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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

if (abi_index != -1) {
			exported = true;
			String base = "res://android/build/libs";
			String type = export_data->debug ? "debug" : "release";
			String abi = abis[abi_index].abi;
			String filename = p_so.path.get_file();
			String dst_path = base.path_join(type).path_join(abi).path_join(filename);
			Vector<uint8_t> data = FileAccess::get_file_as_bytes(p_so.path);
			print_verbose("Copying .so file from " + p_so.path + " to " + dst_path);
			Error err = store_file_at_path(dst_path, data);
			ERR_FAIL_COND_V_MSG(err, err, "Failed to copy .so file from " + p_so.path + " to " + dst_path);
			export_data->libs.push_back(dst_path);
		}
	}
	ERR_FAIL_COND_V_MSG(!exported, FAILED,
			"Cannot determine architecture for library \"" + p_so.path + "\". One of the supported architectures must be used as a tag:" + join_abis(abis, " ", true));
	return OK;
}
bool EditorExportPlatformAndroid::_has_read_write_storage_permission(const Vector<String> &p_permissions) {
	return p_permissions.find("android.permission.READ_EXTERNAL_STORAGE") != -1 || p_permissions.find("android.permission.WRITE_EXTERNAL_STORAGE") != -1;
}
bool EditorExportPlatformAndroid::_has_manage_external_storage_permission(const Vector<String> &p_permissions) {
	return p_permissions.find("android.permission.MANAGE_EXTERNAL_STORAGE") != -1;
}
bool EditorExportPlatformAndroid::_uses_vulkan() {
	String current_renderer = GLOBAL_GET("rendering/renderer/rendering_method.mobile");
	bool uses_vulkan = (current_renderer == "forward_plus" || current_renderer == "mobile") && GLOBAL_GET("rendering/rendering_device/driver.android") == "vulkan";
	return uses_vulkan;
}
void EditorExportPlatformAndroid::_get_permissions(const Ref<EditorExportPreset> &p_preset, bool p_give_internet, Vector<String> &r_permissions) {