[4.3] Refinement: centre-of-mass then batched 2D gaussian

[CSSFrancis]

Centre-of-mass pass, then 2D gaussian refinement through the Wave 1 engine ([1.3] + [1.9]) rather than a per-atom scipy loop.

Must honour the per-atom refine flags set in [4.2] (a flagged-off atom keeps its position and is excluded from the fit).

Benchmark against atomap's own refinement at a realistic atom count.

Part of #74.

---

Plan: RELEASE_0_3_0_PLAN.md

[CSSFrancis]

Delivered in 0.3.0, merged to main via #89.

56d04b1 — feat(atoms): atom finding, GPU refinement, property maps

Closing from the merge rather than automatically: the commits cite issues as (#77) rather than Closes #77, so GitHub linked none of them (#89 reported 0 closing references).