Fix deprecations + updates

Summary

Resolves

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

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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• All automated tests pass
• Reference related issues
• Up-to-date CHANGELOG.md (or not necessary)
• Up-to-date JSON schema (or not necessary)
• Appropriate user and developer documentation (or not necessary)
  • How do I use the software? Assume "stupid" users.
  • How do I develop or debug the software? Assume novice developers.
• Annotations in code (Gitlab comments)
  • Intent of new code
  • Problems with old code
  • Why this implementation?

Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• Up-to-date CHANGELOG.md (or not necessary)
• Appropriate user and developer documentation (or not necessary)
• The test environment setup works and the intended behavior is reproducible in the test environment
• In-code documentation and comments are up-to-date.
• Check: Are there specifications? Are they satisfied?

For further good practices have a look at our review guidelines.

.docker/Dockerfile

@@ -4,7 +4,7 @@ RUN apt-get update
 RUN apt-get install -y cmake
 RUN apt-get install -y lcov
 RUN apt-get install -y doxygen graphviz
-RUN apt-get install -y clang-format-16 clang-tidy
+RUN apt-get install -y clang-format-16 clang-tidy-16
 RUN apt-get install -y python3-pip python3-venv
 RUN apt-get install -y git  
 RUN apt-get install -y curl zip unzip tar