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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 (copy_result != 0) {
			add_message(EXPORT_MESSAGE_ERROR, TTR("Export"), TTR("Unable to copy and rename export file, check gradle project directory for outputs."));
			return ERR_CANT_CREATE;
		}
		print_verbose("Successfully completed Android gradle build.");
		return OK;
	}
	
	print_verbose("Starting legacy build system...");
	if (p_debug) {
		src_apk = p_preset->get("custom_template/debug");
	} else {
		src_apk = p_preset->get("custom_template/release");
	}
	src_apk = src_apk.strip_edges();
	if (src_apk.is_empty()) {
		if (p_debug) {
			src_apk = find_export_template("android_debug.apk");
		} else {
			src_apk = find_export_template("android_release.apk");
		}
		if (src_apk.is_empty()) {
			add_message(EXPORT_MESSAGE_ERROR, TTR("Export"), vformat(TTR("Package not found: \"%s\"."), src_apk));
			return ERR_FILE_NOT_FOUND;
		}
	}
	if (!DirAccess::exists(p_path.get_base_dir())) {
		return ERR_FILE_BAD_PATH;
	}
	Ref<FileAccess> io_fa;