[codex] Derive GNN gate from measurement dimension

[FlorianPfaff]

Summary

• Replace the fixed default GNN gate threshold with gating_probability=0.999 and gating_distance_threshold=None.
• Derive the gate threshold in find_association() from the current measurement dimension.
• Square computed distances when square_dist=True, and use the square-root chi-square threshold when square_dist=False.
• Expand the gating threshold regression test to cover 2-D, 3-D, unsquared, and explicit-threshold behavior.

Root cause

The GNN default gate was a single numeric chi-square threshold tied to 2-D measurements. That made the default inappropriate for other measurement dimensions and left the square_dist setting disconnected from the actual distance scale.

Notes

This PR is stacked on #1845, which removes the accidental extra square from the original default threshold. Once #1845 lands, this can be retargeted to main if desired.

Validation

• Verified the branch diff against codex/fix-gnn-gating-threshold contains only the dimension-aware GNN gating changes and test updates.
• Not run locally; this Codex session has a read-only filesystem, so CI should run the test matrix on the PR.