Fix residue conformational state indexing by group id

[harryswift01]

Summary

This PR fixes residue-level conformational entropy being reported as 0.0. Residue states were stored in a list that was pre-filled with one empty list per group and then appended to, so lookups by group id read the empty placeholders. The residue states and flexible-dihedral counts are now keyed by group id, and the regression baselines affected by the correction are regenerated.

Changes

Key residue conformational state accumulators by group id:

• states_res and flexible_res in conformational_state_builder.py are now dict[int, ...] instead of lists, and the return annotations are updated to match.
• _merge_group_state_data in state_assignment.py takes group_id and assigns states_res[group_id] and flexible_res[group_id] instead of appending.
• Removed the now-unused number_groups.

Update unit tests for group-keyed states:

• Builder tests (no groups, empty group, chunked serial flow) now expect dicts.
• The chunked serial test previously asserted [[], []] for a single group, which encoded the indexing bug.
• The merge test passes a non-zero group_id to check the key is used and not the insertion order.

Update regression baselines:

• Regenerated the baselines for all systems affected by the corrected residue-level conformational entropy.

Impact

• Residue-level conformational entropy changes from 0.0 to a computed value for any run with a residue level. Results will differ from earlier versions.
• On the DNA system from [Bug]: Investigate ambiguous residue conformational state indexing #368 (all atoms, customised_axes: false, frames 0-5 step 2), group 0 residue Conformational goes from 0.0 to 5.292271495278918, matching the issue.
• flexible_res is no longer indexed by position, so skipped or non-contiguous groups can't read another group's value. A missing group now raises KeyError.

[jimboid]

Looks like this fixes a real bug behind at least one reported issue. Happy to merge.

[skfegan]

This looks good. Hopefully the tests ensure that this issue doesn't recur.