Simulation interaction with mixed graphstream / non-gs deployments is broken

[DanySK]

Original file:

incarnation: protelis

network-model:
  type: ConnectWithinDistance
  parameters: [1]

_programs: &programs
  - time-distribution: 1 # This is a frequency
    program: "org:protelis:tutorial:distanceTo"
  - program: send


deployments:
  - type: Grid
    parameters: [-5, -5, 5, 5, 0.5, 0.5, 0.2, 0.2]
    contents:
      - molecule: "source"
        concentration: true
        in:
          type: Circle
          parameters: [0, 0, 0.3]          
    programs: *programs
  - type: GraphStreamDeployment
    parameters: [200, 4, 4, 0.5, "Lobster", [10, 4]]
    programs: *programs
_my_custom_entry:

1. Run the simulation
2. Select and move a bunch of nodes from the top right of the grid
3. Simulator crashes with:

10:49:07.230 [main] ERROR i.u.a.core.implementations.Engine - The simulation engine crashed.
java.lang.IndexOutOfBoundsException: Node -6 does not exist
        at org.graphstream.graph.implementations.AdjacencyListGraph.getNode(AdjacencyListGraph.java:247)
        at it.unibo.alchemist.model.implementations.linkingrules.OffsetGraphStreamLinkingRule.computeNeighborhood(OffsetGraphStreamLinkingRule.kt:30)
        at it.unibo.alchemist.model.implementations.linkingrules.CombinedLinkingRule$computeNeighborhood$1.invoke(CombinedLinkingRule.kt:32)
        at it.unibo.alchemist.model.implementations.linkingrules.CombinedLinkingRule$computeNeighborhood$1.invoke(CombinedLinkingRule.kt:22)
        at kotlin.sequences.FlatteningSequence$iterator$1.ensureItemIterator(Sequences.kt:315)
        at kotlin.sequences.FlatteningSequence$iterator$1.hasNext(Sequences.kt:303)
        at com.google.common.collect.Iterators.addAll(Iterators.java:355)
        at com.google.common.collect.Iterables.addAll(Iterables.java:320)
        at org.danilopianini.util.ImmutableListSet$Builder.addAll(ImmutableListSet.java:49)
        at it.unibo.alchemist.model.implementations.neighborhoods.SimpleNeighborhood.<init>(SimpleNeighborhood.kt:33)
        at it.unibo.alchemist.model.implementations.neighborhoods.Neighborhoods$Companion.make(Neighborhoods.kt:32)
        at it.unibo.alchemist.model.implementations.linkingrules.CombinedLinkingRule.computeNeighborhood(CombinedLinkingRule.kt:28)
        at it.unibo.alchemist.model.implementations.linkingrules.CombinedLinkingRule.computeNeighborhood(CombinedLinkingRule.kt:22)
        at it.unibo.alchemist.model.implementations.environments.AbstractEnvironment.updateNeighborhood(AbstractEnvironment.java:487)
        at it.unibo.alchemist.model.implementations.environments.Abstract2DEnvironment.moveNodeToPosition(Abstract2DEnvironment.java:118)
        at it.unibo.alchemist.model.implementations.environments.Continuous2DEnvironment.moveNodeToPosition(Continuous2DEnvironment.kt:105)
        at it.unibo.alchemist.model.implementations.environments.Continuous2DEnvironment.moveNodeToPosition(Continuous2DEnvironment.kt:30)
        at it.unibo.alchemist.boundary.monitors.Generic2DDisplay$MouseManager.lambda$mouseReleased$1(Generic2DDisplay.java:874)
        at it.unibo.alchemist.core.implementations.Engine.processCommand(Engine.java:352)
        at it.unibo.alchemist.core.implementations.Engine.run(Engine.java:396)
        at it.unibo.alchemist.launch.SingleRunSwingUI.launch(SingleRunSwingUI.kt:48)
        at it.unibo.alchemist.launch.SimulationLauncher.launch(SimulationLauncher.kt:52)
        at it.unibo.alchemist.launch.Launcher$DefaultImpls.invoke(Launcher.kt:44)
        at it.unibo.alchemist.launch.AbstractLauncher.invoke(AbstractLauncher.kt:15)
        at it.unibo.alchemist.Alchemist.launch(Alchemist.kt:170)
        at it.unibo.alchemist.Alchemist.main(Alchemist.kt:128)