Hi, I am just wondering if it is possible to read the content of Web App published to Esri Portal. I want to know what layers have been grouped in which layer group. I think ArcGISOnlineConnector has to be used, but I can only get the general information (even after exposing all available attributes). The Web Application has multiple layer groups with different layers included. 
Yes, it is, I've done similar things before. However I can't remember the exact specifics...
My experience was with the developer version of WebApp Builder, so it might not be exactly the same if its the standard WebApp Builder.
Essentially, the configuration for the layer list widget is JSON. So all you need to do is have FME read in that JSON file (pull it using an httpcaller). You should be able to find the JSON file by opening up developer tools, checking the network tab and reloading the page (you might also need to click on the widget). Then the hard part is finding the exact call but you should be able to filter your calls using 'layerlist'