Clean up documentation

[Herrner]

My suggestion:

• Everyone creates a branch to first get rid of duplicates and deprecated files
• We only store the source files of the documentation in the howto, manuals and quickstart folders (and only the latest version on the mainbranch)
• We create one folder to hold the PDF files that can be directly linked from exmaralda.org and elsewhere (direct linking to the main branch works like this: https://github.com/Exmaralda-Org/exmaralda-docs/raw/main/manuals/coma/Coma_Reference_Manual.pdf

[berndmoos]

I think I did the part with duplicates and deprecated, without branches, though, forgive me. Only docx left now, and quite a lot of version chaos removed. What next?