Upgrade ruff, fix issues, use ruff for import sorting

[akx]

This PR:

• upgrades the version of Ruff used from 0.4.8 to 0.9.4
• copies the exclude rules from pre-commit configuration to the Ruff configuration, to make it possible to run ruff outside of pre-commit
• reapplies ruff format (mechanical)
• fixes other new complaints surfaced by the new version of Ruff
• gets rid of isort for import sorting in favor of just ruff's I rule.
  • This had some manual work go into it, to keep the context of the noqa comments intact.

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Additional details and impacted files

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##             develop    #3380   +/-   ##
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  Files              ?       66           
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  Hits               ?    13446           
  Misses             ?     1006           
  Partials           ?        0           

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[akx]

Well, looks like @nateprewitt did this work some 4 months later in #3495 😄