diff --git a/src/architecture/messaging/CMakeLists.txt b/src/architecture/messaging/CMakeLists.txt
index 3d990fb3cf..bb925c56d7 100644
--- a/src/architecture/messaging/CMakeLists.txt
+++ b/src/architecture/messaging/CMakeLists.txt
@@ -61,23 +61,24 @@ function(generate_messages searchDir generateCCode)
   endforeach()
 endfunction(generate_messages)
 
+set(message_directory_paths
+        "${CMAKE_BINARY_DIR}/Basilisk/architecture/messaging/"
+        "../../msgPayloadDefC/"
+        "../../msgPayloadDefCpp/"
+)
 if(NOT "${EXTERNAL_MODULES_PATH}" STREQUAL "")
-  add_custom_command(
-    OUTPUT ${CMAKE_BINARY_DIR}/Basilisk/architecture/messaging/__init__.py
-    COMMAND
-      ${PYTHON_EXECUTABLE} generatePackageInit.py "${CMAKE_BINARY_DIR}/Basilisk/architecture/messaging/"
-      "../../msgPayloadDefC/" "../../msgPayloadDefCpp/" "${EXTERNAL_MODULES_PATH}/msgPayloadDefC/"
-      "${EXTERNAL_MODULES_PATH}/msgPayloadDefCpp/"
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/msgAutoSource
-    VERBATIM)
-else()
-  add_custom_command(
-    OUTPUT ${CMAKE_BINARY_DIR}/Basilisk/architecture/messaging/__init__.py
-    COMMAND ${PYTHON_EXECUTABLE} generatePackageInit.py "${CMAKE_BINARY_DIR}/Basilisk/architecture/messaging/"
-            "../../msgPayloadDefC/" "../../msgPayloadDefCpp/"
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/msgAutoSource
-    VERBATIM)
-endif(NOT "${EXTERNAL_MODULES_PATH}" STREQUAL "")
+   list(APPEND message_directory_paths
+          "${EXTERNAL_MODULES_PATH}/msgPayloadDefC/"
+          "${EXTERNAL_MODULES_PATH}/msgPayloadDefCpp/")
+endif (NOT "${EXTERNAL_MODULES_PATH}" STREQUAL "")
+
+add_custom_command(
+        OUTPUT ${CMAKE_BINARY_DIR}/Basilisk/architecture/messaging/__init__.py
+        COMMAND
+        ${PYTHON_EXECUTABLE} generateMessagePackageInit.py ${message_directory_paths}
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/msgAutoSource
+        VERBATIM
+)
 
 # Custom target for establishing dependency
 add_custom_target(swigtrick DEPENDS ${CMAKE_BINARY_DIR}/Basilisk/architecture/messaging/__init__.py)
diff --git a/src/architecture/messaging/msgAutoSource/generateMessagePackageInit.py b/src/architecture/messaging/msgAutoSource/generateMessagePackageInit.py
new file mode 100644
index 0000000000..cd266f1b85
--- /dev/null
+++ b/src/architecture/messaging/msgAutoSource/generateMessagePackageInit.py
@@ -0,0 +1,27 @@
+import os
+import pathlib
+import sys
+
+path = os.path.dirname(os.path.abspath(__file__))
+sys.path.append(path + '/../../../../../Basilisk/src/architecture/messaging/msgAutoSource')
+
+if __name__ == "__main__":
+    """
+    In the message package directory create an __init__.py file
+    containing all the message packages. If the file exists, overwrite it.
+    """
+    modulePath = sys.argv[1]
+    isExist = os.path.exists(modulePath)
+    os.makedirs(modulePath, exist_ok=True)
+    mainImportFid = open(modulePath + '/__init__.py', 'w')
+    for i in range(2, len(sys.argv)):
+        headerInputPath = sys.argv[i]
+        for fileName in os.listdir(headerInputPath):
+            if fileName.endswith(".h") or fileName.endswith(".hpp"):
+                className = os.path.splitext(fileName)[0]
+                msgName = className.split('Payload')[0]
+                mainImportFid.write('from Basilisk.architecture.messaging.' + className + ' import *\n')
+    mainImportFid.close()
+    oldModulePath = modulePath.split('messaging')[0] + 'cMsgCInterfacePy'
+    pathlib.Path(oldModulePath).unlink(missing_ok=True)
+    os.symlink(modulePath, oldModulePath)
diff --git a/src/architecture/messaging/msgAutoSource/generatePackageInit.py b/src/architecture/messaging/msgAutoSource/generatePackageInit.py
deleted file mode 100644
index bc825be62b..0000000000
--- a/src/architecture/messaging/msgAutoSource/generatePackageInit.py
+++ /dev/null
@@ -1,22 +0,0 @@
-import os
-import sys
-
-path = os.path.dirname(os.path.abspath(__file__))
-sys.path.append(path + '/../../../../../Basilisk/src/architecture/messaging/msgAutoSource')
-
-if __name__ == "__main__":
-    moduleOutputPath = sys.argv[1]
-    isExist = os.path.exists(moduleOutputPath)
-    if not isExist:
-        os.makedirs(moduleOutputPath, exist_ok=True)
-    mainImportFid = open(moduleOutputPath + '/__init__.py', 'w')
-    for i in range(2, len(sys.argv)):
-        headerInputPath = sys.argv[i]
-        for filePre in os.listdir(headerInputPath):
-            if(filePre.endswith(".h") or filePre.endswith(".hpp")):
-                className = os.path.splitext(filePre)[0]
-                msgName = className.split('Payload')[0]
-                mainImportFid.write('from Basilisk.architecture.messaging.' + className + ' import *\n')
-    mainImportFid.close()
-    setOldPath = moduleOutputPath.split('messaging')[0] + '/cMsgCInterfacePy'
-    os.symlink(moduleOutputPath, setOldPath)