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[dev jul 11] Execution settings are not saved between restarts? Or rather, they are, and show up correctly in Execution Settings in Options window, but if you run something before opening this window your choice of workspace will not be used. After opening it things are OK, no need to even change it. Presumably ExecuteAction.setWorkspace is only called when the setting is deserialized, but ExecuteAction.getWorkspace can be called before then and be wrong. So suggest certain system options be always deserialized early--generally, anything which in its setter methods would call anything but putProperty.
Fixed for SystemOptions used in core, module owners should check their modules, see message http://www.netbeans.org/servlets/ReadMsg?msgId=112617&listName=nbdev
verified this case in dev #20010716
Resolved for 3.4.x or earlier, no new info since then -> closing.