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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, "keystore/release_password", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_SECRET), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::INT, "version/code", PROPERTY_HINT_RANGE, "1,4096,1,or_greater"), 1));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "version/name"), "1.0"));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "package/unique_name", PROPERTY_HINT_PLACEHOLDER_TEXT, "ext.domain.name"), "org.godotengine.$genname", false, true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "package/name", PROPERTY_HINT_PLACEHOLDER_TEXT, "Game Name [default if blank]"), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "package/signed"), true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::INT, "package/app_category", PROPERTY_HINT_ENUM, "Accessibility,Audio,Game,Image,Maps,News,Productivity,Social,Video"), APP_CATEGORY_GAME));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "package/retain_data_on_uninstall"), false));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "package/exclude_from_recents"), false));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, launcher_icon_option, PROPERTY_HINT_FILE, "*.png"), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, launcher_adaptive_icon_foreground_option, PROPERTY_HINT_FILE, "*.png"), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, launcher_adaptive_icon_background_option, PROPERTY_HINT_FILE, "*.png"), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "graphics/opengl_debug"), false));
	r_options->push_back(ExportOption(PropertyInfo(Variant::INT, "xr_features/xr_mode", PROPERTY_HINT_ENUM, "Regular,OpenXR"), XR_MODE_REGULAR, false, true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::INT, "xr_features/hand_tracking", PROPERTY_HINT_ENUM, "None,Optional,Required"), XR_HAND_TRACKING_NONE, false, true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::INT, "xr_features/hand_tracking_frequency", PROPERTY_HINT_ENUM, "Low,High"), XR_HAND_TRACKING_FREQUENCY_LOW));
	r_options->push_back(ExportOption(PropertyInfo(Variant::INT, "xr_features/passthrough", PROPERTY_HINT_ENUM, "None,Optional,Required"), XR_PASSTHROUGH_NONE, false, true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "screen/immersive_mode"), true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "screen/support_small"), true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "screen/support_normal"), true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "screen/support_large"), true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "screen/support_xlarge"), true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "user_data_backup/allow"), false));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "command_line/extra_args"), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::BOOL, "apk_expansion/enable"), false, false, true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "apk_expansion/SALT"), ""));
	r_options->push_back(ExportOption(PropertyInfo(Variant::STRING, "apk_expansion/public_key", PROPERTY_HINT_MULTILINE_TEXT), "", false, true));
	r_options->push_back(ExportOption(PropertyInfo(Variant::PACKED_STRING_ARRAY, "permissions/custom_permissions"), PackedStringArray()));
	const char **perms = android_perms;
	while (*perms) {