diff --git a/.bazelci/presubmit.yml b/.bazelci/presubmit.yml
index e14d56a4a4..1da4d9fb6b 100644
--- a/.bazelci/presubmit.yml
+++ b/.bazelci/presubmit.yml
@@ -28,8 +28,6 @@ buildifier:
   build_targets:
     - "--"
     - "..."
-    # This has its own workspace and needs to run from there
-    - "-//examples/py_proto_library/..."
     # As a regression test for #225, check that wheel targets still build when
     # their package path is qualified with the repo name.
     - "@rules_python//examples/wheel/..."
diff --git a/.bazelrc b/.bazelrc
index 39b28d12e6..32e86e5859 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -3,8 +3,8 @@
 # This lets us glob() up all the files inside the examples to make them inputs to tests
 # (Note, we cannot use `common --deleted_packages` because the bazel version command doesn't support it)
 # To update these lines, run tools/bazel_integration_test/update_deleted_packages.sh
-build --deleted_packages=examples/build_file_generation,examples/build_file_generation/random_number_generator,examples/bzlmod,examples/bzlmod/entry_points,examples/bzlmod/entry_points/tests,examples/bzlmod/libs/my_lib,examples/bzlmod/other_module,examples/bzlmod/other_module/other_module/pkg,examples/bzlmod/runfiles,examples/bzlmod/tests,examples/bzlmod/tests/other_module,examples/bzlmod/whl_mods,examples/bzlmod_build_file_generation,examples/bzlmod_build_file_generation/other_module/other_module/pkg,examples/bzlmod_build_file_generation/runfiles,examples/multi_python_versions/libs/my_lib,examples/multi_python_versions/requirements,examples/multi_python_versions/tests,examples/pip_install,examples/pip_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,tests/compile_pip_requirements,tests/compile_pip_requirements_test_from_external_workspace,tests/ignore_root_user_error,tests/pip_repository_entry_points
-query --deleted_packages=examples/build_file_generation,examples/build_file_generation/random_number_generator,examples/bzlmod,examples/bzlmod/entry_points,examples/bzlmod/entry_points/tests,examples/bzlmod/libs/my_lib,examples/bzlmod/other_module,examples/bzlmod/other_module/other_module/pkg,examples/bzlmod/runfiles,examples/bzlmod/tests,examples/bzlmod/tests/other_module,examples/bzlmod/whl_mods,examples/bzlmod_build_file_generation,examples/bzlmod_build_file_generation/other_module/other_module/pkg,examples/bzlmod_build_file_generation/runfiles,examples/multi_python_versions/libs/my_lib,examples/multi_python_versions/requirements,examples/multi_python_versions/tests,examples/pip_install,examples/pip_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,tests/compile_pip_requirements,tests/compile_pip_requirements_test_from_external_workspace,tests/ignore_root_user_error,tests/pip_repository_entry_points
+build --deleted_packages=examples/build_file_generation,examples/build_file_generation/random_number_generator,examples/bzlmod,examples/bzlmod_build_file_generation,examples/bzlmod_build_file_generation/other_module/other_module/pkg,examples/bzlmod_build_file_generation/runfiles,examples/bzlmod/entry_points,examples/bzlmod/entry_points/tests,examples/bzlmod/libs/my_lib,examples/bzlmod/other_module,examples/bzlmod/other_module/other_module/pkg,examples/bzlmod/runfiles,examples/bzlmod/tests,examples/bzlmod/tests/other_module,examples/bzlmod/whl_mods,examples/multi_python_versions/libs/my_lib,examples/multi_python_versions/requirements,examples/multi_python_versions/tests,examples/pip_install,examples/pip_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/proto,tests/compile_pip_requirements,tests/compile_pip_requirements_test_from_external_workspace,tests/ignore_root_user_error,tests/pip_repository_entry_points
+query --deleted_packages=examples/build_file_generation,examples/build_file_generation/random_number_generator,examples/bzlmod,examples/bzlmod_build_file_generation,examples/bzlmod_build_file_generation/other_module/other_module/pkg,examples/bzlmod_build_file_generation/runfiles,examples/bzlmod/entry_points,examples/bzlmod/entry_points/tests,examples/bzlmod/libs/my_lib,examples/bzlmod/other_module,examples/bzlmod/other_module/other_module/pkg,examples/bzlmod/runfiles,examples/bzlmod/tests,examples/bzlmod/tests/other_module,examples/bzlmod/whl_mods,examples/multi_python_versions/libs/my_lib,examples/multi_python_versions/requirements,examples/multi_python_versions/tests,examples/pip_install,examples/pip_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/proto,tests/compile_pip_requirements,tests/compile_pip_requirements_test_from_external_workspace,tests/ignore_root_user_error,tests/pip_repository_entry_points
 
 test --test_output=errors