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Migrate File/Object Functionality to Prototype #67

@agilgur5

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@agilgur5

E.g. execute shouldn't be called from the executor and passed in an automaton, it should be a function on the automaton's prototype. getCentroid() should be part of the regions's prototype (and possibly stored in the returned region object somewhere too). etc.

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    kind: internalChanges only affect the internals, and _not_ the public API or external-facing docsscope: RegionEditorRelated to the Region Editorscope: SimulatorRelated to the Simulatorscope: SpecEditorRelated to the Spec Editor

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