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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

const char **aperms = android_perms;
	while (*aperms) {
		bool enabled = p_preset->get("permissions/" + String(*aperms).to_lower());
		if (enabled) {
			r_permissions.push_back("android.permission." + String(*aperms));
		}
		aperms++;
	}
	PackedStringArray user_perms = p_preset->get("permissions/custom_permissions");
	for (int i = 0; i < user_perms.size(); i++) {
		String user_perm = user_perms[i].strip_edges();
		if (!user_perm.is_empty()) {
			r_permissions.push_back(user_perm);
		}
	}
	if (p_give_internet) {
		if (r_permissions.find("android.permission.INTERNET") == -1) {
			r_permissions.push_back("android.permission.INTERNET");
		}
	}
	int xr_mode_index = p_preset->get("xr_features/xr_mode");
	if (xr_mode_index == XR_MODE_OPENXR) {
		int hand_tracking_index = p_preset->get("xr_features/hand_tracking"); 
		if (hand_tracking_index > XR_HAND_TRACKING_NONE) {
			if (r_permissions.find("com.oculus.permission.HAND_TRACKING") == -1) {
				r_permissions.push_back("com.oculus.permission.HAND_TRACKING");