diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index d779f6d1..029441b7 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -24,7 +24,7 @@ jobs:
 
     - name: Run black
       run: |
-        black . --diff --extend-exclude cmake --check
+        black . --diff --extend-exclude=cmake --extend-exclude=submodules --extend-exclude=astrobee/survey_manager/survey_dependencies --check
     - name: Run isort
       run: |
-        isort . --diff --extend-skip cmake --profile black --check-only
+        isort . --diff --extend-skip=cmake --extend-skip=submodules --extend-skip=astrobee/survey_manager/survey_dependencies --profile=black --check-only
diff --git a/.isort.cfg b/.isort.cfg
index 88864386..0f2c426d 100644
--- a/.isort.cfg
+++ b/.isort.cfg
@@ -15,4 +15,4 @@
 # folder, you can auto-update it by running
 # scripts/git/configure_isort_paths.sh.
 
-src_paths = analyst/workspace/scripts,anomaly/gmm-change-detection,anomaly/gmm-change-detection/scripts/gmm,anomaly/image/scripts,astrobee/behaviors/inspection/scripts,astrobee/simulation/acoustics_cam/src,astrobee/survey_manager/survey_planner/tools,dense_map/geometry_mapper/tools,dense_map/volumetric_mapper/scripts,pano/pano_stitch/scripts,pano/pano_view/scripts,scripts/git
+src_paths = analyst/workspace/scripts,anomaly/gmm-change-detection,anomaly/gmm-change-detection/scripts/gmm,anomaly/image/scripts,astrobee/behaviors/inspection/scripts,astrobee/simulation/acoustics_cam/src,astrobee/survey_manager/survey_planner,astrobee/survey_manager/survey_planner/scripts,astrobee/survey_manager/survey_planner/src/survey_planner,astrobee/survey_manager/survey_planner/tools/bak,communications/isaac_msgs/isaac_msgs/test,dense_map/geometry_mapper/tools,dense_map/volumetric_mapper/scripts,pano/pano_stitch/scripts,pano/pano_view/scripts,scripts/git
diff --git a/astrobee/survey_manager/survey_planner/data/jem_survey_dynamic.yaml b/astrobee/survey_manager/survey_planner/data/jem_survey_dynamic.yaml
index f7d8f9ae..69e8d29a 100644
--- a/astrobee/survey_manager/survey_planner/data/jem_survey_dynamic.yaml
+++ b/astrobee/survey_manager/survey_planner/data/jem_survey_dynamic.yaml
@@ -44,7 +44,7 @@ goals:
 - {type: panorama, robot: honey, order: 2, location: jem_bay6}
 - {type: panorama, robot: honey, order: 3, location: jem_bay5}
 # This is the other objective we previously had to comment out for POPF to return a decent plan.
-- {type: stereo, robot: honey, order: 4, trajectory: jem_bay4_to_bay7}
+- {type: stereo, robot: honey, order: 4, trajectory: jem_bay7_to_bay4}
 - {type: robot_at, robot: honey, location: berth2}
 
 init:
diff --git a/astrobee/survey_manager/survey_planner/data/sample_output_plan.yaml b/astrobee/survey_manager/survey_planner/data/sample_output_plan.yaml
index 45b0da90..6a517af3 100644
--- a/astrobee/survey_manager/survey_planner/data/sample_output_plan.yaml
+++ b/astrobee/survey_manager/survey_planner/data/sample_output_plan.yaml
@@ -192,7 +192,7 @@
   action:
     type: stereo
     robot: honey
-    fplan: jem_stereo_mapping_bay4_to_bay7.fplan
+    fplan: ISAAC/jem_stereo_mapping_bay7_to_bay4
     base_name: jem_bay7
     bound_name: jem_bay4
   duration_seconds: '600.000'
@@ -206,7 +206,7 @@
   action:
     type: stereo
     robot: bumble
-    fplan: jem_stereo_mapping_bay1_to_bay3.fplan
+    fplan: ISAAC/jem_stereo_mapping_bay1_to_bay3
     base_name: jem_bay1
     bound_name: jem_bay4
   duration_seconds: '600.000'
diff --git a/astrobee/survey_manager/survey_planner/pddl/problem_jem_survey.pddl b/astrobee/survey_manager/survey_planner/pddl/problem_jem_survey.pddl
index 48d20caf..cd8061c2 100644
--- a/astrobee/survey_manager/survey_planner/pddl/problem_jem_survey.pddl
+++ b/astrobee/survey_manager/survey_planner/pddl/problem_jem_survey.pddl
@@ -1,6 +1,6 @@
 ;; Auto-generated by problem_generator.py. Do not edit!
-;; Command was: ./tools/problem_generator.py
-;; Working directory was: /home/vagrant/isaac/astrobee/survey_manager/survey_planner
+;; Command was: ./tools/problem_generator
+;; Working directory was: /home/vagrant/isaac/src/astrobee/survey_manager/survey_planner
 ;; Problem template: pddl/jem_survey_template.pddl
 ;; Config 1: data/survey_static.yaml
 ;; Config 2: data/jem_survey_dynamic.yaml
diff --git a/astrobee/survey_manager/survey_planner/pddl/problem_jem_survey.ps2.pddl b/astrobee/survey_manager/survey_planner/pddl/problem_jem_survey.ps2.pddl
index f39e5694..02092c24 100644
--- a/astrobee/survey_manager/survey_planner/pddl/problem_jem_survey.ps2.pddl
+++ b/astrobee/survey_manager/survey_planner/pddl/problem_jem_survey.ps2.pddl
@@ -16,7 +16,7 @@ set instance o1 order
 set instance o2 order
 set instance o3 order
 set instance o4 order
-set goal (and (completed-panorama bumble o0 jem_bay4) (completed-panorama bumble o1 jem_bay3) (completed-panorama bumble o2 jem_bay2) (completed-panorama bumble o3 jem_bay1) (completed-stereo bumble o4 jem_bay1 jem_bay4) (completed-panorama honey o0 jem_bay7) (completed-panorama honey o1 jem_bay6) (completed-panorama honey o2 jem_bay5) (robot-at honey berth2))
+set goal (and (completed-panorama bumble o0 jem_bay4) (completed-panorama bumble o1 jem_bay3) (completed-panorama bumble o2 jem_bay2) (completed-panorama bumble o3 jem_bay1) (completed-stereo bumble o4 jem_bay1 jem_bay4) (robot-at bumble berth1) (completed-panorama honey o1 jem_bay7) (completed-panorama honey o2 jem_bay6) (completed-panorama honey o3 jem_bay5) (completed-stereo honey o4 jem_bay7 jem_bay4) (robot-at honey berth2))
 set predicate (move-connected jem_bay0 jem_bay1)
 set predicate (move-connected jem_bay1 jem_bay0)
 set predicate (move-connected jem_bay1 jem_bay2)
@@ -130,6 +130,7 @@ set predicate (location-available jem_bay6)
 set predicate (location-available jem_bay7)
 set predicate (location-available jem_bay8)
 set predicate (need-stereo bumble o4 jem_bay1 jem_bay4)
+set predicate (need-stereo honey o4 jem_bay7 jem_bay4)
 set function (= (order-identity o0) 0)
 set function (= (order-identity o1) 1)
 set function (= (order-identity o2) 2)
diff --git a/astrobee/survey_manager/survey_planner/src/survey_planner/plan_interpreter.py b/astrobee/survey_manager/survey_planner/src/survey_planner/plan_interpreter.py
index 13404b03..82e13f58 100755
--- a/astrobee/survey_manager/survey_planner/src/survey_planner/plan_interpreter.py
+++ b/astrobee/survey_manager/survey_planner/src/survey_planner/plan_interpreter.py
@@ -42,7 +42,8 @@
 from matplotlib import collections as mc
 from matplotlib import patches as mp
 from matplotlib import pyplot as plt
-from problem_generator import (
+
+from survey_planner.problem_generator import (
     DATA_DIR,
     get_stereo_traj,
     load_yaml,
diff --git a/astrobee/survey_manager/survey_planner/src/survey_planner/plan_survey.py b/astrobee/survey_manager/survey_planner/src/survey_planner/plan_survey.py
index c43be3d0..9c2879ee 100755
--- a/astrobee/survey_manager/survey_planner/src/survey_planner/plan_survey.py
+++ b/astrobee/survey_manager/survey_planner/src/survey_planner/plan_survey.py
@@ -29,6 +29,7 @@
 
 import pyparsing as pp
 import yaml
+
 from survey_planner.problem_generator import PDDL_DIR
 
 LocationName = str  # Names PDDL object of type location
diff --git a/scripts/git/configure_isort_paths.sh b/scripts/git/configure_isort_paths.sh
index 318fae8a..1323b50c 100755
--- a/scripts/git/configure_isort_paths.sh
+++ b/scripts/git/configure_isort_paths.sh
@@ -27,7 +27,15 @@ srcdir=$(cd $thisdir/../.. && pwd)
 cd $srcdir
 
 # Generate a comma-separated list of folders containing *.py files
-pydirs=$(find . -name "*.py" -print0 | xargs -0 dirname | cut -c3- | sort | uniq | paste -sd "," -)
+pydirs=$( \
+    find . -name "*.py" -print0 \
+    | xargs -0 dirname \
+    | cut -c3- \
+    | grep -Pv "^cmake|^submodules|^astrobee/survey_manager/survey_dependencies|^scripts/setup/dependencies" \
+    | sort \
+    | uniq \
+    | paste -sd "," - \
+)
 
 # Overwrite the src_paths line in the config file to use the list
 perl -i -ple "if (/^src_paths = /) { \$_ = 'src_paths = $pydirs'; }" .isort.cfg
diff --git a/scripts/git/pre-commit.linter_python b/scripts/git/pre-commit.linter_python
index 6f33ccb9..6ed60178 100755
--- a/scripts/git/pre-commit.linter_python
+++ b/scripts/git/pre-commit.linter_python
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 #
 # Copyright (c) 2021, United States Government, as represented by the
 # Administrator of the National Aeronautics and Space Administration.
@@ -72,12 +72,18 @@ echo "  Analysing python code style with 'isort'."
 # could happen for example if the .isort.cfg src_paths list gets out
 # of date.
 
-if $(isort ${py_changed} --profile black --diff --check-only --quiet >/dev/null); then
+isort_args=(
+    "--extend-skip=cmake"
+    "--extend-skip=submodules"
+    "--extend-skip=astrobee/survey_manager/survey_dependencies"
+    "--profile=black"
+)
+if $(isort . "${isort_args[@]}" --diff --check-only --quiet >/dev/null); then
     echo "Linter checks using 'isort' passed."
 else
     echo "Errors detected with 'isort'. Fixing them. Try to add and commit your files again."
-  isort ${py_changed} --profile black >/dev/null
-  failed_lint=true
+    isort . "${isort_args[@]}" >/dev/null
+    failed_lint=true
 fi
 
 # Cancel commit if linter failed