Hi, when deleting the app from the GUI it should also disappear from the rules.xml.
Concerning the popup dialog -- well, me working from a notebook I actually pretty much like it the way it is now - it pops, yes, but it also informs me in what network I am connected right away, which is handy for me. So even though at first we thought this should get changed, currently I sort of lean to keeping it poping. Perhaps a checkbox in the gui, for Desktop PCs to skip the popup migh be a good compromise?