deps: update to gazelle 0.40.0 (#2403)

This allows us to drop the patch for removing native.sh_binary

Work towards #2378

MODULE.bazel

@@ -84,17 +84,7 @@ bazel_dep(name = "bazel_ci_rules", version = "1.0.0", dev_dependency = True)
 # We use `WORKSPACE.bzlmod` because it is impossible to have dev-only local overrides.
 bazel_dep(name = "rules_go", version = "0.41.0", dev_dependency = True, repo_name = "io_bazel_rules_go")
 bazel_dep(name = "rules_python_gazelle_plugin", version = "0", dev_dependency = True)
-bazel_dep(name = "gazelle", version = "0.33.0", dev_dependency = True, repo_name = "bazel_gazelle")
-single_version_override(
-    module_name = "gazelle",
-    patch_strip = 1,
-    patches = [
-        # Can be removed once https://github.com/bazel-contrib/bazel-gazelle/issues/1959
-        # is fixed and released.
-        "patches/gazelle_native_sh.patch",
-    ],
-    version = "0.33.0",
-)
+bazel_dep(name = "gazelle", version = "0.40.0", dev_dependency = True, repo_name = "bazel_gazelle")
 
 internal_dev_deps = use_extension(
     "//python/private:internal_dev_deps.bzl",