lint md2d.js
rm some obsolete code paths from md2d.js
rm hasChargedAtoms since we have chargedAtomsList

... one fewer item of state to maintain!
simplify chargedAtomsList item removal
endow md2d chargedAtomsList with a reset method

[#57522266]
md2d: reset optimization state on history restore

[#57522266]
remember to store atom trace props in tick history

[#57522266]