[Viewer] Enhance Molstar state management by improving code readability

[p3rcypj]

📌 References

• [CV19 & Viewer] Feature: Refined models #244

📝 Implementation

Previously MolecularStructure.tsx was helding all the logic for PdbeMolstar plugin. We previously made an effort to extract the state into two useHooks -> usePdbPlugin() and usePluginRef(). But that effort wasn't enough as there is a lot of complexity still being held. Due to that complexity, when refined models feature was added, two bugs appeared:

• Refined models not added on init (also applying to overlay items, referring to other pdbs and emdbs at the same time)
• And not updating the MolstarStateRef causing to repeatedly load several instances of the model (duplications)
• Nullable filenames external urls

This PR is a mid-refactor. It's a mid effort of extracting and moving some complexity out and improving readability while solving these mentioned bugs. And this PR isn't even the correct boilerplate of the refactor itself.