> The first Question I have is: what *should* be the contents of “mgnlSystem”?
> If this workspace is used only as temporary storage, should it not be empty 
> of content, except while an activation is in progress?

Yes, indeed, workspace should be empty except for when activation is in 
progress.
 
> 2nd Question:
> I’m not really able to follow the activation code, since I am unsure of the 
> requirements that motivate the use of mgnlSystem etc… It’s all quite 
> complicated! So, what can be the implications of existing content in 
> mgnlSystem on the activation process?

The temporary use of mgnlSystem is necessary in order to be able to rollback 
changes in content in case they can't be pushed to all public nodes.
 
> 3rd Question:
> Can I delete the content of the mgnlSystem workspace in production safely?
> If no, how do I solve this problem in production?
> If yes, can I simply delete the workspace folder for mgnlSystem (since I 
> can’t use the JCR Browser tool in production)?

shutdown, remove or rename /repositories/magnolia/workspaces/mgnlSystem, in DB 
remove all mgnlSystem* tables and indices and start up again (As always, please 
make sure to make a backup before making any modifications to production system 
and preferably test it in other environment first)
 
> Finally, the important question:
> How can I prevent this issue from occurring in the future?
> Might it be a good idea to clear out the mgnlSystem workspace when magnolia 
> starts (since an activation task can’t survive a tomcat reboot anyway)?

Indeed good idea.  Other option would be to use command or groovy script to 
clear it out in system context on demand.
I would still like to know how this error occured in the first place. The only 
way i could think of right now is is server died in middle of activation. Was 
there any such event?

Cheers,
Jan

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