Extend Codon Atlas

[DanielCuevas1208]

Summary

• Complete the next planned milestone for Codon Atlas. Keep the implementation, tests, and documentation aligned.
• Add coverage for the changed behavior.
• Update the supporting documentation.
• Keep the automated checks aligned with the implementation.

Validation

• Ran the repository's available tests.
• Ran type checks and builds when configured.

[DanielCuevas1208]

Closing this superseded or failing automated pass. The repository can be revisited in a fresh run.