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With a helloworld autotools project (with Juno M1), Project -> Reconfigure project (with the project selected in the Project Explorer) appears to do nothing.
The invoking of individual autotools commands also seems to do nothing.
Juno has changed the event we are getting passed to command handlers. A fix has been made to master which works both with Juno and Indigo. This fixes both the reconfigure project and the invoke autotool commands which had the same logic.