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when an external tool launches, the current view deactivates. when the external tool terminates, that view does not reactivate. this causes the selection to appear gray. if you attempt to launch a tool again which depends on the selected resource for one of its arguments, the tool will not resolve the argument, as an inactive view will not return the selection. this is very confusing for a user to see the tool fail. see bug 18407 for details.
I think this has to do with our use of a progress monitor dialog. Maybe this problem will go away if we did not use one for launching programs?
Not a stop ship.
The problem is not related to the progress monitor as I had suggested, instead Chris found the problem comes from showing the log console view (it will take focus). There is no API to show a view without giving it focus. He had some code for a workaround - the only problem was a bit of flicker (remembers the active part, shows the log console, activates the old active part). There is a PR for API to show a view without giving it focus. If we add this in release 3.0, we can solve this problem too.
Can workbench provide this api?
*** This bug has been marked as a duplicate of 15821 ***