Consider system packages as installed if the venv includes them

src/poetry/utils/env/base_env.py

@@ -219,8 +219,11 @@ def platlib(self) -> Path:
 
         return self._platlib
 
+    def _get_lib_dirs(self) -> list[Path]:
+        return [self.purelib, self.platlib]
+
     def is_path_relative_to_lib(self, path: Path) -> bool:
-        for lib_path in [self.purelib, self.platlib]:
+        for lib_path in self._get_lib_dirs():
             with contextlib.suppress(ValueError):
                 path.relative_to(lib_path)
                 return True

src/poetry/utils/env/system_env.py

@@ -2,6 +2,7 @@
 
 import os
 import platform
+import site
 import sys
 import sysconfig
 
@@ -87,3 +88,6 @@ def get_pip_version(self) -> Version:
 
     def is_venv(self) -> bool:
         return self._path != self._base
+
+    def _get_lib_dirs(self) -> list[Path]:
+        return super()._get_lib_dirs() + [Path(d) for d in site.getsitepackages()]

src/poetry/utils/env/virtual_env.py

@@ -3,6 +3,7 @@
 import json
 import os
 import re
+import sys
 
 from contextlib import contextmanager
 from copy import deepcopy
@@ -20,6 +21,7 @@
 from poetry.utils.env.script_strings import GET_PYTHON_VERSION
 from poetry.utils.env.script_strings import GET_SYS_PATH
 from poetry.utils.env.script_strings import GET_SYS_TAGS
+from poetry.utils.env.system_env import SystemEnv
 
 
 if TYPE_CHECKING:
@@ -133,3 +135,14 @@ def temp_environ(self) -> Iterator[None]:
 
     def _updated_path(self) -> str:
         return os.pathsep.join([str(self._bin_dir), os.environ.get("PATH", "")])
+
+    def includes_system_site_packages(self) -> bool:
+        pyvenv_cfg = self._path / "pyvenv.cfg"
+        return "include-system-site-packages = true" in pyvenv_cfg.read_text()
+
+    def is_path_relative_to_lib(self, path: Path) -> bool:
+        system_env = SystemEnv(Path(sys.prefix))
+        return (
+            self.includes_system_site_packages()
+            and system_env.is_path_relative_to_lib(path)
+        ) or super().is_path_relative_to_lib(path)

tests/utils/test_env.py

@@ -1,6 +1,8 @@
 from __future__ import annotations
 
+import contextlib
 import os
+import site
 import subprocess
 import sys
 
@@ -18,6 +20,7 @@
 from poetry.repositories.installed_repository import InstalledRepository
 from poetry.toml.file import TOMLFile
 from poetry.utils._compat import WINDOWS
+from poetry.utils._compat import metadata
 from poetry.utils.env import GET_BASE_PREFIX
 from poetry.utils.env import GET_PYTHON_VERSION_ONELINER
 from poetry.utils.env import EnvCommandError
@@ -1462,8 +1465,25 @@ def test_env_system_packages(tmp_path: Path, poetry: Poetry) -> None:
     pyvenv_cfg = venv_path / "pyvenv.cfg"
 
     EnvManager(poetry).build_venv(path=venv_path, flags={"system-site-packages": True})
+    env = VirtualEnv(venv_path)
 
     assert "include-system-site-packages = true" in pyvenv_cfg.read_text()
+    assert env.includes_system_site_packages()
+
+
+def test_env_system_packages_are_relative_to_lib(
+    tmp_path: Path, poetry: Poetry
+) -> None:
+    venv_path = tmp_path / "venv"
+    EnvManager(poetry).build_venv(path=venv_path, flags={"system-site-packages": True})
+    env = VirtualEnv(venv_path)
+    site_dir = Path(site.getsitepackages()[-1])
+    for dist in metadata.distributions():
+        # Emulate is_relative_to, only available in 3.9+
+        with contextlib.suppress(ValueError):
+            dist._path.relative_to(site_dir)  # type: ignore[attr-defined]
+            break
+    assert env.is_path_relative_to_lib(dist._path)  # type: ignore[attr-defined]
 
 
 @pytest.mark.parametrize(