merge all layersSets

What do you use to select a Tool on screen with the cursor? What do you use to organise and move Layers? etc.

Anyway, please try this: 

// 2020, use it your own risk; 
if (app.documents.length > 0) {
var thedoc = app.activeDocument;
var docName = thedoc.name;
var basename = docName.match(/(.*)\.[^\.]+$/)[1];
var docPath = thedoc.path;	
//
deleteHidden ();
mergeGroups (thedoc, []);
//
psdOpts = new PhotoshopSaveOptions();
psdOpts.embedColorProfile = true;
psdOpts.alphaChannels = false;
psdOpts.layers = true;
psdOpts.spotColors = true;
thedoc.saveAs((new File(docPath+"/"+basename+"_merged"+".psd")),psdOpts,false);
};
// delete hidden layer;
function deleteHidden () {
try {
var id26 = charIDToTypeID( "Dlt " ); 
var desc6 = new ActionDescriptor(); 
var id27 = charIDToTypeID( "null" ); 
var ref6 = new ActionReference(); 
var id28 = charIDToTypeID( "Lyr " ); 
var id29 = charIDToTypeID( "Ordn" ); 
var id30 = stringIDToTypeID( "hidden" ); 
ref6.putEnumerated( id28, id29, id30 ); 
desc6.putReference( id27, ref6 ); 
executeAction( id26, desc6, DialogModes.NO );
}
catch (e) {}
};
// apply layermask;
function applyLayerMask (a) {
try {
app.activeDocument.activeLayer = a;
// =======================================================
var id500 = charIDToTypeID( "Dlt " ); 
var desc96 = new ActionDescriptor(); 
var id501 = charIDToTypeID( "null" ); 
var ref67 = new ActionReference(); 
var id502 = charIDToTypeID( "Chnl" ); 
var id503 = charIDToTypeID( "Chnl" ); 
var id504 = charIDToTypeID( "Msk " ); 
ref67.putEnumerated( id502, id503, id504 ); 
desc96.putReference( id501, ref67 ); 
var id505 = charIDToTypeID( "Aply" ); 
desc96.putBoolean( id505, true ); 
executeAction( id500, desc96, DialogModes.NO );
}
catch (e) {}
};
////// function collect all layers //////
function mergeGroups (theParent, allLayers) {
	if (!allLayers) {var allLayers = new Array} 
	else {};
	for (var m = theParent.layers.length - 1; m >= 0;m--) {
		var theLayer = theParent.layers[m];
// apply the function to layersets;
		if (theLayer.typename == "ArtLayer") {
	//		allLayers.push(theLayer)
			}
		else {
    //		allLayers = (collectLayers(theLayer, allLayers))
            var theB = theLayer.bounds;
            if (theB[0] == theB[2] || theB[1] == theB[3]) {theLayer.remove()}
            else {var theLayer = theLayer.merge()};
            applyLayerMask (theLayer);
// this line includes the layer groups;
			allLayers.push(theLayer);
			}
		};
	return allLayers
	};