Split doxygen generated documentations and include markdown documentation files

[b-kaiser]

DRAFT: This merge request is currently pending, awaiting the incorporation of minor changes due to merge requests #156 and #157. These adjustments will be implemented once both #156 and #157 have been successfully merged into the master branch.

Doxygen encounters limitations when documenting projects with multiple executables, particularly in handling global name clashes. Specifically, Doxygen lacks the capability to distinguish between various main functions, opting to select the first instance it encounters and silently disregarding others. The resulting documentation in incomprehensible and misleading.

Upon extensive research, I have not identified a natural and viable solution to address this challenge within a single Doxygen-generated documentation. Consequently, I have changed our documentation strategy.

This merge request splits the documentation process by instructing Doxygen to generate separate documentation for each executable within the project. Moreover, doxygen is now instructed to include the markdown files containing additional information such as README.md and HOWTO.md into the documentations it generates.

Furthermore, in the process, I have fixed several minor issues regarding doxygen.

[cuveland]

Thanks! This looks very good. We have now merged the two prerequisite PRs. We will merge this once you remove the draft flag.

[b-kaiser]

Thank you very much!