Does the GCE/Eclipse magic add client IDs automagically?

Or put another way...

I just moved my app from aaa.appspot.com to a new project (and hence new Client ID) called bbb.appspot.com. When I went to add the new Client Id to my GCE API definitions, it was already there!

So, on the one hand, it's magic :-)

On the other hand, is all of this documented anywhere? I have a slight concern about how I would go about overriding this behaviour if ever I want to manually configure the permitted client IDs.

I assume you are talking about the API annotations for GCE like this:

@ApiMethod(
          name = "testAuth",
    clientIds = { WEB_CLIENT_ID,
            APP1_ANDROID_CLIENT_ID, APP1D_ANDROID_CLIENT_ID,
            APP2_ANDROID_CLIENT_ID },
    audiences = { Config.WEB_CLIENT_ID }        
)

These client ID's come from the API console, where they are created based on your app's package and the hash of your app's certificate.

So, you may create a new GAE project for your new app id, and even create a new console project connected to that new GAE project, but your old console project still exists and still has client id's that are specific to your Android project but independent of your GAE project - so they still work.