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***Bugsquad note:** This issue has been confirmed several times already. No need to confirm it further.*

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### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Ubuntu 22.04

### Issue description

I followed this tutorial
https://docs.godotengine.org/en/stable/tutorials/export/android_custom_build.html#doc-android-custom-build.

I want to create Android launcher app to do this i added following code to AndroidManifest.xml in Android Studio.
`<category android:name="android.intent.category.HOME" />
<category android:name="android.intent.category.DEFAULT" />`

But when I export APK my modifications are removed from AndroidManifest.xml.


### Steps to reproduce

Followed this tutorial
https://docs.godotengine.org/en/stable/tutorials/export/android_custom_build.html#doc-android-custom-build.

then open android project in Android studio and edit AndroidManifest.xml.

### Minimal reproduction project

N/A

String build_command;
#ifdef WINDOWS_ENABLED
		build_command = "gradlew.bat";
#else
		build_command = "gradlew";
#endif
		String build_path = ProjectSettings::get_singleton()->get_resource_path().path_join("android/build");
		build_command = build_path.path_join(build_command);
		String package_name = get_package_name(p_preset->get("package/unique_name"));
		String version_code = itos(p_preset->get("version/code"));
		String version_name = p_preset->get("version/name");
		String min_sdk_version = p_preset->get("gradle_build/min_sdk");
		if (!min_sdk_version.is_valid_int()) {
			min_sdk_version = itos(VULKAN_MIN_SDK_VERSION);
		}
		String target_sdk_version = p_preset->get("gradle_build/target_sdk");
		if (!target_sdk_version.is_valid_int()) {
			target_sdk_version = itos(DEFAULT_TARGET_SDK_VERSION);
		}
		String enabled_abi_string = join_abis(enabled_abis, "|", false);
		String sign_flag = should_sign ? "true" : "false";
		String zipalign_flag = "true";
		Vector<PluginConfigAndroid> enabled_plugins = get_enabled_plugins(p_preset);
		String local_plugins_binaries = PluginConfigAndroid::get_plugins_binaries(PluginConfigAndroid::BINARY_TYPE_LOCAL, enabled_plugins);
		String remote_plugins_binaries = PluginConfigAndroid::get_plugins_binaries(PluginConfigAndroid::BINARY_TYPE_REMOTE, enabled_plugins);
		String custom_maven_repos = PluginConfigAndroid::get_plugins_custom_maven_repos(enabled_plugins);
		bool clean_build_required = is_clean_build_required(enabled_plugins);
		List<String> cmdline;
		if (clean_build_required) {
			cmdline.push_back("clean");