diff --git a/tests_integration/nativeapp/test_bundle.py b/tests_integration/nativeapp/test_bundle.py
index 5c5eb933ba..2bcfa1bd6a 100644
--- a/tests_integration/nativeapp/test_bundle.py
+++ b/tests_integration/nativeapp/test_bundle.py
@@ -23,6 +23,7 @@
 from tests_integration.testing_utils import (
     assert_that_result_failed_with_message_containing,
 )
+from tests_integration.testing_utils.project_fixtures import *
 
 
 @pytest.fixture
@@ -323,10 +324,13 @@ def test_nativeapp_bundle_deletes_existing_deploy_root(template_setup):
 
 
 @pytest.mark.integration
-def test_nativeapp_can_bundle_with_subdirs(runner, nativeapp_project_directory):
+def test_nativeapp_can_bundle_with_subdirs(
+    runner, nativeapp_teardown, setup_v2_project_w_subdir
+):
     command = "app bundle --package-entity-id=pkg_v1"
     subdir = "v1"
-    with nativeapp_project_directory("napp_stage_subdirs") as project_root:
+    project_name, project_root = setup_v2_project_w_subdir()
+    with nativeapp_teardown():
         result = runner.invoke_json(split(command))
         assert result.exit_code == 0
 
@@ -337,9 +341,12 @@ def test_nativeapp_can_bundle_with_subdirs(runner, nativeapp_project_directory):
 
 
 @pytest.mark.integration
-def test_nativeapp_bundle_subdirs_dont_overwrite(runner, nativeapp_project_directory):
+def test_nativeapp_bundle_subdirs_dont_overwrite(
+    runner, nativeapp_teardown, setup_v2_project_w_subdir_w_snowpark
+):
+    project_name, project_root = setup_v2_project_w_subdir_w_snowpark()
 
-    with nativeapp_project_directory("napp_stage_subdirs_w_snowpark") as project_root:
+    with nativeapp_teardown():
         result_1 = runner.invoke_json(split("app bundle --package-entity-id=pkg_v1"))
         assert result_1.exit_code == 0
 
diff --git a/tests_integration/nativeapp/test_deploy.py b/tests_integration/nativeapp/test_deploy.py
index be29b3e10e..d0879ee95b 100644
--- a/tests_integration/nativeapp/test_deploy.py
+++ b/tests_integration/nativeapp/test_deploy.py
@@ -17,12 +17,13 @@
 
 from snowflake.cli.api.project.util import TEST_RESOURCE_SUFFIX_VAR
 from tests.nativeapp.utils import touch
-
+from tests_integration.testing_utils.project_fixtures import *
 from tests.project.fixtures import *
 from tests_integration.test_utils import (
     contains_row_with,
     not_contains_row_with,
     row_from_snowflake_session,
+    row_from_cursor,
 )
 from tests_integration.testing_utils import (
     assert_that_result_failed_with_message_containing,
@@ -108,7 +109,7 @@ def test_nativeapp_deploy(
 
 @pytest.mark.integration
 def test_nativeapp_deploy_w_stage_subdir(
-    nativeapp_project_directory,
+    nativeapp_teardown,
     runner,
     snowflake_session,
     default_username,
@@ -116,9 +117,13 @@ def test_nativeapp_deploy_w_stage_subdir(
     sanitize_deploy_output,
     snapshot,
     print_paths_as_posix,
+    setup_v2_project_w_subdir,
 ):
-    project_name = "stage_w_subdirs_pkg"
-    with nativeapp_project_directory("napp_stage_subdirs"):
+    (
+        project_name,
+        _,
+    ) = setup_v2_project_w_subdir()  # make this a fixture, don't pass temp_dir
+    with nativeapp_teardown():
         result = runner.invoke_with_connection(
             split("app deploy --package-entity-id=pkg_v1")
         )
@@ -127,8 +132,9 @@ def test_nativeapp_deploy_w_stage_subdir(
         assert sanitize_deploy_output(result.output) == snapshot
 
         # package exist
-        package_name = f"{project_name}_{default_username}{resource_suffix}".upper()
-        app_name = f"{project_name}_{default_username}{resource_suffix}".upper()
+        package_name = f"{project_name}_pkg_{default_username}{resource_suffix}".upper()
+        app_name = f"{project_name}_app_v1_{default_username}{resource_suffix}".upper()
+
         assert contains_row_with(
             row_from_snowflake_session(
                 snowflake_session.execute_string(
@@ -139,7 +145,7 @@ def test_nativeapp_deploy_w_stage_subdir(
         )
 
         # manifest file exists
-        stage_name = "app_src.stage/v1"  # as defined in native-apps-templates/basic
+        stage_name = "app_src.stage/v1"
         stage_files = runner.invoke_with_connection_json(
             ["stage", "list-files", f"{package_name}.{stage_name}"]
         )
@@ -274,17 +280,17 @@ def test_nativeapp_deploy_prune_w_stage_subdir(
     command,
     contains,
     not_contains,
-    nativeapp_project_directory,
+    nativeapp_teardown,
     runner,
     snapshot,
     print_paths_as_posix,
     default_username,
     resource_suffix,
     sanitize_deploy_output,
+    setup_v2_project_w_subdir,
 ):
-    test_project = "napp_stage_subdirs"
-    project_name = "stage_w_subdirs_pkg"
-    with nativeapp_project_directory(test_project):
+    project_name, _ = setup_v2_project_w_subdir()
+    with nativeapp_teardown():
         result = runner.invoke_with_connection_json(
             ["app", "deploy", "--package-entity-id=pkg_v1"]
         )
@@ -299,7 +305,7 @@ def test_nativeapp_deploy_prune_w_stage_subdir(
         assert sanitize_deploy_output(result.output) == snapshot
 
         # verify the file does not exist on the stage
-        package_name = f"{project_name}_{default_username}{resource_suffix}".upper()
+        package_name = f"{project_name}_pkg_{default_username}{resource_suffix}".upper()
         stage_name = "app_src.stage/v1"  # as defined in native-apps-templates/basic
         stage_files = runner.invoke_with_connection_json(
             ["stage", "list-files", f"{package_name}.{stage_name}"]
@@ -355,16 +361,17 @@ def test_nativeapp_deploy_files(
 
 @pytest.mark.integration
 def test_nativeapp_deploy_files_w_stage_subdir(
-    nativeapp_project_directory,
+    nativeapp_teardown,
     runner,
     snapshot,
     print_paths_as_posix,
     default_username,
     resource_suffix,
     sanitize_deploy_output,
+    setup_v2_project_w_subdir,
 ):
-    project_name = "stage_w_subdirs_pkg"
-    with nativeapp_project_directory("napp_stage_subdirs"):
+    project_name, _ = setup_v2_project_w_subdir()
+    with nativeapp_teardown():
         # sync only two specific files to stage
         touch("app/v2/file.txt")
         result = runner.invoke_with_connection(
@@ -379,7 +386,7 @@ def test_nativeapp_deploy_files_w_stage_subdir(
         assert sanitize_deploy_output(result.output) == snapshot
 
         # manifest and script files exist, readme doesn't exist
-        package_name = f"{project_name}_{default_username}{resource_suffix}".upper()
+        package_name = f"{project_name}_pkg_{default_username}{resource_suffix}".upper()
         stage_name = "app_src.stage/v2"  # as defined in native-apps-templates/basic
         stage_files = runner.invoke_with_connection_json(
             ["stage", "list-files", f"{package_name}.{stage_name}"]
diff --git a/tests_integration/nativeapp/test_version.py b/tests_integration/nativeapp/test_version.py
index 12bf881d40..fc272fb9f2 100644
--- a/tests_integration/nativeapp/test_version.py
+++ b/tests_integration/nativeapp/test_version.py
@@ -12,6 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 from shlex import split
+from textwrap import dedent
 from typing import Any, Union
 
 import yaml
@@ -102,13 +103,6 @@ def temporary_role(request, snowflake_session, resource_suffix):
             "ws version drop --entity-id=pkg",
             "napp_init_v2",
         ],
-        [
-            "stage_w_subdirs",
-            "app version create --package-entity-id=pkg_v1",
-            "app version list --package-entity-id=pkg_v1",
-            "app version drop --package-entity-id=pkg_v1",
-            "napp_stage_subdirs",
-        ],
     ],
 )
 def test_nativeapp_version_create_and_drop(
@@ -155,6 +149,51 @@ def test_nativeapp_version_create_and_drop(
         assert len(actual.json) == 0
 
 
+@pytest.mark.integration
+def test_nativeapp_version_create_and_drop_stage_subdir(
+    runner,
+    snowflake_session,
+    default_username,
+    resource_suffix,
+    nativeapp_teardown,
+    setup_v2_project_w_subdir,
+):
+    project_name, _ = setup_v2_project_w_subdir()
+    drop_command = "app version drop --package-entity-id=pkg_v1"
+    list_command = "app version list --package-entity-id=pkg_v1"
+    create_command = "app version create --package-entity-id=pkg_v1"
+    with nativeapp_teardown():
+        result_create = runner.invoke_with_connection_json(
+            [*split(create_command), "v1", "--force", "--skip-git-check"]
+        )
+        assert result_create.exit_code == 0
+
+        # package exist
+        package_name = f"{project_name}_pkg_{default_username}{resource_suffix}".upper()
+        assert contains_row_with(
+            row_from_snowflake_session(
+                snowflake_session.execute_string(
+                    f"show application packages like '{package_name}'",
+                )
+            ),
+            dict(name=package_name),
+        )
+
+        # app package contains version v1
+        expect = snowflake_session.execute_string(
+            f"show versions in application package {package_name}"
+        )
+        actual = runner.invoke_with_connection_json(split(list_command))
+        assert actual.json == row_from_snowflake_session(expect)
+
+        result_drop = runner.invoke_with_connection_json(
+            [*split(drop_command), "v1", "--force"]
+        )
+        assert result_drop.exit_code == 0
+        actual = runner.invoke_with_connection_json(split(list_command))
+        assert len(actual.json) == 0
+
+
 # Tests upgrading an app from an existing loose files installation to versioned installation.
 @pytest.mark.integration
 @pytest.mark.parametrize(
@@ -207,15 +246,16 @@ def test_nativeapp_upgrade_w_subdirs(
     snowflake_session,
     default_username,
     resource_suffix,
-    nativeapp_project_directory,
+    nativeapp_teardown,
+    setup_v2_project_w_subdir,
 ):
-    project_name = "stage_w_subdirs"
+    project_name, _ = setup_v2_project_w_subdir()
     create_command = (
         "app version create v1 --package-entity-id=pkg_v1 --force --skip-git-check"
     )
     list_command = "app version list --package-entity-id=pkg_v1"
     drop_command = "app version drop --package-entity-id=pkg_v1"
-    with nativeapp_project_directory("napp_stage_subdirs"):
+    with nativeapp_teardown():
         runner.invoke_with_connection_json(["app", "run", "--app-entity-id=app_v1"])
         runner.invoke_with_connection_json(split(create_command))
 
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/README.md b/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/README.md
deleted file mode 100644
index 3107d92de2..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# README
-
-This is the <% ctx.pkg_v1.stage_subdirectory %> version of this package!
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/manifest.yml b/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/manifest.yml
deleted file mode 100644
index 3fa13420db..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/manifest.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-# This is the v2 version of the napp_init_v1 project
-
-manifest_version: 1
-
-version:
-  name: v1
-
-artifacts:
-  setup_script: setup_script.sql
-  readme: README.md
-  extension_code: true
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/setup_script.sql b/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/setup_script.sql
deleted file mode 100644
index 18017841cc..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs/app/v1/setup_script.sql
+++ /dev/null
@@ -1,5 +0,0 @@
-
-CREATE APPLICATION ROLE IF NOT EXISTS app_public;
-
-CREATE OR ALTER VERSIONED SCHEMA core;
-GRANT USAGE ON SCHEMA core TO APPLICATION ROLE app_public;
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/README.md b/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/README.md
deleted file mode 100644
index b6162eae29..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# README
-
-This is the <% ctx.pkg_v2.stage_subdirectory %> version of this package!
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/manifest.yml b/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/manifest.yml
deleted file mode 100644
index ee1f6c99c5..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/manifest.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-# This is the v2 version of the napp_init_v1 project
-
-manifest_version: 1
-
-version:
-  name: v2
-
-artifacts:
-  setup_script: setup_script.sql
-  readme: README.md
-  extension_code: true
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/setup_script.sql b/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/setup_script.sql
deleted file mode 100644
index 18017841cc..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs/app/v2/setup_script.sql
+++ /dev/null
@@ -1,5 +0,0 @@
-
-CREATE APPLICATION ROLE IF NOT EXISTS app_public;
-
-CREATE OR ALTER VERSIONED SCHEMA core;
-GRANT USAGE ON SCHEMA core TO APPLICATION ROLE app_public;
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs/snowflake.yml b/tests_integration/test_data/projects/napp_stage_subdirs/snowflake.yml
deleted file mode 100644
index c93cab9704..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs/snowflake.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-definition_version: 2
-entities:
-  pkg_v1:
-    type: application package
-    identifier: <% fn.concat_ids('stage_w_subdirs_pkg_', ctx.env.USER) %>
-    stage_subdirectory: v1
-    manifest: ""
-    artifacts:
-      - src: app/v1/*
-        dest: ./
-
-  pkg_v2:
-    type: application package
-    identifier: <% fn.concat_ids('stage_w_subdirs_pkg_', ctx.env.USER) %>
-    stage_subdirectory: v2
-    manifest: ""
-    artifacts:
-      - src: app/v2/*
-        dest: ./
-
-  app_v1:
-    type: application
-    from:
-      target: pkg_v1
-    identifier: <% fn.concat_ids('stage_w_subdirs_app_v1_', ctx.env.USER) %>
-
-  app_v2:
-    type: application
-    from:
-      target: pkg_v2
-    identifier: <% fn.concat_ids('stage_w_subdirs_app_v2_', ctx.env.USER) %>
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/README.md b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/README.md
deleted file mode 100644
index 3107d92de2..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# README
-
-This is the <% ctx.pkg_v1.stage_subdirectory %> version of this package!
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/manifest.yml b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/manifest.yml
deleted file mode 100644
index 3fa13420db..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/manifest.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-# This is the v2 version of the napp_init_v1 project
-
-manifest_version: 1
-
-version:
-  name: v1
-
-artifacts:
-  setup_script: setup_script.sql
-  readme: README.md
-  extension_code: true
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/module-echo-v1/echo-v1.py b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/module-echo-v1/echo-v1.py
deleted file mode 100644
index 335b485dd3..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/module-echo-v1/echo-v1.py
+++ /dev/null
@@ -1,13 +0,0 @@
-# This is where you can create python functions, which can further
-# be used to create Snowpark UDFs and Stored Procedures in your setup_script.sql file.
-
-from snowflake.snowpark.functions import udf
-
-# UDF example:
-# decorated example
-@udf(
-    name="echo_fn",
-    native_app_params={"schema": "core", "application_roles": ["app_public"]},
-)
-def echo_fn(data: str) -> str:
-    return "echo_fn, v1 implementation: " + data
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/setup_script.sql b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/setup_script.sql
deleted file mode 100644
index 18017841cc..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v1/setup_script.sql
+++ /dev/null
@@ -1,5 +0,0 @@
-
-CREATE APPLICATION ROLE IF NOT EXISTS app_public;
-
-CREATE OR ALTER VERSIONED SCHEMA core;
-GRANT USAGE ON SCHEMA core TO APPLICATION ROLE app_public;
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/README.md b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/README.md
deleted file mode 100644
index b6162eae29..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# README
-
-This is the <% ctx.pkg_v2.stage_subdirectory %> version of this package!
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/manifest.yml b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/manifest.yml
deleted file mode 100644
index ee1f6c99c5..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/manifest.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-# This is the v2 version of the napp_init_v1 project
-
-manifest_version: 1
-
-version:
-  name: v2
-
-artifacts:
-  setup_script: setup_script.sql
-  readme: README.md
-  extension_code: true
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/module-echo-v2/echo-v2.py b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/module-echo-v2/echo-v2.py
deleted file mode 100644
index 6ae32cf48a..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/module-echo-v2/echo-v2.py
+++ /dev/null
@@ -1,13 +0,0 @@
-# This is where you can create python functions, which can further
-# be used to create Snowpark UDFs and Stored Procedures in your setup_script.sql file.
-
-from snowflake.snowpark.functions import udf
-
-# UDF example:
-# decorated example
-@udf(
-    name="echo_fn",
-    native_app_params={"schema": "core", "application_roles": ["app_public"]},
-)
-def echo_fn(data: str) -> str:
-    return "echo_fn, v2 implementation: " + data
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/setup_script.sql b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/setup_script.sql
deleted file mode 100644
index 18017841cc..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/app/v2/setup_script.sql
+++ /dev/null
@@ -1,5 +0,0 @@
-
-CREATE APPLICATION ROLE IF NOT EXISTS app_public;
-
-CREATE OR ALTER VERSIONED SCHEMA core;
-GRANT USAGE ON SCHEMA core TO APPLICATION ROLE app_public;
diff --git a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/snowflake.yml b/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/snowflake.yml
deleted file mode 100644
index 1f18f52062..0000000000
--- a/tests_integration/test_data/projects/napp_stage_subdirs_w_snowpark/snowflake.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-definition_version: 2
-entities:
-  pkg_v1:
-    type: application package
-    identifier: <% fn.concat_ids('stage_w_subdirs_pkg', ctx.env.suffix) %>
-    stage_subdirectory: v1
-    manifest: ""
-    artifacts:
-      - src: app/v1/*
-        dest: ./
-        processors:
-          - snowpark
-
-  pkg_v2:
-    type: application package
-    identifier: <% fn.concat_ids('stage_w_subdirs_pkg', ctx.env.suffix) %>
-    stage_subdirectory: v2
-    manifest: ""
-    artifacts:
-      - src: app/v2/*
-        dest: ./
-        processors:
-          - snowpark
-
-  app_v1:
-    type: application
-    from:
-      target: pkg_v1
-    identifier: <% fn.concat_ids('stage_w_subdirs_app_v1', ctx.env.suffix) %>
-
-  app_v2:
-    type: application
-    from:
-      target: pkg_v2
-    identifier: <% fn.concat_ids('stage_w_subdirs_app_v2', ctx.env.suffix) %>
-
-env:
-  suffix: <% fn.concat_ids('_', fn.sanitize_id(fn.get_username('unknown_user')) | lower) %>
diff --git a/tests_integration/testing_utils/project_fixtures.py b/tests_integration/testing_utils/project_fixtures.py
new file mode 100644
index 0000000000..16bf5e0653
--- /dev/null
+++ b/tests_integration/testing_utils/project_fixtures.py
@@ -0,0 +1,137 @@
+from textwrap import dedent
+
+import pytest
+
+from tests.nativeapp.factories import (
+    ProjectV2Factory,
+    ApplicationPackageEntityModelFactory,
+    ApplicationEntityModelFactory,
+)
+
+
+MANIFEST_BASIC = dedent(
+    """\
+            manifest_version: 1
+
+            version:
+                name: dev
+
+            artifacts:
+                setup_script: setup_script.sql
+                readme: README.md
+                extension_code: true
+        """
+)
+
+PYTHON_W_SNOWPARK = dedent(
+    """\
+    from snowflake.snowpark.functions import udf
+    @udf(
+        name="echo_fn",
+        native_app_params={"schema": "core", "application_roles": ["app_public"]},
+    )
+    def echo_fn(data: str) -> str:
+        return "echo_fn: " + data
+        """
+)
+
+
+@pytest.fixture
+def setup_v2_project_w_subdir(temp_dir):
+    def wrapper():
+        readme_v1 = (
+            "This is the <% ctx.pkg_v1.stage_subdirectory %> version of this package!"
+        )
+        readme_v2 = (
+            "This is the <% ctx.pkg_v2.stage_subdirectory %> version of this package!"
+        )
+        project_name = "stage_w_subdirs"
+        ProjectV2Factory(
+            pdf__entities=dict(
+                pkg_v1=ApplicationPackageEntityModelFactory(
+                    identifier=f"<% fn.concat_ids('{project_name}_pkg_', ctx.env.USER) %>",
+                    manifest="",
+                    artifacts=[{"src": "app/v1/*", "dest": "./"}],
+                    stage_subdirectory="v1",
+                ),
+                app_v1=ApplicationEntityModelFactory(
+                    fromm__target="pkg_v1",
+                    identifier=f"<% fn.concat_ids('{project_name}_app_v1_', ctx.env.USER) %>",
+                ),
+                pkg_v2=ApplicationPackageEntityModelFactory(
+                    identifier=f"<% fn.concat_ids('{project_name}_pkg_', ctx.env.USER) %>",
+                    manifest="",
+                    artifacts=[{"src": "app/v2/*", "dest": "./"}],
+                    stage_subdirectory="v2",
+                ),
+                app_v2=ApplicationEntityModelFactory(
+                    fromm__target="pkg_v2",
+                    identifier=f"<% fn.concat_ids('{project_name}_app_v2_', ctx.env.USER) %>",
+                ),
+            ),
+            files={
+                "app/v1/manifest.yml": MANIFEST_BASIC,
+                "app/v1/README.md": readme_v1,
+                "app/v1/setup_script.sql": "SELECT 1;",
+                "app/v2/manifest.yml": MANIFEST_BASIC,
+                "app/v2/README.md": readme_v2,
+                "app/v2/setup_script.sql": "SELECT 1;",
+            },
+        )
+        return project_name, temp_dir
+
+    return wrapper
+
+
+@pytest.fixture
+def setup_v2_project_w_subdir_w_snowpark(temp_dir):
+    def wrapper():
+        setup_script = dedent(
+            """\
+                CREATE APPLICATION ROLE IF NOT EXISTS app_public;
+                CREATE OR ALTER VERSIONED SCHEMA core;
+                GRANT USAGE ON SCHEMA core TO APPLICATION ROLE app_public;
+                """
+        )
+        project_name = "stage_w_subdirs"
+        ProjectV2Factory(
+            pdf__entities=dict(
+                pkg_v1=ApplicationPackageEntityModelFactory(
+                    identifier=f"<% fn.concat_ids('{project_name}_pkg_', ctx.env.USER) %>",
+                    manifest="",
+                    artifacts=[
+                        {"src": "app/v1/*", "dest": "./", "processors": ["snowpark"]}
+                    ],
+                    stage_subdirectory="v1",
+                ),
+                app_v1=ApplicationEntityModelFactory(
+                    fromm__target="pkg_v1",
+                    identifier=f"<% fn.concat_ids('{project_name}_app_v1_', ctx.env.USER) %>",
+                ),
+                pkg_v2=ApplicationPackageEntityModelFactory(
+                    identifier=f"<% fn.concat_ids('{project_name}_pkg_', ctx.env.USER) %>",
+                    manifest="",
+                    artifacts=[
+                        {"src": "app/v2/*", "dest": "./", "processors": ["snowpark"]}
+                    ],
+                    stage_subdirectory="v2",
+                ),
+                app_v2=ApplicationEntityModelFactory(
+                    fromm__target="pkg_v2",
+                    identifier=f"<% fn.concat_ids('{project_name}_app_v2_', ctx.env.USER) %>",
+                ),
+            ),
+            files={
+                "app/v1/manifest.yml": MANIFEST_BASIC,
+                "app/v1/README.md": "\n",
+                "app/v1/setup_script.sql": setup_script,
+                "app/v1/module-echo-v1/echo-v1.py": PYTHON_W_SNOWPARK,
+                "app/v2/manifest.yml": MANIFEST_BASIC,
+                "app/v2/README.md": "\n",
+                "app/v2/setup_script.sql": setup_script,
+                "app/v2/module-echo-v2/echo-v2.py": PYTHON_W_SNOWPARK,
+            },
+        )
+        return project_name, temp_dir
+
+    return wrapper