Speed/stability improvements to chemenv/coordination_environments

[lutfia95]

Summary

Major changes:

• Deterministic neighbor ordering
• O(1) lookups instead of linear scans
• Fewer temporary allocations: Reuse lists; avoid building parallel arrays multiple times; prefer list appends over repeated concatenations.
• Precomputation + tighter loops
• Safer normalization
• Serialization robustness
• Minor consistency fixes

Performance notes

• Fewer sorts
• O(1) lookups for neighbor index mapping instead of O(n) scans inside inner loops
• Reduced allocations in grouping and condition precomputation

Backward compatibility

• No public API changes
• All behavior is deterministic where previously order could vary across runs/platforms

Tests

All unit tests for chemenv/coordination_environments (same as before)

[shyuep]

There seems to be merge conflicts. Pls merge the master branch into your fork and fix the conflicts. Thanks.