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It may be worth considering the potential performance benefits of using the new "flat transaction" capability of the CompositeEMFOperation in GMF's CompositeTransactionalCommand, implemented by bug 141051. This could be especially useful for the command created for DestroyElementRequests, as these are known to be potentially quite large.
Created attachment 42047 [details] Possible update to the AbstractEditHelper Attached a patch that demonstrates the performance impact by updating the AbstractEditHelper to always disable transaction nesting. It seems to work in the logic example at least, but may not be applicable in all cases.
Tested and committed the patch.
[target cleanup] 1.0 RC4 was the original target milestone for this bug
[GMF Restructure] Bug 319140 : product GMF and component Runtime Common was the original product and component for this bug