Examples no long work after switching to manual bootstrap

I had an app where all of my docular example were working.  I then had to switch to manual bootstrapping and now they no longer work.  At first I got the error where it said the app was already bootstrapped (expected) so then I set the option autoBootstrap to false.  I no longer get that error but now none of my scripts are loading.  Is there something else I need to do as well?
