refactor: apply Ruff-specific rule checks

[mwtoews]

This PR applies Ruff-specific rule (RUF) checks, with a few exceptions. A breakdown of the rules used in this refactor are:

• RUF002, RUFF003: ambiguous Unicode character
• RUF013: implicit optional
• RUF100: unused noqa
• RUF015: unnecessary iterable allocation for first element, i.e. use next()

[codecov]

Codecov Report

Attention: Patch coverage is 57.89474% with 8 lines in your changes missing coverage. Please review.

Project coverage is 75.9%. Comparing base (bb9824e) to head (1dce63e).
Report is 10 commits behind head on develop.

Files with missing lines	Patch %	Lines
flopy/export/metadata.py	0.0%	4 Missing ⚠️
flopy/export/vtk.py	50.0%	1 Missing ⚠️
flopy/mbase.py	0.0%	1 Missing ⚠️
flopy/plot/crosssection.py	50.0%	1 Missing ⚠️
flopy/utils/mfreadnam.py	50.0%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##           develop   #2377     +/-   ##
=========================================
+ Coverage     68.4%   75.9%   +7.5%     
=========================================
  Files          294     294             
  Lines        59390   61639   +2249     
=========================================
+ Hits         40652   46842   +6190     
+ Misses       18738   14797   -3941     

Files with missing lines	Coverage Δ
flopy/mfusg/mfusgcln.py	66.9% <ø> (+56.6%)	⬆️
flopy/modflow/mfmnw1.py	86.9% <100.0%> (ø)
flopy/modflow/mfmnw2.py	83.9% <ø> (+4.6%)	⬆️
flopy/modflow/mfrch.py	95.9% <100.0%> (+0.5%)	⬆️
flopy/modflow/mfuzf1.py	92.0% <ø> (+0.5%)	⬆️
flopy/utils/compare.py	41.5% <ø> (+27.2%)	⬆️
flopy/utils/gridintersect.py	79.4% <100.0%> (+<0.1%)	⬆️
flopy/utils/utils_def.py	86.7% <100.0%> (+6.6%)	⬆️
flopy/export/vtk.py	78.0% <50.0%> (+9.4%)	⬆️
flopy/mbase.py	72.4% <0.0%> (+2.5%)	⬆️
... and 3 more

... and 218 files with indirect coverage changes

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