I thought the idea too was that you could build one code base for each environment. I know there are quirks, but why is there a separate phonegap.js file for Android, WebOS, etc.?
The lack of documentation has me confused.
In my experience, there are separate files for each but when using phonegap build if you want to include a universal file for the build there is a way, put
<script src="phonegap.js"></script> in your index.html file and don't include any js files, you actually don't even need the phonegap.js file, when I did this and ran it through phonegap build it attached the appropriate .js file to the appropriate build and I suddenly could use the phonegap API's for all the builds I was testing