[4.2] The three atomap GUI functions as anyplotlib overlays

[CSSFrancis]

Reimplement the interactions over our own overlay (model: vector_overlay.py):

• select_atoms_with_gui → polygon select to separate phases/structures into sublattices, with an invert option.
• add_atoms_with_gui → click to add a missed atom, click to remove a spurious one.
• toggle_atom_refine_position_with_gui → click an atom to toggle its refine flag, green ↔ red.

Verified by running the app and looking at screenshots — these are pure interaction and cannot be verified headlessly.

Part of #74.

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Plan: RELEASE_0_3_0_PLAN.md