You can use the Datastore Admin tool available to Python apps that came with 
App Engine 1.3.8 to delete data more easily:
http://googleappengine.blogspot.com/2010/10/new-app-engine-sdk-138-includes-new.html
(under "Delete all (or a part) of your application’s data")

As it says in the blog post you can use it for Java apps, too. I created a 
simple Python application version as version number 1, then uploaded the 
actual Java app as version 2 and set that as the default version. Works 
great.

If you're new to Python like I am there's a little how-to for Java-devs 
here:
https://groups.google.com/d/topic/google-appengine-java/aRLhRzADuF4/discussion

Once you've done that, you can use the command line utility to remove all 
unused indexes:
appcfg.py vacuum_indexes app-root/

More options are described here:
http://code.google.com/appengine/docs/python/tools/uploadinganapp.html

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