diff --git a/.changeset/delete_fewer_files_with_overwrite.md b/.changeset/delete_fewer_files_with_overwrite.md
new file mode 100644
index 000000000..c2e273a39
--- /dev/null
+++ b/.changeset/delete_fewer_files_with_overwrite.md
@@ -0,0 +1,13 @@
+---
+default: major
+---
+
+# Delete fewer files with `--overwrite`
+
+`--overwrite` will no longer delete the entire output directory before regenerating. Instead, it will only delete 
+specific, known directories within that directory. Right now, that is only the generated `models` and `api` directories.
+
+Other generated files, like `README.md`, will be overwritten. Extra files and directories outside of those listed above 
+will be left untouched, so you can any extra modules or files around while still updating `pyproject.toml` automatically.
+
+Closes #1105.
diff --git a/end_to_end_tests/test_end_to_end.py b/end_to_end_tests/test_end_to_end.py
index 2452c3acd..124b801d2 100644
--- a/end_to_end_tests/test_end_to_end.py
+++ b/end_to_end_tests/test_end_to_end.py
@@ -13,7 +13,7 @@
 def _compare_directories(
     record: Path,
     test_subject: Path,
-    expected_differences: dict[Path, str],
+    expected_differences: Optional[dict[Path, str]] = None,
     expected_missing: Optional[set[str]] = None,
     ignore: list[str] = None,
     depth=0,
@@ -298,11 +298,11 @@ def test_update_integration_tests():
     config_path = source_path / "config.yaml"
     _run_command(
         "generate",
-        extra_args=["--meta=none", "--overwrite", f"--output-path={source_path / 'integration_tests'}"],
+        extra_args=["--overwrite", "--meta=pdm", f"--output-path={temp_dir}"],
         url=url,
         config_path=config_path
     )
-    _compare_directories(temp_dir, source_path, expected_differences={})
+    _compare_directories(source_path, temp_dir, ignore=["pyproject.toml"])
     import mypy.api
 
     out, err, status = mypy.api.run([str(temp_dir), "--strict"])
diff --git a/integration-tests/.gitignore b/integration-tests/.gitignore
index ed29cb977..79a2c3d73 100644
--- a/integration-tests/.gitignore
+++ b/integration-tests/.gitignore
@@ -20,4 +20,4 @@ dmypy.json
 .idea/
 
 /coverage.xml
-/.coverage
\ No newline at end of file
+/.coverage
diff --git a/integration-tests/integration_tests/py.typed b/integration-tests/integration_tests/py.typed
new file mode 100644
index 000000000..1aad32711
--- /dev/null
+++ b/integration-tests/integration_tests/py.typed
@@ -0,0 +1 @@
+# Marker file for PEP 561
\ No newline at end of file
diff --git a/integration-tests/pyproject.toml b/integration-tests/pyproject.toml
index 307e9e936..9eaacea87 100644
--- a/integration-tests/pyproject.toml
+++ b/integration-tests/pyproject.toml
@@ -4,12 +4,12 @@ version = "0.0.1"
 description = "A client library for accessing OpenAPI Test Server"
 authors = []
 readme = "README.md"
+requires-python = ">=3.9,<4.0"
 dependencies = [
     "httpx>=0.20.0,<0.29.0",
     "attrs>=21.3.0",
     "python-dateutil>=2.8.0",
 ]
-requires-python = ">=3.8,<4.0"
 
 [tool.pdm]
 distribution = true
diff --git a/openapi_python_client/__init__.py b/openapi_python_client/__init__.py
index 2225d2008..af6944ae4 100644
--- a/openapi_python_client/__init__.py
+++ b/openapi_python_client/__init__.py
@@ -108,13 +108,11 @@ def build(self) -> Sequence[GeneratorError]:
         """Create the project from templates"""
 
         print(f"Generating {self.project_dir}")
-        if self.config.overwrite:
-            shutil.rmtree(self.project_dir, ignore_errors=True)
-
         try:
             self.project_dir.mkdir()
         except FileExistsError:
-            return [GeneratorError(detail="Directory already exists. Delete it or use the --overwrite option.")]
+            if not self.config.overwrite:
+                return [GeneratorError(detail="Directory already exists. Delete it or use the --overwrite option.")]
         self._create_package()
         self._build_metadata()
         self._build_models()
@@ -158,7 +156,7 @@ def _get_errors(self) -> list[GeneratorError]:
 
     def _create_package(self) -> None:
         if self.package_dir != self.project_dir:
-            self.package_dir.mkdir()
+            self.package_dir.mkdir(exist_ok=True)
         # Package __init__.py
         package_init = self.package_dir / "__init__.py"
 
@@ -214,6 +212,7 @@ def _build_setup_py(self) -> None:
     def _build_models(self) -> None:
         # Generate models
         models_dir = self.package_dir / "models"
+        shutil.rmtree(models_dir, ignore_errors=True)
         models_dir.mkdir()
         models_init = models_dir / "__init__.py"
         imports = []
@@ -259,6 +258,7 @@ def _build_api(self) -> None:
 
         # Generate endpoints
         api_dir = self.package_dir / "api"
+        shutil.rmtree(api_dir, ignore_errors=True)
         api_dir.mkdir()
         api_init_path = api_dir / "__init__.py"
         api_init_template = self.env.get_template("api_init.py.jinja")
diff --git a/pyproject.toml b/pyproject.toml
index a311d020d..4e7c63010 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -130,7 +130,7 @@ composite = ["test --cov openapi_python_client tests --cov-report=term-missing"]
 
 [tool.pdm.scripts.regen_integration]
 shell = """
-openapi-python-client generate --overwrite --url https://raw.githubusercontent.com/openapi-generators/openapi-test-server/main/openapi.json --config integration-tests/config.yaml --meta none --output-path integration-tests/integration_tests \
+openapi-python-client generate --overwrite --url https://raw.githubusercontent.com/openapi-generators/openapi-test-server/main/openapi.json --config integration-tests/config.yaml --meta pdm --output-path integration-tests \
 """
 
 [build-system]