Reads popular document formats (PDF, DOCX, PPTX, Images, HTML, AsciiDoc, Markdown) and exports to Markdown and JSON
Repo: github.com/DS4SD/docling
For a clean interface (but poor Zotero integration), Typora is wonderful.
For academic writing with lots of footnotes, Zettlr works well.
If you want to implement a knowledge base in the same platform as your writing, Obsidian is probably your best bet.