I've made wdoc just for that: https://github.com/thiswillbeyourgithub/WDoc
I am a medical student with thousands of pdfs, various anki databases, video conferences, audio recordings, markdown notes etc. It can query into all of them and return extremely high quality output with sources to each original document.
It's still in alpha though and there's only 0.5 user beside me that I know of so there are bugs that have yet to be found!