Thanks for the contribution Ed - if you could elaborate (a little) on
what you mean by/what happens for you when you "copy the jars into the
project" I'd appreciate that.  I've got options selected to run GAE
from my 'WAR' directory, but I'm not aware of any JARs being copied to
my WEB-INF/lib - indeed when they do occasionally get copied, that
stops the datanucleus enrichment from working.  I've also tried with
the 'export' flag set on the build path configuration, with no change
overall.

Some updates/corrections from me:

* The current problem definitely seems to be runtime/classpath/
classloader related - I'm getting ClassNotFound (CNF) exceptions on
JDO implementation classes (i.e. not the implementations, but the
concrete classes needed at runtime).  I'd expect these to be coming
from the GAE class library set - I can find them in jdo-xxx-eb-xx.jar
(sorry for the hazy jar name, I'm in the day job, not in my dev
environment at the time of writing). Annotation/enrichment works fine.
* I'm using an Eclipse Dynamic Web Project, not a Google Web App
Project as originally stated.  As noted before, between SDK upgrades
this works fine so I know that's not a problem.
* I have altered the library order as per other threads (GAE needs to
be before Web App).
* I have seen the thread about long paths in the classpath (known
issue with 1.3.8) - I have copied my plugin/SDK to a much shorter path
location and regconfigured my project and still reproduced the same
runtime CNF problems so that's not the issue.

Given cumulative problems I've experienced with Google's dev
environment/support, I'm now considering ditching the Google approach
and going to a purer, more open cloud hosting model (poss AWS).
Problems for me include:
* facebook apis redundant, but not flagged as such
* no full map/reduce api (got map, but no reduce)
* SDK/plugin instability (this issue)
* interplay problems with GAE and other tools (Vaadin for myself,
looks like Flex also has issues)
* no entry-level adwords/adsense solution for GWT (ajax) front-ends.

Hardly a strong manifesto.

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