I just tried JWowUpdater..and it seems works fine for me but.....
yeap, i always used wau and use with external to have one clean interface folder :)
it's ok with jwow updater but for example Pitbull.
in WAU, there is one option (not unpack addons package i think) to juste have one pitbull folder and all other inside this folder (ie pitbull pvp, pitbull combat etc...) and with jwowupdater i have many folder for just one addon like pitbull, quartz or prat (addons package)
one way to have just one folder for one addon package?
anyways, very nice updater and very easy to use..
The Config page has a description / explanation for each option available.
You can disable split addon package to stop JWU from splitting packages.