Hello again,
Now I see, it is the java no capable of stopping a thread problem. This would need an external monitor of threads (maybe some wrapping of jconsole :-))  
For now maybe is better of having the editor's completion server on a thread. What do you think? Could you point me to the class implementing it?
Also what I would like to do is to have control over the spawned jython process, like the executable and the vm arguments. Do you think is it possible to construct the java command from inside pydev? I want to run a custom configured jython process.

Regards
Kostas

PS. The interpreters should have an internal mechanism of cancelling a halted or deadlocked command when in interactive mode ( like on Flash Actionscript or Matlab I think). 

>It's possible to halt it (and really simple):
>
>E.g.: if the user goes on and writes:
>
>while True:
>print 'something'
>
>and you import that module while it has that logic, you won't regain
>control over it (and that Thread would be lost and would keep one of
>your processors busy until eclipse exits -- as a separate process it
>can still be killed without any further problems in the Eclipse VM).
>
>The class where the logic for handling communication with the shell is
>the AbstractShell.java (so, that's the place you'd change).