As Jeff and others already posted, JPA on AppEngine just don't work as you 
expect (from the JPA point of view), and others just work as you don't. I'm 
the team leader of a running GAE/J application and we are, like Jeff says, *
screaming* because of my decision to use JPA. We were about to consider 
using JDO, due to it's non-RDBMS options, but looks like the best choice is 
another tool like Objectify or Twig-persist.

We are now trying out those tools to do come poof-of-concept in our 
codebase. A good choice is to encapsulate your datastore using a DAO or 
Repository pattern (or even both!), since they may help you to change your 
mind in the future. We did it and now we can try out some other tools on top 
of the Low Level API. In regards of the Objectify library, +1 for the 
helpers on schema migration. This is very (very!) hard to acomplish on a 
real-world web app when using JDO/JPA, and is a very usefull feature.

In any case, now the RemoteApi is also available in Java (as per 1.4.4) and 
this is very useful to do some data export, local fixture loading and 
others. So, it is nice to at least know how the datastore works, it may help 
you in the future.

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