="1" shortname="store" handler="StoreSettings" module="modules/core/settings" values="Stored"/>
+      <dl_setting var="settings_clear_flag" min="1" step="1" max="1" shortname="clear" handler="ClearSettings" module="modules/core/settings" values="Cleared"/>
     </dl_settings>
   </dl_settings>
 </settings>
diff --git a/conf/settings/superbitrf.xml b/conf/settings/superbitrf.xml
index 359f8cf71a..ef351652a6 100644
--- a/conf/settings/superbitrf.xml
+++ b/conf/settings/superbitrf.xml
@@ -3,7 +3,7 @@
 <settings target="!sim|nps">
   <dl_settings>
     <dl_settings NAME="Superbit">
-      <dl_setting var="settings_store_flag" min="1" step="1" max="1" shortname="store" handler="StoreSettings" module="subsystems/settings" values="Store"/>
+      <dl_setting var="settings_store_flag" min="1" step="1" max="1" shortname="store" handler="StoreSettings" module="modules/core/settings" values="Store"/>
       <dl_setting var="superbitrf.bind_mfg_id32" type="uint32" min="0" step="1" max="4294967295" shortname ="mfg_id" persistent="true" module="modules/datalink/superbitrf" handler="set_mfg_id"/>
       <dl_setting var="superbitrf.num_channels" type="uint8" min="0" step="1" max="14" shortname ="#chan" persistent="true" module="modules/datalink/superbitrf"/>
       <dl_setting var="superbitrf.protocol" type="uint8" min="0" step="1" max="32" shortname ="prot" persistent="true" module="modules/datalink/superbitrf" handler="set_protocol"/>
diff --git a/conf/settings/test_settings.xml b/conf/settings/test_settings.xml
index 3a10926980..dcf7f56277 100644
--- a/conf/settings/test_settings.xml
+++ b/conf/settings/test_settings.xml
@@ -4,11 +4,11 @@
   <dl_settings>
     <dl_settings NAME="Group1">
 
-      <dl_setting var="setting_f" min="0" step="0.1" max="42" shortname ="f" persistent="true" type="float" module="test/subsystems/test_settings"/>
+      <dl_setting var="setting_f" min="0" step="0.1" max="42" shortname ="f" persistent="true" type="float" module="test/modules/test_settings"/>
       <dl_setting var="setting_u8" min="0" step="1" max="42" shortname ="u8" persistent="true" type="uint8"/>
       <dl_setting var="setting_d" min="-42" step="0.1" max="42" shortname ="d" persistent="true" type="double"/>
       <dl_setting var="setting_i32" min="0" step="1" max="4242" shortname ="i32" persistent="true" type="int32"/>
-      <dl_setting var="settings_store_flag" min="0" step="1" max="1" shortname="store" handler="StoreSettings" module="subsystems/settings"/>
+      <dl_setting var="settings_store_flag" min="0" step="1" max="1" shortname="store" handler="StoreSettings" module="modules/core/settings"/>
 
     </dl_settings>
   </dl_settings>
diff --git a/doc/sphinx/source/developer_guide/abi.rst b/doc/sphinx/source/developer_guide/abi.rst
index 209922f440..c0f9b10b41 100644
--- a/doc/sphinx/source/developer_guide/abi.rst
+++ b/doc/sphinx/source/developer_guide/abi.rst
@@ -41,7 +41,7 @@ Include header and declare an ``abi_event`` as a global ``static`` variable (but
 
 .. code-block:: C
 
-    #include "subsystems/abi.h"
+    #include "modules/core/abi.h"
 
     static abi_event ev;
 
@@ -60,7 +60,7 @@ The first parameter is the sender ID you want to receive the message from.
 
 * ``ABI_BROADCAST`` is used to receive messages from all senders.
 * ``ABI_DISABLE`` disable the callback (it will never be called).
-* Senders IDs can be found in the file ``sw/airborne/subsystems/abi_sender_ids.h``
+* Senders IDs can be found in the file ``sw/airborne/modules/core/abi_sender_ids.h``
 
 The second parameter is a pointer to the global ``abi_event`` you declared. This variable **can't** be reused for another bind. You must declare one abi_event per bind.
 
@@ -80,7 +80,7 @@ Include header, then call the send function with the appropriate parameters
     struct foo f;
     AbiSendMsgDATA(SENDER_ID, var, s, &f);
 
-Replace ``SENDER_ID`` by your sender ID defined in ``sw/airborne/subsystems/abi_sender_ids.h``.
+Replace ``SENDER_ID`` by your sender ID defined in ``sw/airborne/modules/core/abi_sender_ids.h``.
 
 Your sender ID identifier should be constructed as the concatenation of the name of the message and the name of your module, suffixed with ``_ID``.
 
@@ -98,7 +98,7 @@ Your sender ID identifier should be constructed as the concatenation of the name
 Code generation
 ---------------
 
-The generated code will be in ``var/include/abi_messages.h`` and include some structure definition from ``sw/airborne/subsystems/abi_common.h`` (``sw/airborne/subsystems/abi.h`` is a convenience header that only includes ``var/include/abi_messages.h``).
+The generated code will be in ``var/include/abi_messages.h`` and include some structure definition from ``sw/airborne/modules/core/abi_common.h`` (``sw/airborne/modules/core/abi.h`` is a convenience header that only includes ``var/include/abi_messages.h``).
 
 Bind and Send functions are generated, as well as callback type definition. A linked list is used to store the binded callbacks for each message. The head of the list is in an array to allow a fast access. 
 
@@ -110,16 +110,16 @@ In depth
 Generated code
 ______________
 
-Here is the code of ``sw/airborne/subsystems/abi_common.h``:
+Here is the code of ``sw/airborne/modules/core/abi_common.h``:
 
 .. code-block:: C
 
     /* Include here headers with structure definition you may want to use with ABI
-     * Ex: '#include "subsystems/gps.h"' in order to use the GpsState structure
+     * Ex: '#include "modules/gps/gps.h"' in order to use the GpsState structure
      */
-    #include "subsystems/gps.h"
+    #include "modules/gps/gps.h"
 
-    #include "subsystems/abi_sender_ids.h"
+    #include "modules/core/abi_sender_ids.h"
 
     #ifdef ABI_C
     #define ABI_EXTERN
@@ -156,7 +156,7 @@ The generated code in ``var/include/abi_messages.h`` for the message defined abo
 .. code-block:: C
 
     // Code generated in var/include/abi_messages.h
-    #include "subsystems/abi_common.h
+    #include "modules/core/abi_common.h
     // Message IDs
     #define ABI_DATA_ID 0
     
@@ -195,5 +195,5 @@ If you want to use ABI outside of one of the Paparazzi firmwares (``rotorcraft``
 .. code-block:: C
 
     #define ABI_C 1
-    #include "subsystems/abi.h"
+    #include "modules/core/abi.h"
 
diff --git a/sw/airborne/arch/chibios/mcu_periph/adc_arch.c b/sw/airborne/arch/chibios/mcu_periph/adc_arch.c
index adcf33b735..c608e6da58 100644
--- a/sw/airborne/arch/chibios/mcu_periph/adc_arch.c
+++ b/sw/airborne/arch/chibios/mcu_periph/adc_arch.c
@@ -216,7 +216,7 @@ static void adc_sample_time_on_all_channels(uint32_t *smpr1, uint32_t *smpr2, ui
  * is collected). Since we are assuming continuous ADC conversion, the ADC state is
  * never equal to ADC_COMPLETE.
  *
- * @note    Averaging is done when the subsystems ask for ADC values
+ * @note    Averaging is done when the modules ask for ADC values
  * @param[in] adcp pointer to a @p ADCDriver object
  * @param[in] buffer pointer to a @p buffer with samples
  * @param[in] n number of samples
diff --git a/sw/airborne/boards/krooz/baro_board.h b/sw/airborne/boards/krooz/baro_board.h
index ec571679cc..c7da64d4e9 100644
--- a/sw/airborne/boards/krooz/baro_board.h
+++ b/sw/airborne/boards/krooz/baro_board.h
@@ -2,7 +2,7 @@
 /*
  * board specific interface for the KroozSD board
  *
- * It uses the subsystems/sensors/baro_ms5611_i2c.c driver
+ * It uses the modules/sensors/baro_ms5611_i2c.c driver
  */
 
 #ifndef BOARDS_KROOZ_BARO_H
diff --git a/sw/airborne/modules/imu/imu_vectornav.c b/sw/airborne/modules/imu/imu_vectornav.c
index 122fbe31a8..a3103ef171 100644
--- a/sw/airborne/modules/imu/imu_vectornav.c
+++ b/sw/airborne/modules/imu/imu_vectornav.c
@@ -23,7 +23,7 @@
 /**
  * @file modules/imu/imu_vectornav.c
  *
- * Vectornav VN-200 IMU subsystems, to be used with other AHRS/INS algorithms.
+ * Vectornav VN-200 IMU module, to be used with other AHRS/INS algorithms.
  */
 
 #include "modules/imu/imu_vectornav.h"
diff --git a/sw/airborne/modules/imu/imu_vectornav.h b/sw/airborne/modules/imu/imu_vectornav.h
index c27e650651..e95c87a514 100644
--- a/sw/airborne/modules/imu/imu_vectornav.h
+++ b/sw/airborne/modules/imu/imu_vectornav.h
@@ -23,7 +23,7 @@
 /**
  * @file modules/imu/imu_vectornav.h
  *
- * Vectornav VN-200 IMU subsystems, to be used with other AHRS/INS algorithms.
+ * Vectornav VN-200 IMU module, to be used with other AHRS/INS algorithms.
  */
 
 #ifndef IMU_VECTORNAV_H
diff --git a/sw/airborne/modules/ins/ins_vectornav.h b/sw/airborne/modules/ins/ins_vectornav.h
index c9aa511f23..54151acff2 100644
--- a/sw/airborne/modules/ins/ins_vectornav.h
+++ b/sw/airborne/modules/ins/ins_vectornav.h
@@ -22,14 +22,14 @@
 /**
  * @file ins_vectornav.h
  *
- * Vectornav VN-200 INS subsystem
+ * Vectornav VN-200 INS module
  *
  * @author Michal Podhradsky <michal.podhradsky@aggiemail.usu.edu>
  */
 #ifndef INS_VECTORNAV_H
 #define INS_VECTORNAV_H
 
-// Subsystems
+// Modules
 #include "modules/gps/gps.h"
 #include "modules/ins/ins.h"
 
diff --git a/sw/airborne/modules/sensors/baro.h b/sw/airborne/modules/sensors/baro.h
index 7addb301c4..13c9b9b1fe 100644
--- a/sw/airborne/modules/sensors/baro.h
+++ b/sw/airborne/modules/sensors/baro.h
@@ -28,8 +28,8 @@
  *
  */
 
-#ifndef SUBSYSTEMS_SENSORS_BARO_H
-#define SUBSYSTEMS_SENSORS_BARO_H
+#ifndef SENSORS_BARO_H
+#define SENSORS_BARO_H
 
 #include BOARD_CONFIG
 
@@ -43,4 +43,4 @@
 extern void baro_init(void);
 extern void baro_periodic(void);
 
-#endif /* SUBSYSTEMS_SENSORS_BARO_H */
+#endif /* SENSORS_BARO_H */
diff --git a/sw/airborne/test/subsystems/test_ahrs.c b/sw/airborne/test/modules/test_ahrs.c
similarity index 100%
rename from sw/airborne/test/subsystems/test_ahrs.c
rename to sw/airborne/test/modules/test_ahrs.c
diff --git a/sw/airborne/test/subsystems/test_imu.c b/sw/airborne/test/modules/test_imu.c
similarity index 100%
rename from sw/airborne/test/subsystems/test_imu.c
rename to sw/airborne/test/modules/test_imu.c
diff --git a/sw/airborne/test/subsystems/test_radio_control.c b/sw/airborne/test/modules/test_radio_control.c
similarity index 100%
rename from sw/airborne/test/subsystems/test_radio_control.c
rename to sw/airborne/test/modules/test_radio_control.c
diff --git a/sw/airborne/test/subsystems/test_settings.c b/sw/airborne/test/modules/test_settings.c
similarity index 100%
rename from sw/airborne/test/subsystems/test_settings.c
rename to sw/airborne/test/modules/test_settings.c
diff --git a/sw/airborne/test/subsystems/test_settings.h b/sw/airborne/test/modules/test_settings.h
similarity index 100%
rename from sw/airborne/test/subsystems/test_settings.h
rename to sw/airborne/test/modules/test_settings.h
diff --git a/sw/lib/python/paparazzi.py b/sw/lib/python/paparazzi.py
index 98a0b29ef5..c63e6e2299 100755
--- a/sw/lib/python/paparazzi.py
+++ b/sw/lib/python/paparazzi.py
@@ -20,10 +20,10 @@ PAPARAZZI_HOME  = getenv("PAPARAZZI_HOME", PAPARAZZI_SRC)
 # Directories
 conf_dir        = path.join(PAPARAZZI_HOME, "conf/")
 
-firmwares_dir   = path.join(conf_dir, "firmwares/")
+firmwares_dir   = path.join(conf_dir, "modules/firmwares/")
 modules_dir     = path.join(conf_dir, "modules/")
 airframes_dir   = path.join(conf_dir, "airframes/")
-boards_dir      = path.join(conf_dir, "boards/")
+boards_dir      = path.join(conf_dir, "modules/boards/")
 
 flight_plan_dir = path.join(conf_dir, "flight_plans/")
 
@@ -83,16 +83,10 @@ def get_list_of_modules():
     return get_list_of_files( modules_dir, ".xml")
 
 def get_list_of_firmwares():
-    return get_list_of_files( firmwares_dir, ".makefile")
+    return get_list_of_files( firmwares_dir, ".xml")
 
 def get_list_of_boards():
-    return get_list_of_files( boards_dir, ".makefile")
-
-def get_list_of_subsystems(firmware):
-    subsys_dir = path.join( firmwares_dir, "subsystems/" + firmware + "/")
-    # \todo how about shared
-    #subsys_dir = path.join( firmwares_dir, "subsystems/shared/" )
-    return get_list_of_files(subsys_dir, ".makefile")
+    return get_list_of_files( boards_dir, ".xml")
 
 def get_list_of_flight_plan_files():
     mylist = glob.glob(path.join(flight_plan_dir, "*.xml"))
@@ -135,14 +129,8 @@ if __name__ == '__main__':
     boards = get_list_of_boards()
     for b in boards:
       print(" - ```" + b + "```" )
-    print("\nFIRMWARES - SUBSYSTEMS\n---------\n")
+    print("\nFIRMWARES\n---------\n")
     firmwares = get_list_of_firmwares()
-    firmwares.append("shared")
-    for f in firmwares:
-        print(" - " + f)
-        subsystems = get_list_of_subsystems(f)
-        for s in subsystems:
-            print("   - ```", s, "```")
     print("\nMODULES\n-------\n")
     modules  = get_list_of_modules()
     for m in modules:
diff --git a/sw/misc/rctx/main_rctx.c b/sw/misc/rctx/main_rctx.c
index c1e3a69541..76d457e80b 100644
--- a/sw/misc/rctx/main_rctx.c
+++ b/sw/misc/rctx/main_rctx.c
@@ -74,10 +74,10 @@ LED_TOGGLE(3);
 #include "uart_hw.h"
 #include "uart.h"
 #include "autopilot.h"
-#include "subsystems/datalink/datalink.h"
+#include "modules/datalink/datalink.h"
 
 #include "messages.h"
-#include "subsystems/datalink/downlink.h"
+#include "modules/datalink/downlink.h"
 
 #if ((AC_ID > 0x108) || (AC_ID < (0x101)))
 //#error aircraft ID should be 0x101..0x108 for RC transmitter
diff --git a/sw/supervision/python/lib/database.py b/sw/supervision/python/lib/database.py
index 8cdae0efbe..f773ba314b 100644
--- a/sw/supervision/python/lib/database.py
+++ b/sw/supervision/python/lib/database.py
@@ -86,7 +86,6 @@ class Target(object):
         self.name = name
         self.board = board
 
-        self.subsystems = None
         self.defines = None
 
     def __repr__(self):
diff --git a/sw/tools/airframe_editor/airframe_editor.py b/sw/tools/airframe_editor/airframe_editor.py
index 7eba433f48..14a586ec27 100755
--- a/sw/tools/airframe_editor/airframe_editor.py
+++ b/sw/tools/airframe_editor/airframe_editor.py
@@ -56,11 +56,6 @@ class AirframeEditor:
         list_of_modules = paparazzi.get_list_of_modules()
         self.update_combo(self.modules_combo, list_of_modules)
 
-    def find_subsystems(self, widget):
-        self.textbox.set_text(self.firmwares_combo.get_active_text())
-        list_of_subsystems = paparazzi.get_list_of_subsystems(self.firmwares_combo.get_active_text())
-        self.update_combo(self.subsystems_combo, list_of_subsystems)
-
     def find_boards(self, widget):
         list_of_boards = paparazzi.get_list_of_boards()
         self.update_combo(self.boards_combo, list_of_boards)
@@ -248,9 +243,6 @@ class AirframeEditor:
         self.btnFirmwares = Gtk.Button("Firmwares")
         self.btnFirmwares.connect("clicked", self.find_firmwares)
 
-        self.btnSubSystem = Gtk.Button("SubSystems")
-        self.btnSubSystem.connect("clicked", self.find_subsystems)
-
         self.btnModules = Gtk.Button("Add Modules")
         self.btnModules.connect("clicked", self.find_modules)
 
@@ -272,9 +264,6 @@ class AirframeEditor:
 
         self.firmwares_combo = Gtk.ComboBoxText.new_with_entry()
         self.find_firmwares(self.firmwares_combo)
-        self.firmwares_combo.connect("changed", self.find_subsystems)
-
-        self.subsystems_combo = Gtk.ComboBoxText.new_with_entry()
 
         self.boards_combo = Gtk.ComboBoxText.new_with_entry()
         self.find_boards(self.boards_combo)
@@ -282,10 +271,8 @@ class AirframeEditor:
 
         self.firmwarebar = Gtk.HBox()
         self.firmwarebar.pack_start(self.btnFirmwares, True, True, 0)
-        self.firmwarebar.pack_start(self.btnSubSystem, True, True, 0)
         self.firmwarebar.pack_start(self.firmwares_combo, True, True, 0)
         self.firmwarebar.pack_start(self.boards_combo, True, True, 0)
-        self.firmwarebar.pack_start(self.subsystems_combo, True, True, 0)
 
         self.modules_combo = Gtk.ComboBoxText.new_with_entry()
         self.find_modules(self.modules_combo)
diff --git a/sw/tools/tcp_aircraft_server/phoenix/__init__.py b/sw/tools/tcp_aircraft_server/phoenix/__init__.py
index 1c49530ff6..e2f5b878f1 100644
--- a/sw/tools/tcp_aircraft_server/phoenix/__init__.py
+++ b/sw/tools/tcp_aircraft_server/phoenix/__init__.py
@@ -103,7 +103,6 @@ DEBUG_MESSAGES = {
 """
 Binary logs
 
-See format description in sw/airborne/subsystems/datalink/fms_link.c
 
 """
 
diff --git a/tests/modules/test_arch/subsystems/actuators/actuators_dualpwm_arch.h b/tests/modules/test_arch/modules/actuators/actuators_dualpwm_arch.h
similarity index 95%
rename from tests/modules/test_arch/subsystems/actuators/actuators_dualpwm_arch.h
rename to tests/modules/test_arch/modules/actuators/actuators_dualpwm_arch.h
index 2d2bd24311..16661ca7a8 100644
--- a/tests/modules/test_arch/subsystems/actuators/actuators_dualpwm_arch.h
+++ b/tests/modules/test_arch/modules/actuators/actuators_dualpwm_arch.h
@@ -19,7 +19,7 @@
  * Boston, MA 02111-1307, USA.
  */
 
-/** @file subsystems/actuators/actuators_dualpwm_arch.h
+/** @file modules/actuators/actuators_dualpwm_arch.h
  *  dummy servos handling for test
  */
 
diff --git a/tests/modules/test_arch/subsystems/actuators/actuators_pwm_arch.h b/tests/modules/test_arch/modules/actuators/actuators_pwm_arch.h
similarity index 95%
rename from tests/modules/test_arch/subsystems/actuators/actuators_pwm_arch.h
rename to tests/modules/test_arch/modules/actuators/actuators_pwm_arch.h
index 225c3ba13e..b599aa72da 100644
--- a/tests/modules/test_arch/subsystems/actuators/actuators_pwm_arch.h
+++ b/tests/modules/test_arch/modules/actuators/actuators_pwm_arch.h
@@ -19,7 +19,7 @@
  * Boston, MA 02111-1307, USA.
  */
 
-/** @file subsystems/actuators/actuators_pwm_arch.h
+/** @file modules/actuators/actuators_pwm_arch.h
  *  dummy servos handling for test
  */
 
diff --git a/tests/modules/test_arch/subsystems/actuators/servos_4015_MAT_hw.h b/tests/modules/test_arch/modules/actuators/servos_4015_MAT_hw.h
similarity index 100%
rename from tests/modules/test_arch/subsystems/actuators/servos_4015_MAT_hw.h
rename to tests/modules/test_arch/modules/actuators/servos_4015_MAT_hw.h
diff --git a/tests/modules/test_arch/subsystems/actuators/servos_4017_hw.h b/tests/modules/test_arch/modules/actuators/servos_4017_hw.h
similarity index 100%
rename from tests/modules/test_arch/subsystems/actuators/servos_4017_hw.h
rename to tests/modules/test_arch/modules/actuators/servos_4017_hw.h
diff --git a/tests/modules/test_arch/subsystems/actuators/servos_ppm_hw.h b/tests/modules/test_arch/modules/actuators/servos_ppm_hw.h
similarity index 100%
rename from tests/modules/test_arch/subsystems/actuators/servos_ppm_hw.h
rename to tests/modules/test_arch/modules/actuators/servos_ppm_hw.h