refactor(expired deprecation): remaining references to SpatialReference

[mwtoews]

This cleans-up a few remaining references to SpatialReference or related (e.g. "sr"). This extends beyond #1200 and #1892.

Details of changes:

• Some related docstrings improved and expanded
• Remove unused method _set_sr_coord_info from flopy/discretization/grid.py
• Spatial metadata in flopy/modflow/mfdis.py was not actually ignored, but now it actually is ignored and removed, as this should be in classic NAM files

Note that these changes are not related to flopy.mf6.utils.reference.SpatialReference, which is not deprecated.

[codecov]

Codecov Report

Merging #1914 (56a256a) into develop (99f680f) will increase coverage by 0.0%.
The diff coverage is 57.1%.

@@           Coverage Diff           @@
##           develop   #1914   +/-   ##
=======================================
  Coverage     72.5%   72.6%           
=======================================
  Files          257     257           
  Lines        56279   56210   -69     
=======================================
- Hits         40854   40841   -13     
+ Misses       15425   15369   -56     

Files Changed	Coverage Δ
flopy/discretization/grid.py	76.0% <ø> (+0.6%)	⬆️
flopy/mbase.py	69.6% <ø> (+0.2%)	⬆️
flopy/modflow/mfdis.py	91.9% <ø> (+7.4%)	⬆️
flopy/modflow/mfsfr2.py	87.5% <ø> (ø)
flopy/mt3d/mt.py	72.6% <ø> (+0.4%)	⬆️
flopy/pakbase.py	81.5% <ø> (+0.1%)	⬆️
flopy/plot/plotutil.py	53.2% <ø> (ø)
flopy/utils/binaryfile.py	81.2% <ø> (+0.4%)	⬆️
flopy/utils/reference.py	90.9% <ø> (ø)
flopy/export/shapefile_utils.py	83.4% <57.1%> (-0.2%)	⬇️

... and 1 file with indirect coverage changes