Basically from what I understand is that if my app wants to use serial communication via the dock connector (pins 12 / 13) the app has to live outside the app sandbox folder. Now I don't want to have to ssh into my phone and copy theAppFolder.app to /Applications/ everytime I click Run in Xcode (that would just be silly).
Now while doing some research I came across this blog post. Down in the comments, someone gives the idea of what I am talking about in this question.
Now is his solution the best way to do what I am thinking of doing, or is there a more elegant solution?
A bit late, but I use Xcode's build command with a post-build script to get my app on my jailbroken iOS device and also start it using a tool from Cydia (it will actually run the app from the /Applications directory). Check out my answer here for more info. The thing still missing is the ability to debug, but I've gotten used to using NSLog and tailing the syslog.