experiments: preserve file permissions across tmpdir execution (#4890)

* tree: use file_mode in upload() for trees that support modes

* experiments: preserve file_mode for files in the workspace

* skip permissions tests on windows

* LocalTree: separate chmod from protect

* fix rebase issue

tests/func/experiments/test_experiments.py

@@ -1,4 +1,6 @@
 import logging
+import os
+import stat
 
 import pytest
 from funcy import first
@@ -19,6 +21,18 @@ def test_new_simple(tmp_dir, scm, dvc, exp_stage, mocker):
     ).read_text() == "foo: 2"
 
 
+@pytest.mark.skipif(os.name == "nt", reason="Not supported for Windows.")
+def test_file_permissions(tmp_dir, scm, dvc, exp_stage, mocker):
+    mode = 0o755
+    os.chmod(tmp_dir / "copy.py", mode)
+    scm.add(["copy.py"])
+    scm.commit("set exec")
+
+    tmp_dir.gen("params.yaml", "foo: 2")
+    dvc.experiments.run(exp_stage.addressing)
+    assert stat.S_IMODE(os.stat(tmp_dir / "copy.py").st_mode) == mode
+
+
 def test_failed_exp(tmp_dir, scm, dvc, exp_stage, mocker, caplog):
     from dvc.stage.exceptions import StageCmdFailedError