I'm a PhoneGap developer using Build, and disagree with this merge. PhoneGap has split off one part of its product, the engine, and the two will diverge more as time goes on. PhoneGap Build is probably going to dominate phonegap questions in the near future.
Also, it's very likely someone else will come along and use the Cordova engine to do something similar to PhoneGap, and will spin off their own distro. The article a commenter mentioned, PhoneGap, Cordova, and what’s in a name?, mentioned the WebKit analogy and I think that's an appropriate way to look at it. A question might use chrome, safari, and/or webkit (or any combination of the three), but they are still separate tags.
They are different things even if developers using PhoneGap may not know where one ends and the other begins. (I know I often don't!) This is compounded by the fact that lots of code that used to be PhoneGap is now Cordova.
The blurring is not entirely unlike someone not understanding if a problem they are facing is in (e.g.) Safari or in WebKit. (As far as I know, this analogy was first popularized by Brian LeRoux.)
The fact that they are different things may be easier to see by their different code bases:
PhoneGap depends on Cordova but Cordova can be used without PhoneGap. You can see this by looking in the
In theory, other projects may arise (or perhaps already have--I don't know much about Icenium etc.) that use Cordova as the underlying engine. Therefore, having separate tags is probably useful.