From cc5d692dfcd86dc091cc3deda7608b758a4586a1 Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 08:55:19 +0900
Subject: [PATCH 01/14] stop chmoding

---
 python/private/python_repository.bzl | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/python/private/python_repository.bzl b/python/private/python_repository.bzl
index cb0731e6eb..f79b3bc74f 100644
--- a/python/private/python_repository.bzl
+++ b/python/private/python_repository.bzl
@@ -130,13 +130,6 @@ def _python_repository_impl(rctx):
     #
     # Note, when on Windows the `chmod` may not work
     if "windows" not in platform and "windows" != repo_utils.get_platforms_os_name(rctx):
-        repo_utils.execute_checked(
-            rctx,
-            op = "python_repository.MakeReadOnly",
-            arguments = [repo_utils.which_checked(rctx, "chmod"), "-R", "ugo-w", "lib"],
-            logger = logger,
-        )
-
         # If the user is not ignoring the warnings, then proceed to run a check,
         # otherwise these steps can be skipped, as they both result in some warning.
         if not rctx.attr.ignore_root_user_error:

From 788b358224edad15fcb7abd241674265088f7fae Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 08:56:51 +0900
Subject: [PATCH 02/14] make ignore_root_user_error noop in python_repository

---
 python/private/python_repository.bzl | 55 +++++-----------------------
 1 file changed, 10 insertions(+), 45 deletions(-)

diff --git a/python/private/python_repository.bzl b/python/private/python_repository.bzl
index f79b3bc74f..16c522f398 100644
--- a/python/private/python_repository.bzl
+++ b/python/private/python_repository.bzl
@@ -123,38 +123,6 @@ def _python_repository_impl(rctx):
             logger = logger,
         )
 
-    # Make the Python installation read-only. This is to prevent issues due to
-    # pycs being generated at runtime:
-    # * The pycs are not deterministic (they contain timestamps)
-    # * Multiple processes trying to write the same pycs can result in errors.
-    #
-    # Note, when on Windows the `chmod` may not work
-    if "windows" not in platform and "windows" != repo_utils.get_platforms_os_name(rctx):
-        # If the user is not ignoring the warnings, then proceed to run a check,
-        # otherwise these steps can be skipped, as they both result in some warning.
-        if not rctx.attr.ignore_root_user_error:
-            exec_result = repo_utils.execute_unchecked(
-                rctx,
-                op = "python_repository.TestReadOnly",
-                arguments = [repo_utils.which_checked(rctx, "touch"), "lib/.test"],
-                logger = logger,
-            )
-
-            # The issue with running as root is the installation is no longer
-            # read-only, so the problems due to pyc can resurface.
-            if exec_result.return_code == 0:
-                stdout = repo_utils.execute_checked_stdout(
-                    rctx,
-                    op = "python_repository.GetUserId",
-                    arguments = [repo_utils.which_checked(rctx, "id"), "-u"],
-                    logger = logger,
-                )
-                uid = int(stdout.strip())
-                if uid == 0:
-                    logger.warn("The current user is root, which can cause spurious cache misses or build failures with the hermetic Python interpreter. See https://github.com/bazel-contrib/rules_python/pull/713.")
-                else:
-                    logger.warn("The current user has CAP_DAC_OVERRIDE set, which can cause spurious cache misses or build failures with the hermetic Python interpreter. See https://github.com/bazel-contrib/rules_python/pull/713.")
-
     python_bin = "python.exe" if ("windows" in platform) else "bin/python3"
 
     if "linux" in platform:
@@ -179,17 +147,15 @@ def _python_repository_impl(rctx):
                 break
 
     glob_include = []
-    glob_exclude = []
-    if rctx.attr.ignore_root_user_error or "windows" in platform:
-        glob_exclude += [
-            # These pycache files are created on first use of the associated python files.
-            # Exclude them from the glob because otherwise between the first time and second time a python toolchain is used,"
-            # the definition of this filegroup will change, and depending rules will get invalidated."
-            # See https://github.com/bazel-contrib/rules_python/issues/1008 for unconditionally adding these to toolchains so we can stop ignoring them."
-            # pyc* is ignored because pyc creation creates temporary .pyc.NNNN files
-            "**/__pycache__/*.pyc*",
-            "**/__pycache__/*.pyo*",
-        ]
+    glob_exclude = [
+        # These pycache files are created on first use of the associated python files.
+        # Exclude them from the glob because otherwise between the first time and second time a python toolchain is used,"
+        # the definition of this filegroup will change, and depending rules will get invalidated."
+        # See https://github.com/bazel-contrib/rules_python/issues/1008 for unconditionally adding these to toolchains so we can stop ignoring them."
+        # pyc* is ignored because pyc creation creates temporary .pyc.NNNN files
+        "**/__pycache__/*.pyc*",
+        "**/__pycache__/*.pyo*",
+    ]
 
     if "windows" in platform:
         glob_include += [
@@ -242,7 +208,6 @@ define_hermetic_runtime_toolchain_impl(
         "coverage_tool": rctx.attr.coverage_tool,
         "distutils": rctx.attr.distutils,
         "distutils_content": rctx.attr.distutils_content,
-        "ignore_root_user_error": rctx.attr.ignore_root_user_error,
         "name": rctx.attr.name,
         "netrc": rctx.attr.netrc,
         "patch_strip": rctx.attr.patch_strip,
@@ -292,7 +257,7 @@ For more information see {attr}`py_runtime.coverage_tool`.
         ),
         "ignore_root_user_error": attr.bool(
             default = True,
-            doc = "Whether the check for root should be ignored or not. This causes cache misses with .pyc files.",
+            doc = "Noop, will be removed in the next major release",
             mandatory = False,
         ),
         "netrc": attr.string(

From fe08b6a725dacb7ca77505f774133f09f116b703 Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 09:00:18 +0900
Subject: [PATCH 03/14] remove ignore_root from the python extension

---
 python/private/python.bzl     | 34 ++-------------
 tests/python/python_tests.bzl | 79 +----------------------------------
 2 files changed, 5 insertions(+), 108 deletions(-)

diff --git a/python/private/python.bzl b/python/private/python.bzl
index a1fe80e0ce..613bf36efe 100644
--- a/python/private/python.bzl
+++ b/python/private/python.bzl
@@ -76,13 +76,6 @@ def parse_modules(*, module_ctx, logger, _fail = fail):
     # Map of string Major.Minor or Major.Minor.Patch to the toolchain_info struct
     global_toolchain_versions = {}
 
-    ignore_root_user_error = None
-
-    # if the root module does not register any toolchain then the
-    # ignore_root_user_error takes its default value: True
-    if not module_ctx.modules[0].tags.toolchain:
-        ignore_root_user_error = True
-
     config = _get_toolchain_config(modules = module_ctx.modules, _fail = _fail)
 
     default_python_version = _compute_default_python_version(module_ctx)
@@ -115,15 +108,6 @@ def parse_modules(*, module_ctx, logger, _fail = fail):
                 # * The root module is allowed to override the rules_python default.
                 is_default = default_python_version == toolchain_version
 
-                # Also only the root module should be able to decide ignore_root_user_error.
-                # Modules being depended upon don't know the final environment, so they aren't
-                # in the right position to know or decide what the correct setting is.
-
-                # If an inconsistency in the ignore_root_user_error among multiple toolchains is detected, fail.
-                if ignore_root_user_error != None and toolchain_attr.ignore_root_user_error != ignore_root_user_error:
-                    fail("Toolchains in the root module must have consistent 'ignore_root_user_error' attributes")
-
-                ignore_root_user_error = toolchain_attr.ignore_root_user_error
             elif mod.name == "rules_python" and not default_toolchain:
                 # This branch handles when the root module doesn't declare a
                 # Python toolchain
@@ -166,7 +150,6 @@ def parse_modules(*, module_ctx, logger, _fail = fail):
                 global_toolchain_versions[toolchain_version] = toolchain_info
                 if debug_info:
                     debug_info["toolchains_registered"].append({
-                        "ignore_root_user_error": ignore_root_user_error,
                         "module": {"is_root": mod.is_root, "name": mod.name},
                         "name": toolchain_name,
                     })
@@ -185,8 +168,6 @@ def parse_modules(*, module_ctx, logger, _fail = fail):
             elif toolchain_info:
                 toolchains.append(toolchain_info)
 
-    config.default.setdefault("ignore_root_user_error", ignore_root_user_error)
-
     # A default toolchain is required so that the non-version-specific rules
     # are able to match a toolchain.
     if default_toolchain == None:
@@ -711,7 +692,6 @@ def _process_global_overrides(*, tag, default, _fail = fail):
         default["minor_mapping"] = tag.minor_mapping
 
     forwarded_attrs = sorted(AUTH_ATTRS) + [
-        "ignore_root_user_error",
         "base_url",
         "register_all_versions",
     ]
@@ -963,7 +943,6 @@ def _create_toolchain_attrs_struct(
         is_default = is_default,
         python_version = python_version if python_version else tag.python_version,
         configure_coverage_tool = getattr(tag, "configure_coverage_tool", False),
-        ignore_root_user_error = getattr(tag, "ignore_root_user_error", True),
     )
 
 _defaults = tag_class(
@@ -1075,16 +1054,9 @@ Then the python interpreter will be available as `my_python_name`.
         "ignore_root_user_error": attr.bool(
             default = True,
             doc = """\
-The Python runtime installation is made read only. This improves the ability for
-Bazel to cache it by preventing the interpreter from creating `.pyc` files for
-the standard library dynamically at runtime as they are loaded (this often leads
-to spurious cache misses or build failures).
-
-However, if the user is running Bazel as root, this read-onlyness is not
-respected. Bazel will print a warning message when it detects that the runtime
-installation is writable despite being made read only (i.e. it's running with
-root access) while this attribute is set `False`, however this messaging can be ignored by setting
-this to `False`.
+:::{versionchanged} VERSION_NEXT_FEATURE
+Noop, will be removed in the next major release.
+:::
 """,
             mandatory = False,
         ),
diff --git a/tests/python/python_tests.bzl b/tests/python/python_tests.bzl
index f2e87274f8..781d55d833 100644
--- a/tests/python/python_tests.bzl
+++ b/tests/python/python_tests.bzl
@@ -75,7 +75,6 @@ def _override(
         auth_patterns = {},
         available_python_versions = [],
         base_url = "",
-        ignore_root_user_error = True,
         minor_mapping = {},
         netrc = "",
         register_all_versions = False):
@@ -83,7 +82,6 @@ def _override(
         auth_patterns = auth_patterns,
         available_python_versions = available_python_versions,
         base_url = base_url,
-        ignore_root_user_error = ignore_root_user_error,
         minor_mapping = minor_mapping,
         netrc = netrc,
         register_all_versions = register_all_versions,
@@ -164,11 +162,9 @@ def _test_default_from_rules_python_when_rules_python_is_root(env):
     env.expect.that_collection(py.config.kwargs).has_size(0)
     env.expect.that_collection(py.config.default.keys()).contains_exactly([
         "base_url",
-        "ignore_root_user_error",
         "tool_versions",
         "platforms",
     ])
-    env.expect.that_bool(py.config.default["ignore_root_user_error"]).equals(True)
     env.expect.that_str(py.default_python_version).equals("3.11")
 
     want_toolchain = struct(
@@ -220,76 +216,6 @@ def _test_default_with_patch_version(env):
 
 _tests.append(_test_default_with_patch_version)
 
-def _test_default_non_rules_python_ignore_root_user_error(env):
-    py = parse_modules(
-        module_ctx = _mock_mctx(
-            _mod(
-                name = "my_module",
-                toolchain = [_toolchain("3.12", ignore_root_user_error = False)],
-                is_root = True,
-            ),
-            _rules_python_module(),
-        ),
-        logger = repo_utils.logger(verbosity_level = 0, name = "python"),
-    )
-
-    env.expect.that_bool(py.config.default["ignore_root_user_error"]).equals(False)
-    env.expect.that_str(py.default_python_version).equals("3.12")
-
-    my_module_toolchain = struct(
-        name = "python_3_12",
-        python_version = "3.12",
-        register_coverage_tool = False,
-    )
-    rules_python_toolchain = struct(
-        name = "python_3_11",
-        python_version = "3.11",
-        register_coverage_tool = False,
-    )
-    env.expect.that_collection(py.toolchains).contains_exactly([
-        rules_python_toolchain,
-        my_module_toolchain,
-    ]).in_order()
-
-_tests.append(_test_default_non_rules_python_ignore_root_user_error)
-
-def _test_default_non_rules_python_ignore_root_user_error_non_root_module(env):
-    """Verify a non-root intermediate module has its ignore_root_user_error setting ignored."""
-    py = parse_modules(
-        module_ctx = _mock_mctx(
-            _mod(name = "my_module", is_root = True, toolchain = [_toolchain("3.13")]),
-            _mod(name = "some_module", toolchain = [_toolchain("3.12", ignore_root_user_error = False)]),
-            _rules_python_module(),
-        ),
-        logger = repo_utils.logger(verbosity_level = 0, name = "python"),
-    )
-
-    env.expect.that_str(py.default_python_version).equals("3.13")
-    env.expect.that_bool(py.config.default["ignore_root_user_error"]).equals(True)
-
-    my_module_toolchain = struct(
-        name = "python_3_13",
-        python_version = "3.13",
-        register_coverage_tool = False,
-    )
-    some_module_toolchain = struct(
-        name = "python_3_12",
-        python_version = "3.12",
-        register_coverage_tool = False,
-    )
-    rules_python_toolchain = struct(
-        name = "python_3_11",
-        python_version = "3.11",
-        register_coverage_tool = False,
-    )
-    env.expect.that_collection(py.toolchains).contains_exactly([
-        some_module_toolchain,
-        rules_python_toolchain,
-        my_module_toolchain,  # this was the only toolchain, default to that
-    ]).in_order()
-
-_tests.append(_test_default_non_rules_python_ignore_root_user_error_non_root_module)
-
 def _test_toolchain_ordering(env):
     py = parse_modules(
         module_ctx = _mock_mctx(
@@ -510,8 +436,8 @@ def _test_first_occurance_of_the_toolchain_wins(env):
 
     env.expect.that_dict(py.debug_info).contains_exactly({
         "toolchains_registered": [
-            {"ignore_root_user_error": True, "module": {"is_root": True, "name": "my_module"}, "name": "python_3_12"},
-            {"ignore_root_user_error": True, "module": {"is_root": False, "name": "rules_python"}, "name": "python_3_11"},
+            {"module": {"is_root": True, "name": "my_module"}, "name": "python_3_12"},
+            {"module": {"is_root": False, "name": "rules_python"}, "name": "python_3_11"},
         ],
     })
 
@@ -538,7 +464,6 @@ def _test_auth_overrides(env):
 
     env.expect.that_dict(py.config.default).contains_at_least({
         "auth_patterns": {"foo": "bar"},
-        "ignore_root_user_error": True,
         "netrc": "/my/netrc",
     })
     env.expect.that_str(py.default_python_version).equals("3.12")

From a295977f5090c323b2d87a8acbd3d03480f6c7a2 Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 09:00:43 +0900
Subject: [PATCH 04/14] remove ignore_root integration tests

---
 .../ignore_root_user_error/.bazelrc           |  7 ----
 .../ignore_root_user_error/.gitignore         |  1 -
 .../ignore_root_user_error/BUILD.bazel        | 32 ---------------
 .../ignore_root_user_error/MODULE.bazel       | 20 ----------
 .../ignore_root_user_error/README.md          |  2 -
 .../ignore_root_user_error/WORKSPACE          | 14 -------
 .../ignore_root_user_error/bzlmod_test.py     | 40 -------------------
 .../ignore_root_user_error/foo_test.py        | 13 ------
 .../submodule/BUILD.bazel                     |  0
 .../submodule/MODULE.bazel                    |  9 -----
 .../submodule/WORKSPACE                       |  0
 11 files changed, 138 deletions(-)
 delete mode 100644 tests/integration/ignore_root_user_error/.bazelrc
 delete mode 100644 tests/integration/ignore_root_user_error/.gitignore
 delete mode 100644 tests/integration/ignore_root_user_error/BUILD.bazel
 delete mode 100644 tests/integration/ignore_root_user_error/MODULE.bazel
 delete mode 100644 tests/integration/ignore_root_user_error/README.md
 delete mode 100644 tests/integration/ignore_root_user_error/WORKSPACE
 delete mode 100644 tests/integration/ignore_root_user_error/bzlmod_test.py
 delete mode 100644 tests/integration/ignore_root_user_error/foo_test.py
 delete mode 100644 tests/integration/ignore_root_user_error/submodule/BUILD.bazel
 delete mode 100644 tests/integration/ignore_root_user_error/submodule/MODULE.bazel
 delete mode 100644 tests/integration/ignore_root_user_error/submodule/WORKSPACE

diff --git a/tests/integration/ignore_root_user_error/.bazelrc b/tests/integration/ignore_root_user_error/.bazelrc
deleted file mode 100644
index bb7b5742cd..0000000000
--- a/tests/integration/ignore_root_user_error/.bazelrc
+++ /dev/null
@@ -1,7 +0,0 @@
-common --action_env=RULES_PYTHON_BZLMOD_DEBUG=1
-common --lockfile_mode=off
-test --test_output=errors
-
-# Windows requires these for multi-python support:
-build --enable_runfiles
-common:bazel7.x --incompatible_python_disallow_native_rules
diff --git a/tests/integration/ignore_root_user_error/.gitignore b/tests/integration/ignore_root_user_error/.gitignore
deleted file mode 100644
index ac51a054d2..0000000000
--- a/tests/integration/ignore_root_user_error/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-bazel-*
diff --git a/tests/integration/ignore_root_user_error/BUILD.bazel b/tests/integration/ignore_root_user_error/BUILD.bazel
deleted file mode 100644
index 6e3b7b9d24..0000000000
--- a/tests/integration/ignore_root_user_error/BUILD.bazel
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 2024 The Bazel Authors. All rights reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-load("@rules_python//python:py_test.bzl", "py_test")
-load("@rules_python//python/private:bzlmod_enabled.bzl", "BZLMOD_ENABLED")  # buildifier: disable=bzl-visibility
-
-py_test(
-    name = "foo_test",
-    srcs = ["foo_test.py"],
-    visibility = ["//visibility:public"],
-)
-
-py_test(
-    name = "bzlmod_test",
-    srcs = ["bzlmod_test.py"],
-    data = [
-        "@rules_python//python/runfiles",
-        "@rules_python_bzlmod_debug//:debug_info.json",
-    ],
-    target_compatible_with = [] if BZLMOD_ENABLED else ["@platforms//:incompatible"],
-)
diff --git a/tests/integration/ignore_root_user_error/MODULE.bazel b/tests/integration/ignore_root_user_error/MODULE.bazel
deleted file mode 100644
index 15c37c4388..0000000000
--- a/tests/integration/ignore_root_user_error/MODULE.bazel
+++ /dev/null
@@ -1,20 +0,0 @@
-module(name = "ignore_root_user_error")
-
-bazel_dep(name = "rules_python", version = "0.0.0")
-local_path_override(
-    module_name = "rules_python",
-    path = "../../..",
-)
-
-bazel_dep(name = "submodule")
-local_path_override(
-    module_name = "submodule",
-    path = "submodule",
-)
-
-python = use_extension("@rules_python//python/extensions:python.bzl", "python")
-python.toolchain(
-    ignore_root_user_error = True,
-    python_version = "3.11",
-)
-use_repo(python, "rules_python_bzlmod_debug")
diff --git a/tests/integration/ignore_root_user_error/README.md b/tests/integration/ignore_root_user_error/README.md
deleted file mode 100644
index 47da5eb9ad..0000000000
--- a/tests/integration/ignore_root_user_error/README.md
+++ /dev/null
@@ -1,2 +0,0 @@
-# ignore_root_user_errors
-There are cases when we have to run Python targets with root, e.g., in Docker containers, requiring setting `ignore_root_user_error = True` when registering Python toolchain. This test makes sure that rules_python works in this case.
\ No newline at end of file
diff --git a/tests/integration/ignore_root_user_error/WORKSPACE b/tests/integration/ignore_root_user_error/WORKSPACE
deleted file mode 100644
index 7ac0a609eb..0000000000
--- a/tests/integration/ignore_root_user_error/WORKSPACE
+++ /dev/null
@@ -1,14 +0,0 @@
-local_repository(
-    name = "rules_python",
-    path = "../../..",
-)
-
-load("@rules_python//python:repositories.bzl", "py_repositories", "python_register_toolchains")
-
-py_repositories()
-
-python_register_toolchains(
-    name = "python39",
-    ignore_root_user_error = True,
-    python_version = "3.9",
-)
diff --git a/tests/integration/ignore_root_user_error/bzlmod_test.py b/tests/integration/ignore_root_user_error/bzlmod_test.py
deleted file mode 100644
index a1d6dc0630..0000000000
--- a/tests/integration/ignore_root_user_error/bzlmod_test.py
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 2024 The Bazel Authors. All rights reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import json
-import pathlib
-import unittest
-
-from python.runfiles import runfiles
-
-
-class BzlmodTest(unittest.TestCase):
-    def test_ignore_root_user_error_true_for_all_toolchains(self):
-        rf = runfiles.Create()
-        debug_path = pathlib.Path(
-            rf.Rlocation("rules_python_bzlmod_debug/debug_info.json")
-        )
-        debug_info = json.loads(debug_path.read_bytes())
-        actual = debug_info["toolchains_registered"]
-        # Because the root module set ignore_root_user_error=True, that should
-        # be the default for all other toolchains.
-        for entry in actual:
-            self.assertTrue(
-                entry["ignore_root_user_error"],
-                msg=f"Expected ignore_root_user_error=True, but got: {entry}",
-            )
-
-
-if __name__ == "__main__":
-    unittest.main()
diff --git a/tests/integration/ignore_root_user_error/foo_test.py b/tests/integration/ignore_root_user_error/foo_test.py
deleted file mode 100644
index 724cdcb69a..0000000000
--- a/tests/integration/ignore_root_user_error/foo_test.py
+++ /dev/null
@@ -1,13 +0,0 @@
-# Copyright 2019 The Bazel Authors. All rights reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
diff --git a/tests/integration/ignore_root_user_error/submodule/BUILD.bazel b/tests/integration/ignore_root_user_error/submodule/BUILD.bazel
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/tests/integration/ignore_root_user_error/submodule/MODULE.bazel b/tests/integration/ignore_root_user_error/submodule/MODULE.bazel
deleted file mode 100644
index f12870963c..0000000000
--- a/tests/integration/ignore_root_user_error/submodule/MODULE.bazel
+++ /dev/null
@@ -1,9 +0,0 @@
-module(name = "submodule")
-
-bazel_dep(name = "rules_python", version = "0.0.0")
-
-python = use_extension("@rules_python//python/extensions:python.bzl", "python")
-python.toolchain(
-    ignore_root_user_error = False,
-    python_version = "3.10",
-)
diff --git a/tests/integration/ignore_root_user_error/submodule/WORKSPACE b/tests/integration/ignore_root_user_error/submodule/WORKSPACE
deleted file mode 100644
index e69de29bb2..0000000000

From 851a60f83cf9adf7ef6ef571d5fb2cebd17a793d Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 09:05:36 +0900
Subject: [PATCH 05/14] cleanup and changelog

---
 .bazelrc                      |  8 ++++----
 CHANGELOG.md                  |  5 +++++
 tests/integration/BUILD.bazel | 16 ----------------
 3 files changed, 9 insertions(+), 20 deletions(-)

diff --git a/.bazelrc b/.bazelrc
index b5c9c7c1e2..b88b40f334 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -4,13 +4,13 @@
 # (Note, we cannot use `common --deleted_packages` because the bazel version command doesn't support it)
 # To update these lines, execute
 # `bazel run @rules_bazel_integration_test//tools:update_deleted_packages`
-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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,rules_python-repro,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/ignore_root_user_error,tests/integration/ignore_root_user_error/submodule,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
-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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,rules_python-repro,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/ignore_root_user_error,tests/integration/ignore_root_user_error/submodule,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
+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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
+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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
 
 test --test_output=errors
 
-common --deleted_packages=gazelle/examples/bzlmod_build_file_generation
-common --deleted_packages=gazelle/examples/bzlmod_build_file_generation/runfiles
+common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
+common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
 
 # Do NOT implicitly create empty __init__.py files in the runfiles tree.
 # By default, these are created in every directory containing Python source code
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d7403b4f1a..e1e1d2f654 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -55,6 +55,11 @@ END_UNRELEASED_TEMPLATE
 
 {#v0-0-0-removed}
 ### Removed
+* (toolchain) `ignore_root_user_error` has now been flipped to be always enabled and
+  the `chmod` of the python toolchain directories have been removed. From now on `rules_python`
+  always adds the `pyc` files to the glob excludes and in order to avoid any problems when using
+  the toolchains in the repository phase, ensure that you pass `-B` to the python interpreter.
+  ([#2016](https://github.com/bazel-contrib/rules_python/issues/2016))
 * (toolchain) Remove all of the python 3.9 toolchain versions except for the `3.9.25`.
   This version has reached EOL and will no longer receive any security fixes, please update to
   `3.10` or above.
diff --git a/tests/integration/BUILD.bazel b/tests/integration/BUILD.bazel
index 0e47faf91a..673312903d 100644
--- a/tests/integration/BUILD.bazel
+++ b/tests/integration/BUILD.bazel
@@ -75,22 +75,6 @@ rules_python_integration_test(
     workspace_path = "compile_pip_requirements",
 )
 
-rules_python_integration_test(
-    name = "ignore_root_user_error_test",
-    env = {
-        "RULES_PYTHON_BZLMOD_DEBUG": "1",
-    },
-)
-
-rules_python_integration_test(
-    name = "ignore_root_user_error_workspace_test",
-    bzlmod = False,
-    env = {
-        "RULES_PYTHON_BZLMOD_DEBUG": "1",
-    },
-    workspace_path = "ignore_root_user_error",
-)
-
 rules_python_integration_test(
     name = "local_toolchains_test",
     env = {

From 4decbc69d2f3592bf3ffb15cf6cd725ed0a28e14 Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 09:10:07 +0900
Subject: [PATCH 06/14] remove bazelci config

---
 .bazelci/presubmit.yml | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/.bazelci/presubmit.yml b/.bazelci/presubmit.yml
index 1cb3a01365..41f511886b 100644
--- a/.bazelci/presubmit.yml
+++ b/.bazelci/presubmit.yml
@@ -611,19 +611,6 @@ tasks:
     - "git diff --exit-code"
 
 
-  integration_test_ignore_root_user_error_macos_workspace:
-    <<: *reusable_build_test_all
-    <<: *common_workspace_flags
-    name: "ignore_root_user_error: macOS, workspace"
-    working_directory: tests/integration/ignore_root_user_error
-    platform: macos
-  integration_test_ignore_root_user_error_windows_workspace:
-    <<: *reusable_build_test_all
-    <<: *common_workspace_flags
-    name: "ignore_root_user_error: Windows, workspace"
-    working_directory: tests/integration/ignore_root_user_error
-    platform: windows
-
   integration_compile_pip_requirements_test_from_external_repo_ubuntu_min_workspace:
     <<: *minimum_supported_version
     <<: *common_workspace_flags_min_bazel

From 34298becdcb98b56a387facecb2f22ddb5ba734b Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 14:46:57 +0900
Subject: [PATCH 07/14] new run

---
 .bazelrc                | 6 +-----
 .pre-commit-config.yaml | 2 +-
 MODULE.bazel            | 2 +-
 3 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/.bazelrc b/.bazelrc
index b88b40f334..ce4645d34e 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -4,14 +4,10 @@
 # (Note, we cannot use `common --deleted_packages` because the bazel version command doesn't support it)
 # To update these lines, execute
 # `bazel run @rules_bazel_integration_test//tools:update_deleted_packages`
-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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
-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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
+common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/python/private,gazelle/pythonconfig,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
 
 test --test_output=errors
 
-common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
-common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/pythonconfig,gazelle/python/private,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
-
 # Do NOT implicitly create empty __init__.py files in the runfiles tree.
 # By default, these are created in every directory containing Python source code
 # or shared libraries, and every parent directory of those directories,
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 91e449f950..14953d0a89 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -48,6 +48,6 @@ repos:
         language: system
         # 7.x is necessary until https://github.com/bazel-contrib/rules_bazel_integration_test/pull/414
         # is merged and released
-        entry: env USE_BAZEL_VERSION=7.x bazel run @rules_bazel_integration_test//tools:update_deleted_packages
+        entry: bazel run @rules_bazel_integration_test//tools:update_deleted_packages --exclude-dir gazelle
         files: ^((examples|tests)/.*/(MODULE.bazel|WORKSPACE|WORKSPACE.bzlmod|BUILD.bazel)|.bazelrc)$
         pass_filenames: false
diff --git a/MODULE.bazel b/MODULE.bazel
index 6e9b725c53..0f80b3202e 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -215,7 +215,7 @@ use_repo(pip, "rules_python_publish_deps")
 bazel_dep(name = "stardoc", version = "0.7.2", repo_name = "io_bazel_stardoc")
 
 # ===== DEV ONLY DEPS AND SETUP BELOW HERE =====
-bazel_dep(name = "rules_bazel_integration_test", version = "0.27.0", dev_dependency = True)
+bazel_dep(name = "rules_bazel_integration_test", version = "0.34.0", dev_dependency = True)
 bazel_dep(name = "rules_testing", version = "0.6.0", dev_dependency = True)
 bazel_dep(name = "rules_shell", version = "0.3.0", dev_dependency = True)
 bazel_dep(name = "rules_multirun", version = "0.9.0", dev_dependency = True)

From 510c28333a6d2eceb433994ee2ac0b7d978e8b8b Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 14:48:01 +0900
Subject: [PATCH 08/14] fix .bazelignore

---
 .bazelignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.bazelignore b/.bazelignore
index dd58b79e3c..2f50cc2c52 100644
--- a/.bazelignore
+++ b/.bazelignore
@@ -31,6 +31,5 @@ gazelle/examples/bzlmod_build_file_generation/bazel-bzlmod_build_file_generation
 gazelle/examples/bzlmod_build_file_generation/bazel-out
 gazelle/examples/bzlmod_build_file_generation/bazel-testlog
 tests/integration/compile_pip_requirements/bazel-compile_pip_requirements
-tests/integration/ignore_root_user_error/bazel-ignore_root_user_error
 tests/integration/local_toolchains/bazel-local_toolchains
 tests/integration/py_cc_toolchain_registered/bazel-py_cc_toolchain_registered

From dfcb8c320d4a6d5e21be80a8cacece0de324d2b1 Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 14:49:40 +0900
Subject: [PATCH 09/14] fix the gazelle docs exclusion

---
 .bazelrc                | 2 +-
 .pre-commit-config.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.bazelrc b/.bazelrc
index ce4645d34e..9f115ec3b0 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -4,7 +4,7 @@
 # (Note, we cannot use `common --deleted_packages` because the bazel version command doesn't support it)
 # To update these lines, execute
 # `bazel run @rules_bazel_integration_test//tools:update_deleted_packages`
-common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/docs,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/python/private,gazelle/pythonconfig,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
+common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/python/private,gazelle/pythonconfig,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
 
 test --test_output=errors
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 14953d0a89..9aa006bda1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -48,6 +48,6 @@ repos:
         language: system
         # 7.x is necessary until https://github.com/bazel-contrib/rules_bazel_integration_test/pull/414
         # is merged and released
-        entry: bazel run @rules_bazel_integration_test//tools:update_deleted_packages --exclude-dir gazelle
+        entry: bazel run @rules_bazel_integration_test//tools:update_deleted_packages --exclude_dir gazelle/docs
         files: ^((examples|tests)/.*/(MODULE.bazel|WORKSPACE|WORKSPACE.bzlmod|BUILD.bazel)|.bazelrc)$
         pass_filenames: false

From a497e697d5412749e268175bf4ad9958b3e9b6b7 Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Fri, 21 Nov 2025 21:52:57 +0900
Subject: [PATCH 10/14] revert to using a previous version of the bazel
 integration test rules and use our shell script to update deleted pkgs

---
 .bazelrc                         | 4 ++--
 .pre-commit-config.yaml          | 2 +-
 MODULE.bazel                     | 2 +-
 tools/update_deleted_packages.sh | 3 ++-
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/.bazelrc b/.bazelrc
index 9f115ec3b0..e93baff4b8 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, execute
-# `bazel run @rules_bazel_integration_test//tools:update_deleted_packages`
-common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,gazelle,gazelle/examples/bzlmod_build_file_generation,gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg,gazelle/examples/bzlmod_build_file_generation/runfiles,gazelle/manifest,gazelle/manifest/generate,gazelle/manifest/hasher,gazelle/manifest/test,gazelle/modules_mapping,gazelle/python,gazelle/python/private,gazelle/pythonconfig,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data,tests/whl_with_build_files/testdata,tests/whl_with_build_files/testdata/somepkg,tests/whl_with_build_files/testdata/somepkg-1.0.dist-info,tests/whl_with_build_files/testdata/somepkg/subpkg
+# `./tools/update_deleted_packages.sh`
+common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,examples/bzlmod/py_proto_library/foo_external,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data
 
 test --test_output=errors
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9aa006bda1..57d31f5f5f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -48,6 +48,6 @@ repos:
         language: system
         # 7.x is necessary until https://github.com/bazel-contrib/rules_bazel_integration_test/pull/414
         # is merged and released
-        entry: bazel run @rules_bazel_integration_test//tools:update_deleted_packages --exclude_dir gazelle/docs
+        entry: ./tools/update_deleted_packages.sh
         files: ^((examples|tests)/.*/(MODULE.bazel|WORKSPACE|WORKSPACE.bzlmod|BUILD.bazel)|.bazelrc)$
         pass_filenames: false
diff --git a/MODULE.bazel b/MODULE.bazel
index 0f80b3202e..6e9b725c53 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -215,7 +215,7 @@ use_repo(pip, "rules_python_publish_deps")
 bazel_dep(name = "stardoc", version = "0.7.2", repo_name = "io_bazel_stardoc")
 
 # ===== DEV ONLY DEPS AND SETUP BELOW HERE =====
-bazel_dep(name = "rules_bazel_integration_test", version = "0.34.0", dev_dependency = True)
+bazel_dep(name = "rules_bazel_integration_test", version = "0.27.0", dev_dependency = True)
 bazel_dep(name = "rules_testing", version = "0.6.0", dev_dependency = True)
 bazel_dep(name = "rules_shell", version = "0.3.0", dev_dependency = True)
 bazel_dep(name = "rules_multirun", version = "0.9.0", dev_dependency = True)
diff --git a/tools/update_deleted_packages.sh b/tools/update_deleted_packages.sh
index 17e33d182a..6333776afd 100755
--- a/tools/update_deleted_packages.sh
+++ b/tools/update_deleted_packages.sh
@@ -23,7 +23,7 @@
 #   2. For each of the directories, get all directories that contains a BUILD.bazel file.
 #   3. Sort and remove duplicates.
 
-set -euxo pipefail
+set -euo pipefail
 
 DIR="$(dirname $0)/.."
 cd $DIR
@@ -35,5 +35,6 @@ sed -i.bak "/^[^#].*--deleted_packages/s#=.*#=$(\
         xargs -n 1 -I{} find {} \( -name BUILD -or -name BUILD.bazel \) |
         xargs -n 1 dirname |
         sort -u |
+        grep -v 'gazelle/docs' |
         paste -sd, -\
 )#" $DIR/.bazelrc && rm .bazelrc.bak

From 8d34217d3e0974fff359fefea25a4949328ef7e9 Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Sat, 22 Nov 2025 14:47:31 +0900
Subject: [PATCH 11/14] split out the deleted packgaes to a separate file

---
 .bazelrc                         |  5 ++--
 .bazelrc.deleted_packages        | 45 ++++++++++++++++++++++++++++++++
 tools/update_deleted_packages.sh | 12 ++++-----
 3 files changed, 53 insertions(+), 9 deletions(-)
 create mode 100644 .bazelrc.deleted_packages

diff --git a/.bazelrc b/.bazelrc
index e93baff4b8..f30f00e306 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -2,9 +2,8 @@
 # Trick bazel into treating BUILD files under examples/* as being regular files
 # 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, execute
-# `./tools/update_deleted_packages.sh`
-common --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/patches,examples/bzlmod/py_proto_library,examples/bzlmod/py_proto_library/example.com/another_proto,examples/bzlmod/py_proto_library/example.com/proto,examples/bzlmod/py_proto_library/foo_external,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_parse,examples/pip_parse_vendored,examples/pip_repository_annotations,examples/py_proto_library,examples/py_proto_library/example.com/another_proto,examples/py_proto_library/example.com/proto,tests/integration/compile_pip_requirements,tests/integration/compile_pip_requirements_test_from_external_repo,tests/integration/custom_commands,tests/integration/local_toolchains,tests/integration/pip_parse,tests/integration/pip_parse/empty,tests/integration/py_cc_toolchain_registered,tests/modules/another_module,tests/modules/other,tests/modules/other/nspkg_delta,tests/modules/other/nspkg_gamma,tests/modules/other/nspkg_single,tests/modules/other/simple_v1,tests/modules/other/simple_v2,tests/modules/other/with_external_data
+# To update the file, execute
+import .bazelrc.deleted_packages
 
 test --test_output=errors
 
diff --git a/.bazelrc.deleted_packages b/.bazelrc.deleted_packages
new file mode 100644
index 0000000000..131c1cb868
--- /dev/null
+++ b/.bazelrc.deleted_packages
@@ -0,0 +1,45 @@
+# Generated via './tools/update_deleted_packages.sh'
+common --deleted_packages=examples/build_file_generation
+common --deleted_packages=examples/build_file_generation/random_number_generator
+common --deleted_packages=examples/bzlmod
+common --deleted_packages=examples/bzlmod/entry_points
+common --deleted_packages=examples/bzlmod/entry_points/tests
+common --deleted_packages=examples/bzlmod/libs/my_lib
+common --deleted_packages=examples/bzlmod/other_module
+common --deleted_packages=examples/bzlmod/other_module/other_module/pkg
+common --deleted_packages=examples/bzlmod/patches
+common --deleted_packages=examples/bzlmod/py_proto_library
+common --deleted_packages=examples/bzlmod/py_proto_library/example.com/another_proto
+common --deleted_packages=examples/bzlmod/py_proto_library/example.com/proto
+common --deleted_packages=examples/bzlmod/py_proto_library/foo_external
+common --deleted_packages=examples/bzlmod/runfiles
+common --deleted_packages=examples/bzlmod/tests
+common --deleted_packages=examples/bzlmod/tests/other_module
+common --deleted_packages=examples/bzlmod/whl_mods
+common --deleted_packages=examples/multi_python_versions/libs/my_lib
+common --deleted_packages=examples/multi_python_versions/requirements
+common --deleted_packages=examples/multi_python_versions/tests
+common --deleted_packages=examples/pip_parse
+common --deleted_packages=examples/pip_parse_vendored
+common --deleted_packages=examples/pip_repository_annotations
+common --deleted_packages=examples/py_proto_library
+common --deleted_packages=examples/py_proto_library/example.com/another_proto
+common --deleted_packages=examples/py_proto_library/example.com/proto
+common --deleted_packages=gazelle/examples/bzlmod_build_file_generation
+common --deleted_packages=gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg
+common --deleted_packages=gazelle/examples/bzlmod_build_file_generation/runfiles
+common --deleted_packages=tests/integration/compile_pip_requirements
+common --deleted_packages=tests/integration/compile_pip_requirements_test_from_external_repo
+common --deleted_packages=tests/integration/custom_commands
+common --deleted_packages=tests/integration/local_toolchains
+common --deleted_packages=tests/integration/pip_parse
+common --deleted_packages=tests/integration/pip_parse/empty
+common --deleted_packages=tests/integration/py_cc_toolchain_registered
+common --deleted_packages=tests/modules/another_module
+common --deleted_packages=tests/modules/other
+common --deleted_packages=tests/modules/other/nspkg_delta
+common --deleted_packages=tests/modules/other/nspkg_gamma
+common --deleted_packages=tests/modules/other/nspkg_single
+common --deleted_packages=tests/modules/other/simple_v1
+common --deleted_packages=tests/modules/other/simple_v2
+common --deleted_packages=tests/modules/other/with_external_data
diff --git a/tools/update_deleted_packages.sh b/tools/update_deleted_packages.sh
index 6333776afd..ab7c4e2f2b 100755
--- a/tools/update_deleted_packages.sh
+++ b/tools/update_deleted_packages.sh
@@ -29,12 +29,12 @@ DIR="$(dirname $0)/.."
 cd $DIR
 
 # The sed -i.bak pattern is compatible between macos and linux
-sed -i.bak "/^[^#].*--deleted_packages/s#=.*#=$(\
-    find examples/*/* tests/*/* \( -name WORKSPACE -or -name MODULE.bazel \) |
+{
+    echo "# Generated via './tools/update_deleted_packages.sh'"
+    find examples/*/* tests/*/* gazelle/examples/*/* \( -name WORKSPACE -or -name MODULE.bazel \) |
         xargs -n 1 dirname |
-        xargs -n 1 -I{} find {} \( -name BUILD -or -name BUILD.bazel \) |
+        xargs -I{} find {} \( -name BUILD -or -name BUILD.bazel \) |
         xargs -n 1 dirname |
         sort -u |
-        grep -v 'gazelle/docs' |
-        paste -sd, -\
-)#" $DIR/.bazelrc && rm .bazelrc.bak
+        sed 's/^/common --deleted_packages=/g' 
+} > "$DIR"/.bazelrc.deleted_packages

From ef19ae8091b42dbcac8a0f649a72dbb12a86181f Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Sat, 22 Nov 2025 15:02:41 +0900
Subject: [PATCH 12/14] fix gazelle package deletion

---
 .bazelrc.deleted_packages        | 9 +++++++++
 tools/update_deleted_packages.sh | 7 ++++---
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/.bazelrc.deleted_packages b/.bazelrc.deleted_packages
index 131c1cb868..d11f96d664 100644
--- a/.bazelrc.deleted_packages
+++ b/.bazelrc.deleted_packages
@@ -25,9 +25,18 @@ common --deleted_packages=examples/pip_repository_annotations
 common --deleted_packages=examples/py_proto_library
 common --deleted_packages=examples/py_proto_library/example.com/another_proto
 common --deleted_packages=examples/py_proto_library/example.com/proto
+common --deleted_packages=gazelle
 common --deleted_packages=gazelle/examples/bzlmod_build_file_generation
 common --deleted_packages=gazelle/examples/bzlmod_build_file_generation/other_module/other_module/pkg
 common --deleted_packages=gazelle/examples/bzlmod_build_file_generation/runfiles
+common --deleted_packages=gazelle/manifest
+common --deleted_packages=gazelle/manifest/generate
+common --deleted_packages=gazelle/manifest/hasher
+common --deleted_packages=gazelle/manifest/test
+common --deleted_packages=gazelle/modules_mapping
+common --deleted_packages=gazelle/python
+common --deleted_packages=gazelle/pythonconfig
+common --deleted_packages=gazelle/python/private
 common --deleted_packages=tests/integration/compile_pip_requirements
 common --deleted_packages=tests/integration/compile_pip_requirements_test_from_external_repo
 common --deleted_packages=tests/integration/custom_commands
diff --git a/tools/update_deleted_packages.sh b/tools/update_deleted_packages.sh
index ab7c4e2f2b..4e5c6d65a9 100755
--- a/tools/update_deleted_packages.sh
+++ b/tools/update_deleted_packages.sh
@@ -23,7 +23,7 @@
 #   2. For each of the directories, get all directories that contains a BUILD.bazel file.
 #   3. Sort and remove duplicates.
 
-set -euo pipefail
+set -euxo pipefail
 
 DIR="$(dirname $0)/.."
 cd $DIR
@@ -31,10 +31,11 @@ cd $DIR
 # The sed -i.bak pattern is compatible between macos and linux
 {
     echo "# Generated via './tools/update_deleted_packages.sh'"
-    find examples/*/* tests/*/* gazelle/examples/*/* \( -name WORKSPACE -or -name MODULE.bazel \) |
+    find examples tests gazelle \( -name WORKSPACE -or -name MODULE.bazel \) |
         xargs -n 1 dirname |
         xargs -I{} find {} \( -name BUILD -or -name BUILD.bazel \) |
         xargs -n 1 dirname |
+        grep -v "gazelle/docs" |
         sort -u |
         sed 's/^/common --deleted_packages=/g' 
-} > "$DIR"/.bazelrc.deleted_packages
+} | tee "$DIR"/.bazelrc.deleted_packages

From f1c91a3fcccd4bdbd2da959f12e956a729734862 Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Sat, 22 Nov 2025 15:02:56 +0900
Subject: [PATCH 13/14] less verbosity

---
 tools/update_deleted_packages.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/update_deleted_packages.sh b/tools/update_deleted_packages.sh
index 4e5c6d65a9..83bed91d16 100755
--- a/tools/update_deleted_packages.sh
+++ b/tools/update_deleted_packages.sh
@@ -23,7 +23,7 @@
 #   2. For each of the directories, get all directories that contains a BUILD.bazel file.
 #   3. Sort and remove duplicates.
 
-set -euxo pipefail
+set -euo pipefail
 
 DIR="$(dirname $0)/.."
 cd $DIR

From 39e064fb855e3f9a7992a55a10c6650c0b0a051d Mon Sep 17 00:00:00 2001
From: Ignas Anikevicius <240938+aignas@users.noreply.github.com>
Date: Sat, 22 Nov 2025 21:00:39 +0900
Subject: [PATCH 14/14] fixup

---
 .bazelrc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.bazelrc b/.bazelrc
index f30f00e306..73035548af 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -3,7 +3,7 @@
 # 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 the file, execute
-import .bazelrc.deleted_packages
+import %workspace%/.bazelrc.deleted_packages
 
 test --test_output=errors