Fix deprecations + updates

Summary

Resolves

• #95 (closed)
• #93 (closed)
• #89 (closed)
• #92 (closed)
• #86 (closed)
• #72 (closed)
• #70

Focus

• Updating to Debian 12 made creating a venv in the Dockerfile necessary
• clang-format-11->clang-format-16
• no more deprecation warnings for inheriting from std::iterator
• boost::string_file was replaced by copying the implementation from boost

Test Environment

How to set up a test environment for manual testing?

Check List for the Author

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• Reference related issues
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• Up-to-date JSON schema (or not necessary)
• Appropriate user and developer documentation (or not necessary)
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Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
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• Appropriate user and developer documentation (or not necessary)
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