Hi Paul,
I deal with this issue on Cordova, but I think it might be helpful (as long as you don't have too much customization you are manually doing in Xcode).
I add and remove the platforms:
cordova platform add ios
...
close Xcode project
cordova platform rm ios
cordova platform add ios
And have a hook that fires on after_platform_add that adds all the plugins I want.
#!/bin/sh
for fileurl in "
http://github.com/foo/barplugin ...
cordova plugin add $fileurl;
done
I realize this is more of a workaround than an answer to your original question, but thought it might be useful. It looks like you are using phonegap cli in local mode, so this should work--I don't think you have hooks in phonegap build.
--
Dan Moore
Developing with Cordova CLI
https://leanpub.com/developingwithcordovacli