diff --git a/tools/cloudharness_utilities/openapi.py b/tools/cloudharness_utilities/openapi.py
index 42bf3d8d..1630c568 100644
--- a/tools/cloudharness_utilities/openapi.py
+++ b/tools/cloudharness_utilities/openapi.py
@@ -20,7 +20,7 @@
 OPENAPI_GEN_URL = 'https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/5.4.0/openapi-generator-cli-5.4.0.jar'
 
 
-def generate_server(app_path):
+def generate_server(app_path, overrides_folder):
     get_dependencies()
     openapi_dir = os.path.join(app_path, 'api')
     openapi_file = glob.glob(os.path.join(openapi_dir, '*.yaml'))[0]
@@ -28,7 +28,7 @@ def generate_server(app_path):
         f"{app_path}/server") else f"server"
     out_path = f"{app_path}/{out_name}"
     command = f"java -jar {CODEGEN} generate -i {openapi_file} -g python-flask -o {out_path} " \
-              f"-c {openapi_dir}/config.json -t {os.path.join(HERE, APPLICATION_TEMPLATE_PATH, 'server')}"
+              f"-c {openapi_dir}/config.json -t {overrides_folder}"
     os.system(command)
 
 
diff --git a/tools/harness-application b/tools/harness-application
index 68e34962..1d9579be 100644
--- a/tools/harness-application
+++ b/tools/harness-application
@@ -4,13 +4,14 @@ import sys
 import os
 import shutil
 import re
+import tempfile
 
 from cloudharness_utilities import HERE
 from cloudharness_utilities.constants import APPLICATION_TEMPLATE_PATH
 import cloudharness_utilities.openapi
 from cloudharness_utilities.openapi import generate_server, APPLICATIONS_SRC_PATH, generate_ts_client
 from cloudharness_utilities.utils import merge_configuration_directories, replaceindir, replace_in_file, \
-    to_python_module
+    to_python_module, copymergedir
 
 # Only allow lowercased alphabetical characters separated by "-".
 name_pattern = re.compile("[a-z]+((-)?[a-z])?")
@@ -54,8 +55,12 @@ if __name__ == "__main__":
 
     app_path = os.path.join(APPLICATIONS_SRC_PATH, args.name)
     for template_name in args.templates:
+
         if template_name == 'server':
-            generate_server(app_path)
+            with tempfile.TemporaryDirectory() as tmp_dirname:
+                copymergedir(os.path.join(HERE, APPLICATION_TEMPLATE_PATH, template_name), tmp_dirname)
+                merge_configuration_directories(app_path, tmp_dirname)
+                generate_server(app_path, tmp_dirname)
 
         for base_path in (HERE, os.getcwd()):
             template_path = os.path.join(base_path, APPLICATION_TEMPLATE_PATH, template_name)