Please add projects to JBIDE-3050 if you got an example that works fine under JBT 2 but breaks on JBT 3...
Ok. But the real system is from my job, so I will try create some kind of functional mock that has the same behavior as soon as possible.
Well, seems that I found one workaround.
Disabling "General > Startup and Shutdown > Refresh workspace on startup" and "General > Workspace > Refresh automatically", turn packaging much more responsive.
I will create some testcase soon.