To be picky, yesterday wasn’t exactly “nothing,” it just felt like it. I spent the day editing out annoying errors from the Word files containing my Renaissance data, making sure each little chunk of information had its source noted, and other picky-but-necessary bits. Today, due to massive sleep deprivation, probably will be a nothing day.
But once I get my brain online, I’d like to move the contents of those files into some format more easily searchable. There’s only so much organizing I can do with headers; I wind up copying paragraphs that apply to more than one thing; and the files themselves become unmanageably long. Database time!
For the last book I used Evernote, but it wasn’t completely satisfactory. My principal gripes were that it stored my notes in its own cloud and that it frequently claimed it was too busy to retrieve things for me. I’d vastly prefer a note-sorting app that allows me to store the notes right here on my own laptop, where I can easily back them up to a flash drive and where I can look at them whenever I need to.
What kind of software do you all use? I’m going to listen to some nice, simple, predictable Baroque music and/or take a nap, those two activities being about I’m up to this morning. Will check back in later, hoping for some software suggestions.
Mad Genius Club 
I use an ad-hoc set of text files for notes. If I forget which file I put something into I can use the “grep” or “rg” (ripgrep) to search all files in the directory. In a text editor I just use Control-F to find. Usually what I am looking for is in the last place I was working so it’s just right there.
At one point in time I used Emacs org-mode which is handy. But you need to run Emacs which may not be handy.
For taking notes in work meetings I like using the pen on my MS Surface tablet and OneNote. I am a tech guy so it is a bit weird but I love writing notes in cursive handwriting using a pen. OneNote can convert to text and search it. If my handwriting is good enough. So it has been quite the incentive to improve my cursive.
For non-fiction I use paper and pen (or pencil if forced to by archive rules). Meaning I am very, very fussy about paper, and use the Levenger note-pads that have space on top for topic, subtopic, page of topic (or subtopic) and date. One margin is blank so I can put citations there in short form, as well as file, box, document, and collection number. The paper doesn’t smear pencil or pen, even fountain pen (although the new glaze they use does allow some show-through. Grrrr.)
For fiction, I just use the book (if I have it), or follow the same system as for non-fiction. All the notes are stored in a three-ring binder with color-coded file tabs. I also have neat, tiny cursive handwriting, so I can get away with a system like this (lots of data per square inch).
Nothing special. Notes go in textfiles called obvious things like notes, or ideas, or origins. Fiction goes in its own single file per work. Real work gets done in RoughDraft, a very old RTF editor that doesn’t add so much gunk and has a good multi-file search function (which stole me away from WordPerfect):
http://rsalsbury.co.uk/rd.htm
I recently outlined something in Freeplane (mind mapping software) and MS Paint.
Overleaf is a browser based LaTeX client/editor that I’ve used recently.
You didn’t specify software for writing, so in theory I could just ramble about what I use for all the tasks. 🙂
Basic summary, is that I install more than one program of a given type, then more or less make a random choice which I use every project, so my use cases might be a terrible series of dumpster fires.
I did that outlining after a long time getting nowhere with pencil and paper. Didn’t make it work, middle of writing it, and don’t want to comment for fear of killing the (non-fiction) project before getting it done.
Manga Studio 😋
Because I *own it*
All text, all the time.
You seem to be a bit computer savvy (not necessarily a guru, you just need to be able to follow instructions) so I would look into using markdown as a “text formatter” to create your notes in simple text but giving then some format so you can export them afterwards if needed to doc, epub, pdf, etc but having simple paragrafs, titles, cursive and the like. You can see your notes nicely formated with any program (there are lots) having a visualization mode for markdown, but inside your notes are simple text and completely searchable with whatever you want to use, like a simple grep like @Zan Lynx suggested.
Around markdown there are other programs to help you organize your notes: Obsidian, Mindforger, Notable, Zettel… You can migrate from one to another with less or more pain depending on how strict they are on the folder structure to organize the notes, but the notes will be there because they are simple text.
The same with backups and version history if you feel you need it, being text files, you can use git to have a version history of your notes.