Eclipse build creates correct Manifest only the first time.

The option in Unity 4.0 that creates an Eclipse project is great. This is my current workflow.

1. Work in Unity, create Eclipse build.

2. In Eclipse, import Android project from Existing code.

3. Rename project name (removing ProxyActivity from it).

4. Work some in Java.

5. Work back in Unity, create new Eclipse build, overwriting previous one.

Thankfully, modifications to the Activity classes are not overwritten. The AndroidManifest.xml is correctly created the first time, referencing the 3 Activity classes that were generated, but each successive build the overwrites the first, creates a manifest that directly calls com.unity3d.player.UnityPlayerProxyActivity instead of your game's Activity class, i.e. com.yourpackage.whatever.YourGameProxyActivity. Is this a bug or something I've not got right in the workflow? If you need to back and forth between Unity and Java to test, I don't see any other practical way. So far the only solution I've come up with is to copy the original manifest, and then copy over the bad one after each new eclipse build out of Unity.

*note... skipping step 3 doesn't make a difference.