Add callback to get return value of plugin methods

[#49933495]
MD2D: also include each plugin's state in getState

[#49933495]
QD: implement getState to save photon history

[#49933495]
MD2D: new 'utils' module with extendArrays
Simplify photon table handling
MD2D: rm throwaway object creation in integration
rm md2d test that kept obsolete interface around

(keeping the test commented out for now so we can extract the important bits to a new test using more up to date modeler interface)

[#50074251]
MD2D: expose 'raw' atoms as part of modelState

[#50086079]
md2d: rename modelOutputState -> modelState
MD2D: rm cruft
MD2D: to client code, 'results' is just 'atoms'
refactor updateViewAtoms, rm resizeViewAtomsArray
MD2D: comments referencing stories about 'results'