I kept all my dissertation items as plain text and then, over my subsequent career, converted anything that was not plain text to plain text (like a book manuscript, minus the footnotes, though I could also dump those).
Then I kept them in a directory tree. Thousands of pages. Probably 6000 pages by the end of my career. Then I could fire up Powergrep and blaze through those files in seconds. People would often marvel at my “memory” because I could locate almost any passage they were looking for.
I found having a programming background surprisingly useful as a historian. I never met another historian who knew what a regex was until I started teaching my students. In commemoration of just how useful it is, there is a 3-year-old steeper named Regex living im Florida in the family farm of one of my former students.
Plus, of course, as our layout tool changed from WordPerfext to Word to InDesign, these files were already “converted”.
Plain text rules.
I keep Notepad++ open all the time. If I have a new topic, I just open a new tab. Since it auto saves, I don’t even name the files or save them until the notes appear to have long-term utility. In the meantime, they’re just there in a tab anytime I start up Notepad++
