Move deprecating flags to bzlmod only

Author: restingbull

examples/android/.bazelrc

@@ -2,9 +2,6 @@ common --lockfile_mode=off
 test --test_output=all
 build --config=android_worker
 
-common --incompatible_disable_native_repo_rules=true
-common --incompatible_autoload_externally=
-
 # Worker configuration
 build:android_worker \
   --worker_max_instances=auto \

src/main/kotlin/io/bazel/kotlin/test/BazelIntegrationTestRunner.kt

@@ -168,7 +168,11 @@ object BazelIntegrationTestRunner {
       }
 
       override fun workspaceFlag(isBzlMod: Boolean): Array<String> = if (isBzlMod) {
-        arrayOf("--enable_bzlmod=true")
+        arrayOf(
+          "--enable_bzlmod=true",
+          "--incompatible_disable_native_repo_rules=true",
+          "--incompatible_autoload_externally=",
+        )
       } else if (major >= 7) {
         arrayOf("--enable_workspace=true", "--enable_bzlmod=false")
       } else {