fix(config): clear markers overridden by unconditional set_env values (tox-dev#4077)

Clear a previous marker when a later unconditional `set_env` assignment
or environment-file value overrides the variable. Otherwise, a false
marker still suppresses the replacement value.

Adds regression coverage for inline INI assignments and environment-file
overrides in INI and TOML.

Fixes tox-dev#4076.

Validation: Python 3.14 full suite (8,153 passed, 12 skipped), Python
3.10 config suite (6,749 passed, 2 skipped), ty/mypy/pyrefly,
pre-commit, package checks, and strict Sphinx build with visual
changelog inspection. The full suite used a process-local PATH excluding
the host's legacy Python 2 installation to avoid interpreter-discovery
warnings in JSON output. Checks ran directly with the project's
dependency groups to reuse local environments.

- [x] ran the linter to address style issues (`pre-commit run
--all-files --show-diff-on-failure`)
- [x] wrote descriptive pull request text
- [x] ensured there are test(s) validating the fix
- [x] added news fragment in `docs/changelog` folder
- [x] updated/extended the documentation (changelog)

Author: jakezwang

docs/changelog/4076.bugfix.rst

@@ -0,0 +1 @@
+Clear obsolete markers when unconditional ``set_env`` values override conditional entries, including environment files.

src/tox/config/set_env.py

@@ -72,6 +72,8 @@ def __init__(  # ruff:ignore[complex-structure, too-many-branches]
                         keys_after_file.add(key)
                         if marker:
                             self._markers[key] = Marker(marker)
+                        else:
+                            self._markers.pop(key, None)
 
     def _parse_dict(self, raw: dict[str, str | SetEnvEntry]) -> None:
         keys_after_file: set[str] = set()
@@ -109,6 +111,7 @@ def use_replacer(self, value: Replacer, args: ConfigLoadArgs) -> None:
             for key, val in self._stream_env_file(filename, args):
                 if key not in keys_after:
                     self._raw[key] = val
+                    self._markers.pop(key, None)
 
     def _stream_env_file(self, filename: str, args: ConfigLoadArgs) -> Iterator[tuple[str, str]]:
         # Our rules in the documentation, some upstream environment file rules (we follow mostly the docker one):

tests/config/test_set_env.py

@@ -513,6 +513,33 @@ def test_set_env_escaped_semicolon() -> None:
     assert set_env.load("FOO") == "a;b"
 
 
+@pytest.mark.parametrize(
+    ("of_type", "config"),
+    [
+        pytest.param(
+            "ini",
+            "[testenv]\npackage=skip\nset_env=FOO=conditional; sys_platform == 'nonexistent'\n FOO=unconditional",
+            id="inline",
+        ),
+        pytest.param(
+            "ini",
+            "[testenv]\npackage=skip\nset_env=FOO=conditional; sys_platform == 'nonexistent'\n file|.env",
+            id="ini-file",
+        ),
+        pytest.param(
+            "toml",
+            '[env_run_base]\npackage="skip"\n'
+            'set_env = {FOO={value="conditional", marker="sys_platform == \'nonexistent\'"}, file=".env"}',
+            id="toml-file",
+        ),
+    ],
+)
+def test_set_env_unconditional_override(eval_set_env: EvalSetEnv, of_type: ConfigFileFormat, config: str) -> None:
+    set_env = eval_set_env(config, of_type=of_type, extra_files={".env": "FOO=unconditional\n"})
+    assert "FOO" in set_env
+    assert set_env.load("FOO") == "unconditional"
+
+
 def test_set_env_marker_mixed(eval_set_env: EvalSetEnv) -> None:
     marker = f"sys_platform == '{sys.platform}'"
     config = (