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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

r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "custom_template/debug", PROPERTY_HINT_GLOBAL_FILE, "*.apk"), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "custom_template/release", PROPERTY_HINT_GLOBAL_FILE, "*.apk"), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "gradle_build/use_gradle_build"), false, false, true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::INT, "gradle_build/export_format", PROPERTY_HINT_ENUM, "Export APK,Export AAB"), EXPORT_FORMAT_APK, false, true));
	
	
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "gradle_build/min_sdk", PROPERTY_HINT_PLACEHOLDER_TEXT, vformat("%d (default)", VULKAN_MIN_SDK_VERSION)), "", false, true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "gradle_build/target_sdk", PROPERTY_HINT_PLACEHOLDER_TEXT, vformat("%d (default)", DEFAULT_TARGET_SDK_VERSION)), "", false, true));
	Vector<PluginConfigAndroid> plugins_configs = get_plugins();
	for (int i = 0; i < plugins_configs.size(); i++) {
		print_verbose("Found Android plugin " + plugins_configs[i].name);
		r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, vformat("%s/%s", PNAME("plugins"), plugins_configs[i].name)), false));
	}
	plugins_changed.clear();
	
	
	const Vector<ABI> abis = get_abis();
	for (int i = 0; i < abis.size(); ++i) {
		const String abi = abis[i].abi;
		
		
		const bool is_default = abi == "arm64-v8a";
		r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, vformat("%s/%s", PNAME("architectures"), abi)), is_default));
	}
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "keystore/debug", PROPERTY_HINT_GLOBAL_FILE, "*.keystore,*.jks", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_SECRET), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "keystore/debug_user", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_SECRET), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "keystore/debug_password", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_SECRET), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "keystore/release", PROPERTY_HINT_GLOBAL_FILE, "*.keystore,*.jks", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_SECRET), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "keystore/release_user", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_SECRET), ""));