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Even if there is no active connection, the user is doing nothing in the remote systems view (but view is visible in perspective) and performing usual edit/compile cycles, RSE seems to listen to _any_ resource change propagated by Eclipse. Frequently the "Remote System Explorer Operation..." jobs can be observed within the progress view in the described state. RSE should not do anything, including scheduling unnecessary jobs, if a event is not relevant for RSE.
In RSE, there is a) The TempFileListener b) Profile Save Jobs c) UI update jobs in the SystemView. and probably more, would need some investigation. (a) would be fixed by deferred plugin activation (bug 181939). (b) might partially have been fixed by avoiding profile saves (bug 203365). (c) is necessary for passing the UI/Non-UI gap. Those Jobs might have to be converted into System jobs such that they are not user visible in the Progress view (calling Job#setSystem(true)).
Dave, I'm passing this one to you since you own bug 181939. Let me know whether that's something you plan on dealing with anytime soon.
moving to 3.1