Move timeout and progress reports to Simulation

[pjonsson]

This moves the code for handling timeouts
and progress reports from LogScriptEngine to Simulation.

[pjonsson]

@nfi Added the commit that migrates the progress report to this PR. It's the last set timeout that should get precedence. I'm not sure what decides the order.

[nfi]

I get an exception when I deactivate and then reactivate a simulation script:

java.lang.IllegalStateException: Event is already scheduled: org.contikios.cooja.Simulation$1@19eff8d7
	at org.contikios.cooja.EventQueue.addEvent(EventQueue.java:95)
	at org.contikios.cooja.Simulation.scheduleEvent(Simulation.java:534)
	at org.contikios.cooja.Simulation.lambda$setTimeout$1(Simulation.java:556)
	at org.contikios.cooja.Simulation.lambda$new$0(Simulation.java:212)
	at java.base/java.lang.Thread.run(Thread.java:833)

[pjonsson]

Fixed in latest update.

[nfi]

If you run a simulation until timeout, and then reload the simulation, the new simulation will immediately timeout without running anything. Also, it is no longer possible to continue running a simulation after first timeout.

[pjonsson]

Fixed.