diff --git a/Makefile b/Makefile
index 31640064..8e19f4f8 100755
--- a/Makefile
+++ b/Makefile
@@ -3,18 +3,19 @@
 #
 BUILDTYPE ?= debug
 INSTALLPREFIX ?= exe
-FSWBUILDDIR ?= $(CURDIR)/fsw/build
-GSWBUILDDIR ?= $(CURDIR)/gsw/build
-SIMBUILDDIR ?= $(CURDIR)/sims/build
+NOS3BUILDDIR ?= /tmp/nos3
+FSWBUILDDIR ?= $(NOS3BUILDDIR)/fsw
+GSWBUILDDIR ?= $(NOS3BUILDDIR)/gsw
+SIMBUILDDIR ?= $(NOS3BUILDDIR)/sims
 
 export CFS_APP_PATH = ../components
-export MISSION_DEFS = ../cfg/build/
-export MISSIONCONFIG = ../cfg/build/nos3
+export MISSION_DEFS = /tmp/nos3/cfg/nos3_defs
+export MISSIONCONFIG = nos3
 
 # The "prep" step requires extra options that are specified via enviroment variables.
 # Certain special ones should be passed via cache (-D) options to CMake.
 # These are only needed for the "prep" target but they are computed globally anyway.
-PREP_OPTS :=
+PREP_OPTS := -DMISSION_DEFS=$(MISSION_DEFS)
 
 ifneq ($(INSTALLPREFIX),)
 PREP_OPTS += -DCMAKE_INSTALL_PREFIX=$(INSTALLPREFIX)
@@ -48,7 +49,7 @@ all:
 
 build-cryptolib:
 	mkdir -p $(GSWBUILDDIR)
-	cd $(GSWBUILDDIR) && cmake $(PREP_OPTS) -DSUPPORT=1 ../../components/cryptolib
+	cd $(GSWBUILDDIR) && cmake -DSUPPORT=1 $(CURDIR)/components/cryptolib
 	$(MAKE) --no-print-directory -C $(GSWBUILDDIR)
 
 build-fsw:
@@ -56,13 +57,13 @@ ifeq ($(FLIGHT_SOFTWARE), fprime)
 	cd fsw/fprime/fprime-nos3 && fprime-util generate && fprime-util build
 else
 	mkdir -p $(FSWBUILDDIR)
-	cd $(FSWBUILDDIR) && cmake $(PREP_OPTS) ../cfe
+	cd $(FSWBUILDDIR) && cmake $(PREP_OPTS) $(CURDIR)/fsw/cfe
 	$(MAKE) --no-print-directory -C $(FSWBUILDDIR) mission-install
 endif
 
 build-sim:
 	mkdir -p $(SIMBUILDDIR)
-	cd $(SIMBUILDDIR) && cmake -DCMAKE_INSTALL_PREFIX=$(SIMBUILDDIR) ..
+	cd $(SIMBUILDDIR) && cmake -DCMAKE_INSTALL_PREFIX=$(SIMBUILDDIR) $(CURDIR)/sims
 	$(MAKE) --no-print-directory -C $(SIMBUILDDIR) install
 
 build-test:
@@ -70,7 +71,7 @@ ifeq ($(FLIGHT_SOFTWARE), fprime)
 	# TODO
 else
 	mkdir -p $(FSWBUILDDIR)
-	cd $(FSWBUILDDIR) && cmake $(PREP_OPTS) -DENABLE_UNIT_TESTS=true ../cfe
+	cd $(FSWBUILDDIR) && cmake $(PREP_OPTS) -DENABLE_UNIT_TESTS=true $(CURDIR)/fsw/cfe
 	$(MAKE) --no-print-directory -C $(FSWBUILDDIR) mission-install
 endif
 
@@ -81,22 +82,19 @@ clean:
 	$(MAKE) clean-fsw
 	$(MAKE) clean-sim
 	$(MAKE) clean-gsw
-	rm -rf cfg/build
+	./scripts/clean.sh
 
 clean-fsw:
-	rm -rf cfg/build/nos3_defs
-	rm -rf fsw/build
 	rm -rf fsw/fprime/fprime-nos3/build-artifacts
 	rm -rf fsw/fprime/fprime-nos3/build-fprime-automatic-native
 	rm -rf fsw/fprime/fprime-nos3/fprime-venv
+	./scripts/fsw/fsw_clean.sh
 
 clean-sim:
-	rm -rf sims/build
+	./scripts/sim/sim_clean.sh
 
 clean-gsw:
-	rm -rf gsw/build
-	rm -rf gsw/cosmos/build
-	rm -rf /tmp/nos3
+	./scripts/gsw/gsw_clean.sh
 
 config:
 	./scripts/cfg/config.sh
@@ -105,17 +103,17 @@ debug:
 	./scripts/debug.sh
 
 fsw: 
-	./cfg/build/fsw_build.sh
+	$(NOS3BUILDDIR)/cfg/fsw_build.sh $(CURDIR)
 
 gsw:
 	./scripts/gsw/build_cryptolib.sh
-	./cfg/build/gsw_build.sh
+	$(NOS3BUILDDIR)/cfg/gsw_build.sh $(CURDIR)
 
 igniter:
 	./scripts/igniter_launch.sh
 
 launch:
-	./cfg/build/launch.sh
+	$(NOS3BUILDDIR)/cfg/launch.sh $(CURDIR)
 
 log:
 	./scripts/log.sh
@@ -130,7 +128,7 @@ prep-sat:
 	./scripts/cfg/prep_sat.sh
 
 sim:
-	./scripts/build_sim.sh
+	./scripts/sim/build_sim.sh
 
 start-gsw:
 	./scripts/gsw/launch_gsw.sh
diff --git a/cfg/InOut/Inp_Graphics.txt b/cfg/InOut/Inp_Graphics.txt
index 34966368..7aa7ae54 100644
--- a/cfg/InOut/Inp_Graphics.txt
+++ b/cfg/InOut/Inp_Graphics.txt
@@ -3,7 +3,7 @@
 Skymap09.txt                       !  Star Catalog File Name
 TRUE                               !  Map Window Exists
 FALSE                              !  Orrery Window Exists
-TRUE                               !  Unit Sphere Window Exists
+FALSE                              !  Unit Sphere Window Exists
 ******************************* POV *********************************
 FALSE                              !  Pause at Startup
 TRACK_HOST                         !  POV Mode (TRACK_HOST, TRACK_TARGET, FIXED_IN_HOST)
diff --git a/cfg/nos3_defs/targets.cmake b/cfg/nos3_defs/targets.cmake
index c5c220ee..7d13c421 100644
--- a/cfg/nos3_defs/targets.cmake
+++ b/cfg/nos3_defs/targets.cmake
@@ -97,7 +97,7 @@ list(APPEND MISSION_GLOBAL_APPLIST
         fm
         lc
         sbn
-        sbn_tcp
+        sbn/modules/protocol/sbn_tcp
         sbn_client
         sc
         sch
diff --git a/scripts/cfg/config.sh b/scripts/cfg/config.sh
index 5718fef6..6028f6bf 100755
--- a/scripts/cfg/config.sh
+++ b/scripts/cfg/config.sh
@@ -6,13 +6,19 @@
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 source $SCRIPT_DIR/../env.sh
 
-# Make flight software configuration directory
-mkdir -p $BASE_DIR/cfg/build
+# Make build directories
+mkdir -p $USER_NOS3_BUILD_DIR/cfg
+mkdir -p $USER_NOS3_BUILD_DIR/fsw
+mkdir -p $USER_NOS3_BUILD_DIR/gsw
+mkdir -p $USER_NOS3_BUILD_DIR/sims
 
 # Copy baseline configurations into build directory
-cp -r $BASE_DIR/cfg/InOut $BASE_DIR/cfg/build/
-cp -r $BASE_DIR/cfg/nos3_defs $BASE_DIR/cfg/build/
-cp -r $BASE_DIR/cfg/sims $BASE_DIR/cfg/build/
+cp -r $BASE_DIR/cfg/InOut $USER_NOS3_BUILD_DIR/cfg/
+cp -r $BASE_DIR/cfg/nos3_defs $USER_NOS3_BUILD_DIR/cfg/
+cp -r $BASE_DIR/cfg/sims $USER_NOS3_BUILD_DIR/cfg/
 
 # Configure flight software
 python3 $SCRIPT_DIR/cfg/configure.py
+
+# Set permissions
+chmod 777 -R $USER_NOS3_BUILD_DIR
diff --git a/scripts/cfg/configure.py b/scripts/cfg/configure.py
old mode 100644
new mode 100755
index ccc27aee..49941c05
--- a/scripts/cfg/configure.py
+++ b/scripts/cfg/configure.py
@@ -24,12 +24,12 @@
 
 if (fsw_cfg == 'fprime'):
     fsw_identified = 1
-    os.system('cp ./scripts/fsw/fsw_fprime_build.sh ./cfg/build/fsw_build.sh')
-    os.system('cp ./scripts/fsw/fsw_fprime_launch.sh ./cfg/build/launch.sh')
+    os.system('cp ./scripts/fsw/fsw_fprime_build.sh /tmp/nos3/cfg/fsw_build.sh')
+    os.system('cp ./scripts/fsw/fsw_fprime_launch.sh /tmp/nos3/cfg/launch.sh')
 if (fsw_cfg == 'cfs'):
     fsw_identified = 1
-    os.system('cp ./scripts/fsw/fsw_cfs_build.sh ./cfg/build/fsw_build.sh')
-    os.system('cp ./scripts/fsw/fsw_cfs_launch.sh ./cfg/build/launch.sh')
+    os.system('cp ./scripts/fsw/fsw_cfs_build.sh /tmp/nos3/cfg/fsw_build.sh')
+    os.system('cp ./scripts/fsw/fsw_cfs_launch.sh /tmp/nos3/cfg/launch.sh')
 if (fsw_identified == 0):
     print('Invalid FSW in configuration file!')
     print('Exiting due to error...')
@@ -41,25 +41,25 @@
 
 gsw_identified = 0
 if (gsw_cfg == 'openc3'):
-    # Copy openc3 scripts into ./cfg/build
+    # Copy openc3 scripts into /tmp/nos3
     gsw_identified = 1
-    os.system('cp ./scripts/gsw/gsw_openc3_build.sh ./cfg/build/gsw_build.sh')
-    os.system('cp ./scripts/gsw/gsw_openc3_launch.sh ./cfg/build/gsw_launch.sh')
+    os.system('cp ./scripts/gsw/gsw_openc3_build.sh /tmp/nos3/cfg/gsw_build.sh')
+    os.system('cp ./scripts/gsw/gsw_openc3_launch.sh /tmp/nos3/cfg/gsw_launch.sh')
 if (gsw_cfg == 'cosmos'):
-    # Copy cosmos scripts into ./cfg/build
+    # Copy cosmos scripts into /tmp/nos3
     gsw_identified = 1
-    os.system('cp ./scripts/gsw/gsw_cosmos_build.sh ./cfg/build/gsw_build.sh')
-    os.system('cp ./scripts/gsw/gsw_cosmos_launch.sh ./cfg/build/gsw_launch.sh')
+    os.system('cp ./scripts/gsw/gsw_cosmos_build.sh /tmp/nos3/cfg/gsw_build.sh')
+    os.system('cp ./scripts/gsw/gsw_cosmos_launch.sh /tmp/nos3/cfg/gsw_launch.sh')
 if (gsw_cfg == 'fprime'):
-    # Copy fprime scripts into ./cfg/build
+    # Copy fprime scripts into /tmp/nos3
     gsw_identified = 1
-    os.system('cp ./scripts/gsw/gsw_fprime_build.sh ./cfg/build/gsw_build.sh')
-    os.system('cp ./scripts/gsw/gsw_fprime_launch.sh ./cfg/build/gsw_launch.sh')
+    os.system('cp ./scripts/gsw/gsw_fprime_build.sh /tmp/nos3/cfg/gsw_build.sh')
+    os.system('cp ./scripts/gsw/gsw_fprime_launch.sh /tmp/nos3/cfg/gsw_launch.sh')
 if (gsw_cfg == 'ait'):
-    # Copy ait scripts into ./cfg/build
+    # Copy ait scripts into /tmp/nos3
     gsw_identified = 1
-    os.system('cp ./scripts/gsw/gsw_ait_build.sh ./cfg/build/gsw_build.sh')
-    os.system('cp ./scripts/gsw/gsw_ait_launch.sh ./cfg/build/gsw_launch.sh')
+    os.system('cp ./scripts/gsw/gsw_ait_build.sh /tmp/nos3/cfg/gsw_build.sh')
+    os.system('cp ./scripts/gsw/gsw_ait_launch.sh /tmp/nos3/cfg/gsw_launch.sh')
 if (gsw_identified == 0):
     print('Invalid GSW in configuration file!')
     print('Exiting due to error...')
@@ -242,7 +242,7 @@
         lines.insert(sc_startup_eof, cf_line)
                         
         # Write startup script file
-        with open('./cfg/build/nos3_defs/cpu1_cfe_es_startup.scr', 'w') as fp:
+        with open('/tmp/nos3/cfg/nos3_defs/cpu1_cfe_es_startup.scr', 'w') as fp:
             lines = "".join(lines)
             fp.write(lines)
 
@@ -273,7 +273,7 @@
         lines[date_index] = mission_start_time_utc.strftime('%m %d %Y') + '  !  Date (UTC) (Month, Day, Year)\n'
         lines[time_index] = mission_start_time_utc.strftime('%H %M %S') + '  !  Time (UTC) (Hr,Min,Sec)\n'
 
-        with open('./cfg/build/InOut/Inp_Sim.txt', 'w') as fp:
+        with open('/tmp/nos3/cfg/InOut/Inp_Sim.txt', 'w') as fp:
             lines = "".join(lines)
             fp.write(lines)
 
@@ -288,7 +288,7 @@
         
         lines[tipoff_index] = sc_orbit_tipoff_x + ' ' + sc_orbit_tipoff_y + ' ' + sc_orbit_tipoff_z + '  ! Ang Vel (deg/sec)\n'
 
-        with open('./cfg/build/InOut/SC_NOS3.txt', 'w') as fp:
+        with open('/tmp/nos3/cfg/InOut/SC_NOS3.txt', 'w') as fp:
             lines = "".join(lines)
             fp.write(lines)
 
@@ -385,7 +385,7 @@
         if (sc_thruster_en != 'true'):
             lines[thruster_index] = ipc_off
 
-        with open('./cfg/build/InOut/Inp_IPC.txt', 'w') as fp:
+        with open('/tmp/nos3/cfg/InOut/Inp_IPC.txt', 'w') as fp:
             lines = "".join(lines)
             fp.write(lines)
 
@@ -408,7 +408,7 @@
         torquer_index = 999
         thruster_index = 999
 
-        with open('./cfg/build/sims/nos3-simulator.xml', 'r') as fp:
+        with open('/tmp/nos3/cfg/sims/nos3-simulator.xml', 'r') as fp:
             lines = fp.readlines()
             for line in lines:
                 if line.find('camsim</name>') != -1:
@@ -487,6 +487,6 @@
         if (sc_thruster_en != 'true'):
             lines[thruster_index] = sim_disabled
 
-        with open('./cfg/build/sims/nos3-simulator.xml', 'w') as fp:
+        with open('/tmp/nos3/cfg/sims/nos3-simulator.xml', 'w') as fp:
             lines = "".join(lines)
             fp.write(lines)
diff --git a/scripts/clean.sh b/scripts/clean.sh
new file mode 100755
index 00000000..03713d5e
--- /dev/null
+++ b/scripts/clean.sh
@@ -0,0 +1,19 @@
+#!/bin/bash -i
+#
+# Convenience script for NOS3 development
+# Use with the Dockerfile in the deployment repository
+# https://github.com/nasa-itc/deployment
+#
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+source $SCRIPT_DIR/env.sh
+
+# Check that NOS3 build directory exists
+if [ -d $USER_NOS3_BUILD_DIR ]; then
+
+    # Cleanup all build files
+    $DFLAGS -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name "nos_clean" -w $BASE_DIR $DBOX rm -rf $USER_NOS3_BUILD_DIR/*
+
+    # Remove build directory
+    yes | rm -r $USER_NOS3_BUILD_DIR 2> /dev/null
+fi
diff --git a/scripts/debug.sh b/scripts/debug.sh
index 05f479db..d5e18a79 100755
--- a/scripts/debug.sh
+++ b/scripts/debug.sh
@@ -9,4 +9,4 @@ SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 source $SCRIPT_DIR/env.sh
 
 mkdir -p $BASE_DIR/fsw/build
-$DFLAGS_CPUS -v $BASE_DIR:$BASE_DIR -v $USER_NOS3_DIR:$USER_NOS3_DIR -w $BASE_DIR --sysctl fs.mqueue.msg_max=10000 --ulimit rtprio=99 --cap-add=sys_nice --name "nos3_debug" $DBOX bash
+$DFLAGS_CPUS -v $BASE_DIR:$BASE_DIR -v $USER_NOS3_DIR:$USER_NOS3_DIR -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR -w $BASE_DIR --sysctl fs.mqueue.msg_max=10000 --ulimit rtprio=99 --cap-add=sys_nice --name "nos3_debug" $DBOX bash
diff --git a/scripts/env.sh b/scripts/env.sh
index 546eaa34..2d9a0f99 100755
--- a/scripts/env.sh
+++ b/scripts/env.sh
@@ -5,21 +5,24 @@
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 BASE_DIR=$(cd `dirname $SCRIPT_DIR` && pwd)
-FSW_DIR=$BASE_DIR/fsw/build/exe/cpu1
+
+USERDIR=$(cd ~/ && pwd)
+USER_NOS3_DIR=$USERDIR/.nos3
+USER_NOS3_BUILD_DIR=/tmp/nos3
+
+FSW_DIR=$USER_NOS3_BUILD_DIR/fsw/exe/cpu1
 GSW_BIN=$BASE_DIR/gsw/cosmos/build/openc3-cosmos-nos3
 GSW_DIR=$BASE_DIR/gsw/cosmos
-SIM_DIR=$BASE_DIR/sims/build
+SIM_DIR=$USER_NOS3_BUILD_DIR/sims
 SIM_BIN=$SIM_DIR/bin
 
-if [ -d $SIM_DIR/bin ]; then
-    SIMS=$(ls $SIM_BIN/nos3*simulator) 
-fi 
+#if [ -d $SIM_DIR/bin ]; then
+#    SIMS=$(ls $SIM_BIN/nos3*simulator) 
+#fi 
 
 DATE=$(date "+%Y%m%d%H%M")
 NUM_CPUS="$( nproc )"
 
-USERDIR=$(cd ~/ && pwd)
-USER_NOS3_DIR=$(cd ~/ && pwd)/.nos3
 OPENC3_DIR=$USER_NOS3_DIR/cosmos
 OPENC3_PATH=$OPENC3_DIR/openc3.sh
 
@@ -39,7 +42,7 @@ INFLUXDB_ADMIN_PASSWORD=admin_password
 #    DNETWORK="docker network"
 #else
     DCALL="docker"
-    DFLAGS="docker run --rm -it -v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro -u $(id -u $(stat -c '%U' $SCRIPT_DIR/env.sh)):$(getent group $(stat -c '%G' $SCRIPT_DIR/env.sh) | cut -d: -f3)"
+    DFLAGS="docker run --rm -it -v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro -u $(id -u):$(getent group $(stat -c '%G' $SCRIPT_DIR/env.sh) | cut -d: -f3)"
     DFLAGS_CPUS="$DFLAGS --cpus=$NUM_CPUS"
     DCREATE="docker create --rm -it"
     DNETWORK="docker network"
diff --git a/scripts/fsw/fsw_cfs_build.sh b/scripts/fsw/fsw_cfs_build.sh
index f9e4e261..b0566f6e 100755
--- a/scripts/fsw/fsw_cfs_build.sh
+++ b/scripts/fsw/fsw_cfs_build.sh
@@ -5,9 +5,8 @@
 # https://github.com/nasa-itc/deployment
 #
 
-# Note this is copied to ./cfg/build as part of `make config`
-SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-source $SCRIPT_DIR/../../scripts/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
 
 # Check that local NOS3 directory exists
 if [ ! -d $USER_NOS3_DIR ]; then
@@ -18,15 +17,12 @@ if [ ! -d $USER_NOS3_DIR ]; then
 fi
 
 # Check that configure build directory exists
-if [ ! -d $BASE_DIR/cfg/build ]; then
+if [ ! -d $USER_NOS3_BUILD_DIR/cfg ]; then
     echo ""
     echo "    Need to run make config first!"
     echo ""
     exit 1
 fi
 
-# Make flight software build directory
-mkdir -p $BASE_DIR/fsw/build
-
 # Build
-$DFLAGS_CPUS -v $BASE_DIR:$BASE_DIR --name "nos_build_fsw" -w $BASE_DIR $DBOX make -j$NUM_CPUS -e FLIGHT_SOFTWARE=cfs build-fsw
+$DFLAGS_CPUS -v $BASE_DIR:$BASE_DIR -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name "nos_build_fsw" -w $BASE_DIR $DBOX make -j$NUM_CPUS -e FLIGHT_SOFTWARE=cfs build-fsw
diff --git a/scripts/fsw/fsw_cfs_launch.sh b/scripts/fsw/fsw_cfs_launch.sh
index 9dd354a8..20ce8e29 100755
--- a/scripts/fsw/fsw_cfs_launch.sh
+++ b/scripts/fsw/fsw_cfs_launch.sh
@@ -5,9 +5,8 @@
 # https://github.com/nasa-itc/deployment
 #
 
-# Note this is copied to ./cfg/build as part of `make config`
-SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-source $SCRIPT_DIR/../../scripts/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
 
 # Check that local NOS3 directory exists
 if [ ! -d $USER_NOS3_DIR ]; then
@@ -18,7 +17,7 @@ if [ ! -d $USER_NOS3_DIR ]; then
 fi
 
 # Check that configure build directory exists
-if [ ! -d $BASE_DIR/cfg/build ]; then
+if [ ! -d $USER_NOS3_BUILD_DIR/cfg ]; then
     echo ""
     echo "    Need to run make config first!"
     echo ""
@@ -53,7 +52,7 @@ echo ""
 
 echo "Launch GSW..."
 echo ""
-source $BASE_DIR/cfg/build/gsw_launch.sh
+source $USER_NOS3_BUILD_DIR/cfg/gsw_launch.sh $BASE_DIR
 
 echo "Create NOS interfaces..."
 export GND_CFG_FILE="-f nos3-simulator.xml"
@@ -88,7 +87,7 @@ do
 
     echo $SC_NUM " - 42..."
     rm -rf $USER_NOS3_DIR/42/NOS3InOut
-    cp -r $BASE_DIR/cfg/build/InOut $USER_NOS3_DIR/42/NOS3InOut
+    cp -r $USER_NOS3_BUILD_DIR/cfg/InOut $USER_NOS3_DIR/42/NOS3InOut
     xhost +local:*
     gnome-terminal --tab --title=$SC_NUM" - 42" -- $DFLAGS -e DISPLAY=$DISPLAY -v $USER_NOS3_DIR:$USER_NOS3_DIR -v /tmp/.X11-unix:/tmp/.X11-unix:ro --name $SC_NUM"_fortytwo" -h fortytwo --network=$SC_NETNAME -w $USER_NOS3_DIR/42 -t $DBOX $USER_NOS3_DIR/42/42 NOS3InOut
     echo ""
@@ -101,12 +100,12 @@ do
     cd $FSW_DIR
     # Debugging
     # Replace `--tab` with `--window-with-profile=KeepOpen` once you've created this gnome-terminal profile manually
-    gnome-terminal --title=$SC_NUM" - NOS3 Flight Software" -- $DFLAGS -v $BASE_DIR:$BASE_DIR --name $SC_NUM"_nos_fsw" -h nos_fsw --network=$SC_NETNAME -w $FSW_DIR --sysctl fs.mqueue.msg_max=10000 --ulimit rtprio=99 --cap-add=sys_nice $DBOX $SCRIPT_DIR/fsw/fsw_respawn.sh &
+    gnome-terminal --title=$SC_NUM" - NOS3 Flight Software" -- $DFLAGS -v $BASE_DIR:$BASE_DIR -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name $SC_NUM"_nos_fsw" -h nos_fsw --network=$SC_NETNAME -w $FSW_DIR --sysctl fs.mqueue.msg_max=10000 --ulimit rtprio=99 --cap-add=sys_nice $DBOX $SCRIPT_DIR/fsw/fsw_respawn.sh &
     #gnome-terminal --window-with-profile=KeepOpen --title=$SC_NUM" - NOS3 Flight Software" -- $DFLAGS -v $BASE_DIR:$BASE_DIR --name $SC_NUM"_nos_fsw" -h nos_fsw --network=$SC_NETNAME -w $FSW_DIR --sysctl fs.mqueue.msg_max=10000 --ulimit rtprio=99 --cap-add=sys_nice $DBOX $FSW_DIR/core-cpu1 -R PO &
     echo ""
 
     echo $SC_NUM " - CryptoLib..."
-    gnome-terminal --tab --title=$SC_NUM" - CryptoLib" -- $DFLAGS -v $BASE_DIR:$BASE_DIR --name $SC_NUM"_cryptolib"  --network=$SC_NETNAME --network-alias=cryptolib -w $BASE_DIR/gsw/build $DBOX ./support/standalone
+    gnome-terminal --tab --title=$SC_NUM" - CryptoLib" -- $DFLAGS -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name $SC_NUM"_cryptolib"  --network=$SC_NETNAME --network-alias=cryptolib -w $USER_NOS3_BUILD_DIR/gsw $DBOX ./support/standalone
     echo ""
 
     echo $SC_NUM " - Simulators..."
diff --git a/scripts/fsw/fsw_clean.sh b/scripts/fsw/fsw_clean.sh
new file mode 100755
index 00000000..38173093
--- /dev/null
+++ b/scripts/fsw/fsw_clean.sh
@@ -0,0 +1,15 @@
+#!/bin/bash -i
+#
+# Convenience script for NOS3 development
+# Use with the Dockerfile in the deployment repository
+# https://github.com/nasa-itc/deployment
+#
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+source $SCRIPT_DIR/env.sh
+
+# Check that NOS3 build directory exists
+if [ -d $USER_NOS3_BUILD_DIR/fsw ]; then
+    # Cleanup all build files
+    $DFLAGS -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name "nos_clean" -w $BASE_DIR $DBOX rm -rf $USER_NOS3_BUILD_DIR/fsw/*
+fi
diff --git a/scripts/fsw/fsw_fprime_build.sh b/scripts/fsw/fsw_fprime_build.sh
index 199c10be..c449364b 100755
--- a/scripts/fsw/fsw_fprime_build.sh
+++ b/scripts/fsw/fsw_fprime_build.sh
@@ -5,9 +5,8 @@
 # https://github.com/nasa-itc/deployment
 #
 
-SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[1]}" )/scripts" && pwd )
-source $SCRIPT_DIR/env.sh
-
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
 
 # Check that local NOS3 directory exists
 if [ ! -d $USER_NOS3_DIR ]; then
@@ -18,7 +17,7 @@ if [ ! -d $USER_NOS3_DIR ]; then
 fi
 
 # Check that configure build directory exists
-if [ ! -d $BASE_DIR/cfg/build ]; then
+if [ ! -d $USER_NOS3_BUILD_DIR/cfg ]; then
     echo ""
     echo "    Need to run make config first!"
     echo ""
diff --git a/scripts/fsw/fsw_fprime_launch.sh b/scripts/fsw/fsw_fprime_launch.sh
index 4d041f4d..3b60e1bc 100755
--- a/scripts/fsw/fsw_fprime_launch.sh
+++ b/scripts/fsw/fsw_fprime_launch.sh
@@ -5,9 +5,8 @@
 # https://github.com/nasa-itc/deployment
 #
 
-# Note this is copied to ./cfg/build as part of `make config`
-SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-source $SCRIPT_DIR/../../scripts/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
 
 # Check that local NOS3 directory exists
 if [ ! -d $USER_NOS3_DIR ]; then
@@ -18,7 +17,7 @@ if [ ! -d $USER_NOS3_DIR ]; then
 fi
 
 # Check that configure build directory exists
-if [ ! -d $BASE_DIR/cfg/build ]; then
+if [ ! -d $USER_NOS3_BUILD_DIR/cfg ]; then
     echo ""
     echo "    Need to run make config first!"
     echo ""
@@ -51,8 +50,9 @@ $DNETWORK create \
     nos3_core
 echo ""
 
-#echo "Launch GSW..."
-$BASE_DIR/cfg/build/gsw_launch.sh
+echo "Launch GSW..."
+echo ""
+source $USER_NOS3_BUILD_DIR/cfg/gsw_launch.sh $BASE_DIR
 echo ""
 
 echo "Create NOS interfaces..."
@@ -88,7 +88,7 @@ do
 
     echo $SC_NUM " - 42..."
     rm -rf $USER_NOS3_DIR/42/NOS3InOut
-    cp -r $BASE_DIR/cfg/build/InOut $USER_NOS3_DIR/42/NOS3InOut
+    cp -r $USER_NOS3_BUILD_DIR/cfg/InOut $USER_NOS3_DIR/42/NOS3InOut
     xhost +local:*
     gnome-terminal --tab --title=$SC_NUM" - 42" -- $DFLAGS -e DISPLAY=$DISPLAY -v $USER_NOS3_DIR:$USER_NOS3_DIR -v /tmp/.X11-unix:/tmp/.X11-unix:ro --name $SC_NUM"_fortytwo" -h fortytwo --network=$SC_NETNAME -w $USER_NOS3_DIR/42 -t $DBOX $USER_NOS3_DIR/42/42 NOS3InOut
     echo ""
@@ -102,7 +102,7 @@ do
     # Replace `--tab` with `--window-with-profile=KeepOpen` once you've created this gnome-terminal profile manually
 
     echo $SC_NUM " - CryptoLib..."
-    gnome-terminal --tab --title=$SC_NUM" - CryptoLib" -- $DFLAGS -v $BASE_DIR:$BASE_DIR --name $SC_NUM"_cryptolib"  --network=$SC_NETNAME --network-alias=cryptolib -w $BASE_DIR/gsw/build $DBOX ./support/standalone
+    gnome-terminal --tab --title=$SC_NUM" - CryptoLib" -- $DFLAGS -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name $SC_NUM"_cryptolib"  --network=$SC_NETNAME --network-alias=cryptolib -w $USER_NOS3_BUILD_DIR/gsw $DBOX ./support/standalone
     echo ""
 
     echo $SC_NUM " - Simulators..."
diff --git a/scripts/fsw/onair_launch.sh b/scripts/fsw/onair_launch.sh
old mode 100644
new mode 100755
diff --git a/scripts/gsw/build_cryptolib.sh b/scripts/gsw/build_cryptolib.sh
index c8f47e94..d03849ac 100755
--- a/scripts/gsw/build_cryptolib.sh
+++ b/scripts/gsw/build_cryptolib.sh
@@ -17,15 +17,12 @@ if [ ! -d $USER_NOS3_DIR ]; then
 fi
 
 # Check that configure build directory exists
-if [ ! -d $BASE_DIR/cfg/build ]; then
+if [ ! -d $USER_NOS3_BUILD_DIR/cfg ]; then
     echo ""
     echo "    Need to run make config first!"
     echo ""
     exit 1
 fi
 
-# Make ground software build directory
-mkdir -p $BASE_DIR/gsw/build
-
 # Build
-$DFLAGS_CPUS -v $BASE_DIR:$BASE_DIR --name "nos_build_cryptolib" -w $BASE_DIR $DBOX make -j$NUM_CPUS build-cryptolib
+$DFLAGS_CPUS -v $BASE_DIR:$BASE_DIR -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name "nos_build_cryptolib" -w $BASE_DIR $DBOX make -j$NUM_CPUS build-cryptolib
diff --git a/scripts/gsw/gsw_ait_build.sh b/scripts/gsw/gsw_ait_build.sh
index 1ab46d11..73ed59aa 100755
--- a/scripts/gsw/gsw_ait_build.sh
+++ b/scripts/gsw/gsw_ait_build.sh
@@ -3,9 +3,8 @@
 # Convenience script for NOS3 development
 #
 
-CFG_BUILD_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-SCRIPT_DIR=$CFG_BUILD_DIR/../../scripts
-source $SCRIPT_DIR/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
 
 echo "AIT build..."
 $DCALL image pull ghcr.io/sphinxdefense/gsw-ait:main
diff --git a/scripts/gsw/gsw_ait_launch.sh b/scripts/gsw/gsw_ait_launch.sh
index 02d304e3..096bed69 100755
--- a/scripts/gsw/gsw_ait_launch.sh
+++ b/scripts/gsw/gsw_ait_launch.sh
@@ -3,9 +3,9 @@
 # Convenience script for NOS3 development
 #
 
-CFG_BUILD_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-SCRIPT_DIR=$CFG_BUILD_DIR/../../scripts
-source $SCRIPT_DIR/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
+
 export GSW="ait"
 
 echo "AIT launch..."
diff --git a/scripts/gsw/gsw_clean.sh b/scripts/gsw/gsw_clean.sh
new file mode 100755
index 00000000..69e5ff57
--- /dev/null
+++ b/scripts/gsw/gsw_clean.sh
@@ -0,0 +1,15 @@
+#!/bin/bash -i
+#
+# Convenience script for NOS3 development
+# Use with the Dockerfile in the deployment repository
+# https://github.com/nasa-itc/deployment
+#
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+source $SCRIPT_DIR/env.sh
+
+# Check that NOS3 build directory exists
+if [ -d $USER_NOS3_BUILD_DIR/gsw ]; then
+    # Cleanup all build files
+    $DFLAGS -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name "nos_clean" -w $BASE_DIR $DBOX rm -rf $USER_NOS3_BUILD_DIR/gsw/*
+fi
diff --git a/scripts/gsw/gsw_cosmos_build.sh b/scripts/gsw/gsw_cosmos_build.sh
index 6f48393c..8300f801 100755
--- a/scripts/gsw/gsw_cosmos_build.sh
+++ b/scripts/gsw/gsw_cosmos_build.sh
@@ -3,9 +3,8 @@
 # Convenience script for NOS3 development
 #
 
-CFG_BUILD_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-SCRIPT_DIR=$CFG_BUILD_DIR/../../scripts
-source $SCRIPT_DIR/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
 
 echo "COSMOS build..."
 $DCALL image pull ballaerospace/cosmos:4.5.0
diff --git a/scripts/gsw/gsw_cosmos_launch.sh b/scripts/gsw/gsw_cosmos_launch.sh
index 9d41b671..2b835ce3 100755
--- a/scripts/gsw/gsw_cosmos_launch.sh
+++ b/scripts/gsw/gsw_cosmos_launch.sh
@@ -3,9 +3,9 @@
 # Convenience script for NOS3 development
 #
 
-CFG_BUILD_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-SCRIPT_DIR=$CFG_BUILD_DIR/../../scripts
-source $SCRIPT_DIR/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
+
 export GSW="cosmos_openc3-operator_1"
 
 # Debugging
diff --git a/scripts/gsw/gsw_openc3_build.sh b/scripts/gsw/gsw_openc3_build.sh
index c5c88e3f..d9b23ae0 100755
--- a/scripts/gsw/gsw_openc3_build.sh
+++ b/scripts/gsw/gsw_openc3_build.sh
@@ -3,9 +3,8 @@
 # Convenience script for NOS3 development
 #
 
-CFG_BUILD_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-SCRIPT_DIR=$CFG_BUILD_DIR/../../scripts
-source $SCRIPT_DIR/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
 
 # Check that local NOS3 directory exists
 if [ ! -d $USER_NOS3_DIR ]; then
diff --git a/scripts/gsw/gsw_openc3_launch.sh b/scripts/gsw/gsw_openc3_launch.sh
index 11d306a5..1529fbd6 100755
--- a/scripts/gsw/gsw_openc3_launch.sh
+++ b/scripts/gsw/gsw_openc3_launch.sh
@@ -3,9 +3,9 @@
 # Convenience script for NOS3 development
 #
 
-CFG_BUILD_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-SCRIPT_DIR=$CFG_BUILD_DIR/../../scripts
-source $SCRIPT_DIR/env.sh
+# Note the first argument passed is expected to be the BASE_DIR of the NOS3 repository
+source $1/scripts/env.sh
+
 export GSW="cosmos_openc3-operator_1"
 
 # Debugging
diff --git a/scripts/build_sim.sh b/scripts/sim/build_sim.sh
similarity index 72%
rename from scripts/build_sim.sh
rename to scripts/sim/build_sim.sh
index 92a33145..f2b612fe 100755
--- a/scripts/build_sim.sh
+++ b/scripts/sim/build_sim.sh
@@ -6,7 +6,7 @@
 #
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-source $SCRIPT_DIR/env.sh
+source $SCRIPT_DIR/../env.sh
 
 # Check that local NOS3 directory exists
 if [ ! -d $USER_NOS3_DIR ]; then
@@ -17,7 +17,7 @@ if [ ! -d $USER_NOS3_DIR ]; then
 fi
 
 # Check that configure build directory exists
-if [ ! -d $BASE_DIR/cfg/build ]; then
+if [ ! -d $USER_NOS3_BUILD_DIR/cfg ]; then
     echo ""
     echo "    Need to run make config first!"
     echo ""
@@ -26,4 +26,4 @@ fi
 
 chmod g+s $BASE_DIR/sims
 mkdir -p $BASE_DIR/sims/build
-$DFLAGS_CPUS -v $BASE_DIR:$BASE_DIR --name "nos_build_sim" -w $BASE_DIR $DBOX make -j$NUM_CPUS build-sim
+$DFLAGS_CPUS -v $BASE_DIR:$BASE_DIR -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name "nos_build_sim" -w $BASE_DIR $DBOX make -j$NUM_CPUS build-sim
diff --git a/scripts/sim/sim_clean.sh b/scripts/sim/sim_clean.sh
new file mode 100755
index 00000000..b9e8e4bf
--- /dev/null
+++ b/scripts/sim/sim_clean.sh
@@ -0,0 +1,15 @@
+#!/bin/bash -i
+#
+# Convenience script for NOS3 development
+# Use with the Dockerfile in the deployment repository
+# https://github.com/nasa-itc/deployment
+#
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+source $SCRIPT_DIR/env.sh
+
+# Check that NOS3 build directory exists
+if [ -d $USER_NOS3_BUILD_DIR/sim ]; then
+    # Cleanup all build files
+    $DFLAGS -v $USER_NOS3_BUILD_DIR:$USER_NOS3_BUILD_DIR --name "nos_clean" -w $BASE_DIR $DBOX rm -rf $USER_NOS3_BUILD_DIR/sim/*
+fi
diff --git a/scripts/stop.sh b/scripts/stop.sh
index bcb11dcd..8def7b14 100755
--- a/scripts/stop.sh
+++ b/scripts/stop.sh
@@ -12,7 +12,7 @@ source $SCRIPT_DIR/env.sh
 rm -rf /tmp/gpio_fake
 
 # NOS3 Stored HK
-rm -rf $BASE_DIR/fsw/build/exe/cpu1/scratch/*
+#rm -rf $BASE_DIR/fsw/build/exe/cpu1/scratch/*
 
 # Docker stop
 cd $SCRIPT_DIR; $DFLAG compose down > /dev/null 2>&1
diff --git a/sims/CMakeLists.txt b/sims/CMakeLists.txt
index 9eea63e5..098010c8 100644
--- a/sims/CMakeLists.txt
+++ b/sims/CMakeLists.txt
@@ -48,8 +48,8 @@ ENDFOREACH()
 
 # Install configuration files to bin
 set(sim_cfg
-    ../cfg/build/sims/nos_engine_server_config.json
-    ../cfg/build/sims/nos3-simulator.xml
-    ../cfg/build/sims/sim_log_config.xml
+    /tmp/nos3/cfg/sims/nos_engine_server_config.json
+    /tmp/nos3/cfg/sims/nos3-simulator.xml
+    /tmp/nos3/cfg/sims/sim_log_config.xml
 )
 install(FILES ${sim_cfg} DESTINATION bin COMPONENT config)