Fix work dir propagation

docs/changelog/2933.bugfix.rst

@@ -0,0 +1 @@
+Fix issue where ``work_dir`` was not correctly including ``tox_root`` for test runs

src/tox/config/sets.py

@@ -189,7 +189,9 @@ def register_config(self) -> None:
         )
 
         def work_dir_builder(conf: Config, env_name: str | None) -> Path:  # noqa: U100
-            return (conf.work_dir if conf.work_dir is not None else cast(Path, self["tox_root"])) / ".tox"
+            if conf.work_dir == conf.src_path.parent:
+                return cast(Path, self["tox_root"]) / ".tox"
+            return conf.work_dir
 
         def work_dir_post_process(value: Path) -> Path:
             return self._conf.work_dir if self._conf.options.work_dir else value

tests/config/test_main.py

@@ -93,3 +93,11 @@ def test_relative_config_paths_resolve(tox_project: ToxProjectCreator) -> None:
     result.assert_success()
     expected = f"[testenv:py]\nchange_dir = {project.path}\nenv_dir = {project.path / '.tox' / 'py'}\n"
     assert result.out == expected
+
+
+def test_tox_root_propagates_to_work_dir(tox_project: ToxProjectCreator) -> None:
+    root_dir = "root"
+    project = tox_project({"tox.ini": "[tox]"})
+    result = project.run("c", "--root", root_dir)
+    result.assert_success()
+    assert result.state.conf.core["work_dir"].parent.name == root_dir