Longrunning transactions should not be stored in a session... but in a 
reference and fixed at the protocol level (locking etc.., see the ws-* 
standards)

The web application should only concentrate on one task, and what you describe 
is a kind of wizard. Multiple pages committing data to one task. Copying them 
over should not be for you to worry, but the container and api of the engine 
(and it does that for you).  Varibables for tasks are stored separately and 
only when ' committed' (task is finished) they are copied to the processlevel 
again.... so I do not see a problem here.

I think you should look at things from a different perspective. Writing your 
own persistece in addition to jBPM is not strange. We've developed our own 
domain models for different apps with  persistency and use jBPM to control some 
flow. We maintain relations between the flow and our domain model by storing 
the processid and relevant tokeid's in our domainmodel

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