diff --git a/misc/deploy.sh b/misc/deploy.sh
index c52cf47a..07d88944 100755
--- a/misc/deploy.sh
+++ b/misc/deploy.sh
@@ -8,9 +8,9 @@ branch=""
 needsReboot=false
 calFile=""
 
-cd ..
-dirPath="$(pwd)"
-dirName="$(basename `pwd`)"
+export dirPath="$(catkin locate)"
+if [ -z "$dirPath" ]; then dirPath=$(dirname "$0"); fi
+dirName="$(basename $dirPath)"
 
 #Functions
 #--------------------------------------------------------------------------
diff --git a/misc/rover_launch_local.sh b/misc/rover_launch_local.sh
index 209e05a4..26422a3b 100755
--- a/misc/rover_launch_local.sh
+++ b/misc/rover_launch_local.sh
@@ -1,3 +1,5 @@
 #!/bin/bash
+export SWARMATHON_APP_ROOT="$(catkin locate)"
+if [ -z "$SWARMATHON_APP_ROOT" ]; then SWARMATHON_APP_ROOT=$(dirname "$0"); fi
 roscore &
-./rover_onboard_node_launch.sh localhost $1
+$SWARMATHON_APP_ROOT/misc/rover_onboard_node_launch.sh localhost $1
diff --git a/run.sh b/run.sh
index 04e3ec16..ba14cb9a 100755
--- a/run.sh
+++ b/run.sh
@@ -1,18 +1,19 @@
 #!/bin/bash
-echo "Running in $PWD" 
 previous_gazebo_model_path=${GAZEBO_MODEL_PATH}
 previous_gazebo_plugin_path=${GAZEBO_PLUGIN_PATH}
-export SWARMATHON_APP_ROOT="$PWD"
-export GAZEBO_MODEL_PATH="$PWD/simulation/models"
-export GAZEBO_PLUGIN_PATH="$PWD/build/gazebo_plugins"
-source "$PWD/devel/setup.bash"
+export SWARMATHON_APP_ROOT="$(catkin locate)"
+if [ -z "$SWARMATHON_APP_ROOT" ]; then SWARMATHON_APP_ROOT=$(dirname "$0"); fi
+echo "Running from: $PWD with repo root: $SWARMATHON_APP_ROOT"
+export GAZEBO_MODEL_PATH="$SWARMATHON_APP_ROOT/simulation/models"
+export GAZEBO_PLUGIN_PATH="$SWARMATHON_APP_ROOT/build/gazebo_plugins"
+source "$SWARMATHON_APP_ROOT/devel/setup.bash"
 echo Cleaning up ROS and Gazebo Processes
 
 #Delete the rqt cache - can take 24 hours for changes in the UI
 # to show up otherwise
 rm ~/.config/ros.org/rqt_gui.ini
 
-./cleanup.sh
+$SWARMATHON_APP_ROOT/cleanup.sh
 echo Killing rosmaster
 pkill rosmaster
 echo Killing roscore
@@ -28,7 +29,7 @@ echo Killing rosmaster
 pkill rosmaster
 echo Killing roscore
 pkill roscore
-./cleanup.sh
+$SWARMATHON_APP_ROOT/cleanup.sh
 # Restore previous environment
 export GAZEBO_MODEL_PATH=$previous_gazebo_model_path
 export GAZEBO_PLUGIN_PATH=$previous_gazebo_plugin_path