refactor(deprecations): deprecate flopy.mf6.utils.reference module

[wpbonelli]

The flopy.mf6.utils.reference module contains spatial reference classes similar to those deprecated/removed in #1914, #1892, and #1200. These are not in use anywhere in the codebase. The flopy.discretization module can/should be used instead?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.9%. Comparing base (bb9824e) to head (f93571a).
Report is 9 commits behind head on develop.

Additional details and impacted files

@@            Coverage Diff            @@
##           develop   #2375     +/-   ##
=========================================
+ Coverage     68.4%   75.9%   +7.5%     
=========================================
  Files          294     294             
  Lines        59390   61638   +2248     
=========================================
+ Hits         40652   46841   +6189     
+ Misses       18738   14797   -3941     

Files with missing lines	Coverage Δ
flopy/mf6/utils/reference.py	0.0% <ø> (ø)

... and 229 files with indirect coverage changes

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[mwtoews]

Sure, looks good. I've pushed a commit to use Sphinx's cross-references.