Add comprehensive narrative documentation for undocumented API#14
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Three new guide pages cover functionality that was previously only discoverable via the auto-generated API reference: - geometry.rst: vertex species composition, distances/vectors, off-centre displacement, radial distortion, angular analysis, vector projections, topology, and identity/utility methods - octahedral-analysis.rst: opposite/adjacent vertex pairs, cis/trans and fac/mer isomer identification, trans-axis orthogonality - orientations.rst: RotationAnalyser, orientation order parameters, and orientation distribution plotting Also expands trajectories.rst with Configuration-level utilities (polyhedra_by_label, central_atoms, coordination_atoms), polyhedron trajectory time-series extraction, and lattice_mc export.
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Summary
geometry.rst): vertex species composition (vertex_count,vertex_labels,vertex_distances_and_labels), distances/vectors, off-centre displacement, radial distortion, angular analysis, vector projections, topology (faces/edges/convex hull), and identity/utility methodsoctahedral-analysis.rst): opposite/adjacent vertex pairs, cis/trans and fac/mer isomer identification, trans-axis orthogonalityorientations.rst):RotationAnalyser, orientation order parameters, and orientation distribution plottingtrajectories.rstwithConfiguration-level utilities (polyhedra_by_label,central_atoms,coordination_atoms), polyhedron trajectory time-series extraction, andlattice_mcexportcore-concepts.rstandindex.rstto integrate the new guides into the navigationAfter this change, every public class, method, and property in the library appears in at least one narrative guide page.