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I'd also check Joplin, there is a desktop application and you can sync with a webdav server (NextCloud for example).
I personally love to use BookStack for these things since I found it a few years ago. It's basically what you are looking for. You can take notes of everything, order them in a hierarchical structure (shelves > books > chapter > pages) and export them to PDF. There is markdown editor for experienced users or a normal WYSIWYG editor with some useful shortcuts. I like to use it as my personal wiki and a quick reference handbook for all the difficult problems that I already solved. The fulltext search is quite fast which was an important requirement for myself.