update deprecation warnings

[atravitz]

Updating to_rbfe_alchemical_network deprecation timeline from v2.0 to next minor release.

Also including lessons learned from:
OpenFreeEnergy/konnektor#250

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Checklist

• Added a news entry

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[github-actions]

No API break detected ✅

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.56%. Comparing base (e4ee296) to head (88b17a5).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #793   +/-   ##
=======================================
  Coverage   98.56%   98.56%           
=======================================
  Files          43       43           
  Lines        2797     2797           
=======================================
  Hits         2757     2757           
  Misses         40       40           

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