I am currently making a plugin for phonegap 3. I have a custom framework to copy using the source-file directive. In the plugin.xml I tried:
Good news: it seems that the Cordova folks are working on this as we speak. There is a feature request as well as a commit to GitHub that claims to resolve this issue. The framework tag will support the custom="true" attribute. For example, here's how you could do it for the AWS iOS SDK Runtime framework:
UPDATE: It seems that this change made it into the current stable release of Cordova on 11/29/2013 (two days ago). Just update your Cordova and Plugman binaries and you should be good to go.
$ npm update -g cordova # if using `cordova plugin add xyz`
$ npm update -g plugman # if using `plugman install --platform x --project y --plugin z`