Move "performActionWithinIntegrationLoop" call before forces update

It seems to be safer, as otherwise e.g. chemical reactions plugin
was causing engine to diverge. I suspect that reason was that new
radial bond was added, however forces and velocities weren't updated
immediately, so bond was unnaturally squeezed or stretched. Now even
if a new bond is added, forces will be updated immediately.

Note that it also affects users actions. In fact all user actions
(or script actions) are executed between .integrate() calls. Not sure
what is correct place to modify model during the integration.

Perhaps we should always updated forces after changing model - some
operations do it, but not all for sure.
Mark bonded atoms as neighbors in Verlet List

It ensures that model won't diverge when the radial bond is removed
(e.g. by chemical reactions engine).

It was the real culprit of divergence in models with chemical
reactions. It also reverts change done be 58c1285bde0076 commit.
clarify mml-parser change with comment
Chemical Reactions: add a new interactive for bonds exchange testing

[#56880370]
Fix and cleanup chemical reactions parameters MML->JSON conversion

[#56880370]
Chemical Reactions: change "bondEnergy" format, add "activationEnergy"

[#56880370]

Don't use matrices. "bondEnergy" needed two dimensional matrix, but
"activationEnergy" would need three dimensional matrix what would
be completely unreadable. Use simpler, more descriptive format
instead, as in most cases authors would modify only a few values.
Make sure scripting api rebinds model on reload

This is a fix for IS [#56962282]

This doesn't fix the issue for the model-specific scripting apis, partly to avoid appearing to have fixed the deeper issues created by the particular way in which 'model' was deglobalized.
table view: command click => discontiguous selection
pendulum and graph: graph min width: 24em
debugging support: add incrementing namespace to MD2D model
numericOutput: update model on modelLoaded event
interactiveController: add getScriptingAPI()
button delegates more to interactiveComponent

A buttonController instance now delegates modelLoaded
events and click action/handler teardown-setup to
interactiveComponent base class.
playBack: inherited _scriptingAPI now full instance
small changes to pendulum examples
wip: explosion for itsi
restore experimentController inputs to retain
Apply heat bath after plugins execute their functions

[#56880370]
Chemical Reactions: implement bonds exchange mechanism

[#56880370]
Chemical Reactions: update "Bonds Exchange" interactive

[#56880370]

Add energy graph, so energy conservation can be tested.