Support explicit polyhedra defined by atom indices

[bjmorgan]

Currently polyhedra are constructed from bonded neighbours detected by distance cutoffs (via BondSpec.max_length). This works well for equilibrium structures but struggles with distorted geometries such as MD trajectories, where bond lengths fluctuate and a fixed cutoff can produce incomplete or over-coordinated polyhedra.

For example, in a MAPbI3 NHC trajectory with a 5.0 A Pb-I cutoff, ~5% of Pb atoms have 5 or 7 I neighbours instead of the expected 6, producing distorted or incorrect octahedra.

It would be useful to allow users to define polyhedra by explicit atom index groups (e.g. centre atom + list of vertex indices), bypassing distance-based detection entirely. This would give reliable results for known coordination environments regardless of geometric distortion.