Apply updated templates with fixes and improvements

[AndrewSazonov]

This PR applies the latest Copier templates and includes several bug fixes and improvements introduced in the templates since the previous version.

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Codecov Report

✅ All modified and coverable lines are covered by tests.
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Additional details and impacted files

@@            Coverage Diff             @@
##             develop     #114   +/-   ##
==========================================
  Coverage           ?   97.68%           
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  Files              ?       36           
  Lines              ?     2328           
  Branches           ?      388           
==========================================
  Hits               ?     2274           
  Misses             ?       33           
  Partials           ?       21           

Flag	Coverage Δ
integration	0.00% <ø> (?)
unittests	97.68% <ø> (?)

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[henrikjacobsenfys]

Looks good to me! I may want to make some changes/improvements to documentation, but I think enough is happening here, so it'll come in a new PR (yet-more-docstrings)