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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

APKExportData ed;
		ed.ep = &ep;
		ed.apk = unaligned_apk;
		err = export_project_files(p_preset, p_debug, ignore_apk_file, &ed, save_apk_so);
	} else {
		if (apk_expansion) {
			err = save_apk_expansion_file(p_preset, p_debug, p_path);
			if (err != OK) {
				add_message(EXPORT_MESSAGE_ERROR, TTR("Export"), TTR("Could not write expansion package file!"));
				return err;
			}
		} else {
			APKExportData ed;
			ed.ep = &ep;
			ed.apk = unaligned_apk;
			err = export_project_files(p_preset, p_debug, save_apk_file, &ed, save_apk_so);
		}
	}
	if (err != OK) {
		unzClose(pkg);
		add_message(EXPORT_MESSAGE_ERROR, TTR("Export"), vformat(TTR("Could not export project files.")));
		CLEANUP_AND_RETURN(ERR_SKIP);
	}
	zip_fileinfo zipfi = get_zip_fileinfo();
	zipOpenNewFileInZip(unaligned_apk,
			"assets/_cl_",
			&zipfi,
			nullptr,
			0,
			nullptr,