Sorry for necroing this thread but I solved my Swiftmend "stacking problem" (when you have the "Prosperity" talent as a RestoDruid) in weakauras with possibly some help of this thread. I have set up three Swiftmend buttons in weakauras, each being triggered (in the trigger tab) by charges = 0 or = 1 or = 2. and also using %s on the text line in the display tab, so you can see how many stacks you currently have available.
The button for =2 is playing sound (custom made "Swiftmend" in text to speech) "on show", =0 is playing the same sound but "on hide". This way you will hear this specific sound only when gaining a stack when it is refreshed by the current 25 second cd. It's obviously not rocket science but it took me a minute or so of thinking before figuring out the obvious answer. Also this works best with a progress bar type of button next to these three buttons, to see how far you are from gaining a stack.
Unfortunatly I don't know the solution for this problem when the skill has a possible higher stack than two, but maybe there is a function that I haven't thought about and/or missed.