diff --git a/aviary/docs/misc_resources/externally_supported_subsystems.ipynb b/aviary/docs/misc_resources/externally_supported_subsystems.ipynb
index 504c0c427..1f3f39ce9 100644
--- a/aviary/docs/misc_resources/externally_supported_subsystems.ipynb
+++ b/aviary/docs/misc_resources/externally_supported_subsystems.ipynb
@@ -23,14 +23,18 @@
     "# Testing Cell\n",
     "import aviary.api as av\n",
     "from aviary.utils.doctape import glue_variable\n",
-    "av.get_path('examples/external_subsystems')\n",
-    "glue_variable('aviary/examples/external_subsystems', md_code=True)"
+    "\n",
+    "folder = av.get_path('examples/external_subsystems')\n",
+    "aviary_top_dir = av.get_path('docs').parent.parent\n",
+    "ext_examples_dir = folder.relative_to(aviary_top_dir)\n",
+    "\n",
+    "glue_variable(str(ext_examples_dir), md_code=True)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "latest_env",
+   "display_name": "av1",
    "language": "python",
    "name": "python3"
   },
@@ -44,7 +48,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.9.18"
   }
  },
  "nbformat": 4,
diff --git a/aviary/docs/misc_resources/modeling_exercise.ipynb b/aviary/docs/misc_resources/modeling_exercise.ipynb
index c905067b8..5dd5ee807 100644
--- a/aviary/docs/misc_resources/modeling_exercise.ipynb
+++ b/aviary/docs/misc_resources/modeling_exercise.ipynb
@@ -36,11 +36,19 @@
    "outputs": [],
    "source": [
     "# Testing Cell\n",
+    "import os\n",
     "import aviary.api as av\n",
     "from aviary.utils.doctape import glue_variable\n",
-    "av.get_path('examples/run_basic_aviary_example.py')\n",
-    "glue_variable('aviary/examples', md_code=True)\n",
-    "glue_variable('run_basic_aviary_example.py', md_code=True)"
+    "\n",
+    "aviary_top_dir = av.get_path('docs').parent.parent\n",
+    "\n",
+    "folder = av.get_path('examples')\n",
+    "examples_dir = folder.relative_to(aviary_top_dir)\n",
+    "glue_variable(str(examples_dir), md_code=True)\n",
+    "\n",
+    "folder = av.get_path('examples/run_basic_aviary_example.py')\n",
+    "run_example_dir = os.path.basename(folder)\n",
+    "glue_variable(run_example_dir, md_code=True)"
    ]
   },
   {
@@ -90,14 +98,8 @@
    "outputs": [],
    "source": [
     "# Testing Cell\n",
-    "from aviary.interface.methods_for_level2 import AviaryGroup\n",
     "from aviary.utils.doctape import glue_variable\n",
-    "\n",
-    "ag = AviaryGroup()\n",
-    "opts = list(ag.options)\n",
-    "for opt in opts:\n",
-    "    if opt == 'phase_info':\n",
-    "        glue_variable('phase_info', md_code=True)\n"
+    "glue_variable('phase_info', md_code=True)"
    ]
   },
   {
@@ -144,8 +146,10 @@
     "# Testing Cell\n",
     "import aviary.api as av\n",
     "from aviary.utils.doctape import glue_variable\n",
-    "av.get_path('examples/reserve_missions/run_reserve_mission_fixedrange.py');\n",
-    "glue_variable('run_reserve_mission_fixedrange.py', md_code=True)"
+    "\n",
+    "folder = av.get_path('examples/reserve_missions/run_reserve_mission_fixedrange.py')\n",
+    "run_reserve_dir = os.path.basename(folder)\n",
+    "glue_variable(run_reserve_dir, md_code=True)"
    ]
   },
   {
diff --git a/aviary/docs/user_guide/SGM_capabilities.ipynb b/aviary/docs/user_guide/SGM_capabilities.ipynb
index 8dfcd0af2..c0886ab5c 100644
--- a/aviary/docs/user_guide/SGM_capabilities.ipynb
+++ b/aviary/docs/user_guide/SGM_capabilities.ipynb
@@ -11,14 +11,9 @@
    "outputs": [],
    "source": [
     "# Testing Cell\n",
-    "from aviary.interface.methods_for_level2 import AviaryGroup\n",
     "from aviary.utils.doctape import glue_variable\n",
-    "#from aviary.interface.default_phase_info.two_dof_fiti import\n",
-    "ag = AviaryGroup()\n",
-    "opts = list(ag.options)\n",
-    "for opt in opts:\n",
-    "    if opt == 'phase_info':  # only need this option to glue\n",
-    "        glue_variable('phase_info', md_code=True)"
+    "\n",
+    "glue_variable('phase_info', md_code=True)"
    ]
   },
   {
diff --git a/aviary/docs/user_guide/aerodynamics.ipynb b/aviary/docs/user_guide/aerodynamics.ipynb
index 2fdc9fd19..0bb0ef53f 100644
--- a/aviary/docs/user_guide/aerodynamics.ipynb
+++ b/aviary/docs/user_guide/aerodynamics.ipynb
@@ -157,9 +157,6 @@
    "source": [
     "# Testing Cell\n",
     "from aviary.api import Aircraft\n",
-    "Aircraft.Wing.MAX_CAMBER_AT_70_SEMISPAN;\n",
-    "Aircraft.Wing.AIRFOIL_TECHNOLOGY;\n",
-    "Aircraft.Design.BASE_AREA;\n",
     "glue_variable(get_variable_name(Aircraft.Wing.MAX_CAMBER_AT_70_SEMISPAN), md_code=True)\n",
     "glue_variable(get_variable_name(Aircraft.Wing.AIRFOIL_TECHNOLOGY), md_code=True)\n",
     "glue_variable(get_variable_name(Aircraft.Design.BASE_AREA), md_code=True)"
diff --git a/aviary/docs/user_guide/aviary_commands.ipynb b/aviary/docs/user_guide/aviary_commands.ipynb
index 2a37c73ff..58a565a78 100644
--- a/aviary/docs/user_guide/aviary_commands.ipynb
+++ b/aviary/docs/user_guide/aviary_commands.ipynb
@@ -125,18 +125,29 @@
    "outputs": [],
    "source": [
     "# Testing Cell\n",
+    "import os\n",
     "import subprocess\n",
+    "import aviary.api as av\n",
     "from aviary.utils.doctape import glue_variable\n",
     "\n",
-    "str_model = 'small_single_aisle_GwGm'\n",
+    "aviary_top_dir = av.get_path('docs').parent.parent\n",
     "str_folder = 'models/small_single_aisle'\n",
-    "command = 'aviary run_mission ' + str_folder + '/' + str_model + '.csv'\n",
+    "folder = av.get_path(str_folder)\n",
+    "model_dir = folder.relative_to(aviary_top_dir)\n",
+    "glue_variable(str(model_dir), md_code=True)\n",
+    "\n",
+    "str_model = 'small_single_aisle_GwGm.csv'\n",
+    "folder = av.get_path(str_folder) / (str_model)\n",
+    "file_name = os.path.basename(folder)\n",
+    "glue_variable(file_name, md_code=False)\n",
+    "\n",
+    "command = 'aviary run_mission ' + str_folder + '/' + str_model\n",
+    "glue_variable(command, md_code=True)\n",
     "command += ' --max_iter 0 --optimizer IPOPT' # max_iter to limit build time, IPOPT to run on CI\n",
     "subprocess.run(command.split()).check_returncode();\n",
     "\n",
-    "glue_variable('aviary run_mission models/small_single_aisle/' + str_model + '.csv', md_code=True)\n",
-    "glue_variable(str_model + '.csv', md_code=False)\n",
-    "glue_variable('aviary/' + str_folder, md_code=True)"
+    "\n",
+    "\n"
    ]
   },
   {
diff --git a/aviary/docs/user_guide/battery_subsystem_example.ipynb b/aviary/docs/user_guide/battery_subsystem_example.ipynb
index 761a7dfae..705ffe763 100644
--- a/aviary/docs/user_guide/battery_subsystem_example.ipynb
+++ b/aviary/docs/user_guide/battery_subsystem_example.ipynb
@@ -1,5 +1,25 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# Testing Cell\n",
+    "import aviary.api as av\n",
+    "from aviary.utils.doctape import glue_variable\n",
+    "\n",
+    "aviary_top_dir = av.get_path('docs').parent.parent\n",
+    "folder = av.get_path('examples/external_subsystems/battery')\n",
+    "examples_dir = folder.relative_to(aviary_top_dir)\n",
+    "glue_variable(str(examples_dir), md_code=True)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -9,7 +29,7 @@
     "## Examining the battery as an example case\n",
     "\n",
     "Let's take a look at how to integrate an external subsystem into Aviary using the example of a battery model.\n",
-    "This battery model and builder are provided in the `aviary/examples/external_subsystems/battery` folder.\n",
+    "This battery model and builder are provided in the {glue:md}`aviary/examples/external_subsystems/battery` folder.\n",
     "\n",
     "We'll show you how to define the builder object, how to specify the pre-mission and mission models, and how to implement the interface methods.\n",
     "In each of these methods, we've removed the initial docstring to increase readability on this page.\n",
@@ -111,7 +131,7 @@
     "# Get all functions of class CoreAerodynamicsBuilder\n",
     "methods = inspect.getmembers(SubsystemBuilderBase, predicate=inspect.isfunction)\n",
     "for name, func in methods:\n",
-    "    if not name.startswith('_'):\n",
+    "    if not name.startswith('_'):  # exclude private functions\n",
     "        glue_variable(name + '()', md_code=True)\n",
     "\n",
     "AviaryValues = av.AviaryValues\n",
diff --git a/aviary/docs/user_guide/features_and_functionalities.ipynb b/aviary/docs/user_guide/features_and_functionalities.ipynb
index 21b181202..8c02ce6ce 100644
--- a/aviary/docs/user_guide/features_and_functionalities.ipynb
+++ b/aviary/docs/user_guide/features_and_functionalities.ipynb
@@ -12,14 +12,9 @@
    "source": [
     "# Testing Cell\n",
     "from aviary.api import LegacyCode\n",
-    "from aviary.interface.methods_for_level2 import AviaryGroup\n",
     "from aviary.utils.doctape import glue_variable\n",
     "\n",
-    "ag = AviaryGroup()\n",
-    "opts = list(ag.options)\n",
-    "for opt in opts:\n",
-    "    if opt == 'phase_info':\n",
-    "        glue_variable('phase_info', md_code=True)\n",
+    "glue_variable('phase_info', md_code=True)\n",
     "glue_variable(LegacyCode.FLOPS.name, md_code=False)\n",
     "glue_variable(LegacyCode.GASP.name, md_code=False)"
    ]
diff --git a/aviary/docs/user_guide/hamilton_standard.ipynb b/aviary/docs/user_guide/hamilton_standard.ipynb
index 796750976..82a7aaa4b 100644
--- a/aviary/docs/user_guide/hamilton_standard.ipynb
+++ b/aviary/docs/user_guide/hamilton_standard.ipynb
@@ -324,25 +324,42 @@
    "outputs": [],
    "source": [
     "# Testing Cell\n",
+    "import os\n",
     "import aviary.api as av\n",
     "from aviary.variable_info.enums import OutMachType\n",
     "from aviary.subsystems.propulsion.propeller.propeller_performance import OutMachs\n",
-    "file_path = av.get_path('models/propellers/general_aviation.prop')\n",
-    "file_path = av.get_path('models/propellers/PropFan.prop')\n",
-    "glue_variable('models/propellers', md_code=True)\n",
-    "glue_variable('general_aviation.prop', md_code=True)\n",
-    "glue_variable('PropFan.prop', md_code=True)\n",
-    "file_path = av.get_path('models/propellers/general_aviation.map')\n",
-    "file_path = av.get_path('models/propellers/PropFan.map')\n",
-    "glue_variable('general_aviation.map', md_code=True)\n",
-    "glue_variable('PropFan.map', md_code=True)\n",
+    "\n",
+    "aviary_top_dir = av.get_path('docs').parent\n",
+    "#print(aviary_top_dir)\n",
+    "\n",
+    "folder_path = av.get_path('models/propellers')\n",
+    "propellers_dir = folder_path.relative_to(aviary_top_dir)\n",
+    "glue_variable(str(propellers_dir), md_code=True)\n",
+    "\n",
+    "file_path = av.get_path(folder_path / 'general_aviation.prop')\n",
+    "prop_file_name = os.path.basename(file_path)\n",
+    "glue_variable(prop_file_name, md_code=True)\n",
+    "\n",
+    "map_file_name = file_path.stem + '.map'\n",
+    "file_path = av.get_path(folder_path / map_file_name)\n",
+    "map_file_name = os.path.basename(file_path)\n",
+    "glue_variable(map_file_name, md_code=True)\n",
+    "\n",
+    "file_path = av.get_path(folder_path / 'PropFan.prop')\n",
+    "prop_file_name = os.path.basename(file_path)\n",
+    "glue_variable(prop_file_name, md_code=True)\n",
+    "\n",
+    "map_file_name = file_path.stem + '.map'\n",
+    "file_path = av.get_path(folder_path / map_file_name)\n",
+    "map_file_name = os.path.basename(file_path)\n",
+    "glue_variable(map_file_name, md_code=True)\n",
     "\n",
     "glue_variable(OutMachType.HELICAL_MACH.name.title(), md_code=True)\n",
     "glue_variable(OutMachType.MACH.name.title(), md_code=True)\n",
     "\n",
-    "check_value(Aircraft.Engine.Propeller.DATA_FILE,'aircraft:engine:propeller:data_file')\n",
+    "check_value(Aircraft.Engine.Propeller.DATA_FILE, 'aircraft:engine:propeller:data_file')\n",
     "glue_variable(get_variable_name(Aircraft.Engine.Propeller.DATA_FILE), md_code=True)\n",
-    "check_value(Dynamic.Atmosphere.MACH,'mach')\n",
+    "check_value(Dynamic.Atmosphere.MACH, 'mach')\n",
     "glue_variable(get_variable_name(Dynamic.Atmosphere.MACH), md_code=True)\n",
     "glue_variable(get_variable_name(OutMachs), md_code=True)\n"
    ]
diff --git a/aviary/docs/user_guide/off_design_missions.ipynb b/aviary/docs/user_guide/off_design_missions.ipynb
index 5b5818987..9a9f0d6ab 100644
--- a/aviary/docs/user_guide/off_design_missions.ipynb
+++ b/aviary/docs/user_guide/off_design_missions.ipynb
@@ -88,9 +88,11 @@
     "# Testing Cell\n",
     "import aviary.api as av\n",
     "from aviary.utils.doctape import glue_variable\n",
-    "str_file_path = 'examples/run_off_design_example.py'\n",
-    "file_path = av.get_path(str_file_path)\n",
-    "glue_variable('aviary/' + str_file_path, md_code=True)"
+    "\n",
+    "aviary_top_dir = av.get_path('docs').parent.parent\n",
+    "\n",
+    "file_path = av.get_path('examples/run_off_design_example.py').relative_to(aviary_top_dir)\n",
+    "glue_variable(str(file_path), md_code=True)"
    ]
   },
   {
diff --git a/aviary/docs/user_guide/postprocessing_and_visualizing_results.ipynb b/aviary/docs/user_guide/postprocessing_and_visualizing_results.ipynb
index 7970a7382..e778ff9ba 100644
--- a/aviary/docs/user_guide/postprocessing_and_visualizing_results.ipynb
+++ b/aviary/docs/user_guide/postprocessing_and_visualizing_results.ipynb
@@ -12,16 +12,34 @@
    "source": [
     "# Testing Cell\n",
     "import inspect\n",
-    "from aviary.utils.functions import get_path\n",
+    "import os\n",
+    "import aviary.api as av\n",
+    "#from aviary.utils.functions import get_path\n",
     "from aviary.utils.doctape import glue_variable\n",
     "from aviary.interface.methods_for_level2 import AviaryProblem\n",
     "\n",
+    "aviary_top_dir = av.get_path('docs').parent.parent\n",
+    "\n",
     "# make sure that the path exists.\n",
-    "str_run_aviary_example = 'run_aviary_example'\n",
-    "get_path('examples/' + str_run_aviary_example + '.py')\n",
-    "glue_variable('aviary/examples', md_code=True)\n",
-    "glue_variable(str_run_aviary_example + '.py', md_code=True)\n",
-    "glue_variable(str_run_aviary_example + '.zip', md_code=True)\n",
+    "folder = av.get_path('examples')\n",
+    "examples_dir = folder.relative_to(aviary_top_dir)\n",
+    "glue_variable(str(examples_dir), md_code=True)\n",
+    "\n",
+    "run_example_dir = os.path.basename(examples_dir)\n",
+    "\n",
+    "str_run_aviary_example = 'run_aviary_example.py'\n",
+    "run_aviary_example = av.get_path(folder / str_run_aviary_example)\n",
+    "examples_dir = run_aviary_example.relative_to(aviary_top_dir)\n",
+    "#print(examples_dir)\n",
+    "\n",
+    "run_example_dir = os.path.basename(examples_dir)\n",
+    "glue_variable(run_example_dir, md_code=True)\n",
+    "#glue_variable(str_run_aviary_example + '.py', md_code=True)\n",
+    "\n",
+    "run_example_dir = os.path.basename(examples_dir.stem + '.zip')\n",
+    "\n",
+    "glue_variable(run_example_dir, md_code=True)\n",
+    "#glue_variable(str_run_aviary_example + '.zip', md_code=True)\n",
     "\n",
     "# Get all functions of class AviaryProblem\n",
     "functs = inspect.getmembers(AviaryProblem, predicate=inspect.isfunction)\n",
@@ -34,8 +52,8 @@
     "sig = inspect.signature(AviaryProblem.run_aviary_problem)\n",
     "arguments = [param.name for param in sig.parameters.values()]\n",
     "for arg in arguments:\n",
-    "    if arg == 'optimization_history_filename':\n",
-    "        glue_variable(arg, md_code=True)"
+    "    #if arg == 'optimization_history_filename':\n",
+    "    glue_variable(arg, md_code=True)"
    ]
   },
   {
@@ -110,7 +128,7 @@
     "        #print(action.dest, action.default)\n",
     "        glue_variable('--' + action.dest, md_code=True)\n",
     "        if action.default is not None and not type(action.default) is bool:\n",
-    "            glue_variable(str(action.default), md_code=True)\n"
+    "            glue_variable(action.default, md_code=True)\n"
    ]
   },
   {
diff --git a/aviary/docs/user_guide/reserve_missions.ipynb b/aviary/docs/user_guide/reserve_missions.ipynb
index 58c2fc4eb..01093fee6 100644
--- a/aviary/docs/user_guide/reserve_missions.ipynb
+++ b/aviary/docs/user_guide/reserve_missions.ipynb
@@ -12,10 +12,10 @@
    "source": [
     "# Testing Cell\n",
     "import inspect\n",
+    "import os\n",
     "import aviary.api as av\n",
     "from aviary.interface.methods_for_level2 import AviaryGroup, AviaryProblem\n",
     "from aviary.utils.doctape import get_variable_name, glue_variable\n",
-    "from aviary.utils.functions import get_path\n",
     "\n",
     "glue_variable(av.EquationsOfMotion.HEIGHT_ENERGY.value, md_code=False)\n",
     "glue_variable(av.EquationsOfMotion.TWO_DEGREES_OF_FREEDOM.value, md_code=False)\n",
@@ -28,24 +28,28 @@
     "str_shooting = str_shooting.split('.')[1].lower()\n",
     "glue_variable(str_shooting, md_code=False)\n",
     "\n",
-    "ag = AviaryGroup()\n",
-    "opts = list(ag.options)\n",
-    "for opt in opts:\n",
-    "    if opt == 'phase_info':\n",
-    "        glue_variable('phase_info', md_code=True)\n",
+    "glue_variable('phase_info', md_code=True)\n",
+    "\n",
+    "aviary_top_dir = av.get_path('docs').parent\n",
+    "folder = av.get_path('examples/reserve_missions')\n",
+    "examples_dir = folder.relative_to(aviary_top_dir)\n",
+    "\n",
+    "str_run_aviary_example = 'run_reserve_mission_multiphase.py'\n",
+    "file_name = os.path.join(examples_dir, str_run_aviary_example)\n",
+    "file_name = os.path.basename(file_name)\n",
+    "glue_variable(str(file_name), md_code=True)\n",
     "\n",
-    "str_run_aviary_example = 'run_reserve_mission_multiphase'\n",
-    "get_path('examples/reserve_missions/' + str_run_aviary_example + '.py')\n",
-    "glue_variable(str_run_aviary_example + '.py', md_code=True)\n",
     "\n",
-    "str_run_aviary_example = 'run_2dof_reserve_mission_multiphase'\n",
-    "get_path('examples/reserve_missions/' + str_run_aviary_example + '.py')\n",
-    "glue_variable(str_run_aviary_example + '.py', md_code=True)\n",
+    "str_run_aviary_example = 'run_2dof_reserve_mission_multiphase.py'\n",
+    "file_name = os.path.join(examples_dir, str_run_aviary_example)\n",
+    "file_name = os.path.basename(file_name)\n",
+    "glue_variable(str(file_name), md_code=True)\n",
     "\n",
     "# Get all functions of class AviaryProblem\n",
     "methods = inspect.getmembers(AviaryProblem, predicate=inspect.isfunction)\n",
     "for name, func in methods:\n",
-    "    if not name.startswith('_') and name in ['check_and_preprocess_inputs', 'load_inputs']:\n",
+    "    #if not name.startswith('_') and name in ['check_and_preprocess_inputs', 'load_inputs']:\n",
+    "    if not name.startswith('_'):  # exclude private functions\n",
     "        glue_variable(name + '()', md_code=True)\n",
     "        glue_variable('prob.' + name + '()', md_code=True)"
    ]
diff --git a/aviary/docs/user_guide/variable_metadata.ipynb b/aviary/docs/user_guide/variable_metadata.ipynb
index 888b62bfd..a6472a12e 100644
--- a/aviary/docs/user_guide/variable_metadata.ipynb
+++ b/aviary/docs/user_guide/variable_metadata.ipynb
@@ -333,19 +333,29 @@
    "source": [
     "# Testing Cell\n",
     "\n",
+    "import os\n",
     "import aviary.api as av\n",
     "from aviary.utils.doctape import get_function_names, glue_variable\n",
     "\n",
-    "glue_variable('utils/merge_hierarchies.py', md_code=False)\n",
-    "glue_variable('utils/merge_variable_metadata.py', md_code=False)\n",
+    "aviary_top_dir = av.get_path('docs').parent\n",
+    "folder = av.get_path('utils')\n",
     "\n",
-    "file_path = av.get_path('utils/merge_hierarchies.py')\n",
+    "utils_dir = folder.relative_to(aviary_top_dir)\n",
+    "print(utils_dir)\n",
+    "\n",
+    "file_path = os.path.join(utils_dir, 'merge_hierarchies.py')\n",
+    "glue_variable(file_path, md_code=False)\n",
+    "file_path = av.get_path(file_path)\n",
     "function_names = get_function_names(file_path)\n",
     "for function_name in function_names:\n",
     "    if not function_name.startswith('_'):\n",
     "        glue_variable(function_name+'()', md_code=True)\n",
     "\n",
-    "file_path = av.get_path('utils/merge_variable_metadata.py')\n",
+    "file_path = os.path.join(utils_dir, 'merge_variable_metadata.py')\n",
+    "glue_variable(file_path, md_code=False)\n",
+    "file_path = av.get_path(file_path)\n",
+    "\n",
+    "file_path = av.get_path(file_path)\n",
     "function_names = get_function_names(file_path)\n",
     "for function_name in function_names:\n",
     "    if not function_name.startswith('_'):\n",
@@ -555,7 +565,7 @@
  "metadata": {
   "celltoolbar": "Tags",
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "av1",
    "language": "python",
    "name": "python3"
   },
@@ -569,7 +579,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.9.18"
   },
   "orphan": true
  },