Personally, I don't get that complex.
I write non-fiction, which I'm sure is a different process from fiction.
I start out by throwing a bunch of notes into an MS Word document. Basically a collection of "here are things I want to talk about". Initially I don't worry about order, structure or consistency. For some things I may just put a sentence or a headline. For another point where I have specific words in my head, I might write several paragraphs.
When I have a bunch of such notes, so that I think I basically have every main idea I want to cover, I group related ideas with some cut-and-paste and put in chapter and section titles. Then I arrange the chapters and sections into a rational order. Then I go throw my notes, generally front to back, and pad out all my notes into full sentences and paragraphs.
I have occasionally thought of using SVN or a similar product to save working versions, but I've never seen enough value to it to actually bother. I'm a software developer by profession so I'm quite familiar with library managers. For programming it makes a lot of sense: You have a history of when changes were made and why. If many people are working on a project, you can see who made what change. If a program used to be working and now is broken, you can go back to the working version. None of these apply to writing a book. I don't produce a "working version" of a book and then make incremental changes to it. Even if I did, there isn't a clear distinction between "working" and "not working" like there is in software: in real life, I can't imagine saying, "Oh, a reader has pointed out a mistake in my book. I'd better hastily restore to an earlier version that doesn't have this mistake, and then rework the changes until they are correct." Etc. I do occasionally make back-up copies of a draft, mostly so that if I make some clumsy mistake in editing, like accidentally deleting a chapter, I can get it back. Maybe this is a lazy version of a repository.
I don't see what the advantage would be of writing a book with a plain text editor and then later migrating it to MS Word (or some other word processing program). If I'm going to put in italics or block quotes or whatever formatting, it seems a whole lot easier to do it as I'm going alone then to have it all in plain text and go back and add the formatting later. As I'm writing it, I know what formatting I want. If I tried to put it in later I'd have to figure it out all over again. I suppose if you're going to keep your book in Git or whatever, repository software works a whole lot better with plain text than with a docx.
I've never used "note keeping" software. It seems to me a whole lot easier to just throw all my notes into MS Word, and then when I'm writing the book, I just edit the notes as I go along.
For books, when I've got the text complete and I'm happy with it, I export it to PDF to send to the printer or publisher. For magazine articles, the magazine usually wants to be able to edit, so they want them in Word or something editable.
Of course if I have illustrations I'll use some sort of drawing software. Usually CorelDraw.
As always on mechanical things like this, I'm happy to drone on about the process I use and why I like it, but it comes down to, What works for you? I know writers who prefer to write on paper and not put it on the computer until they have a good draft. I find this incredibly awkward -- you lose all the advantages of the editing features of the software, the ability to easily backspace and fix a mistake, switch sentences or paragraphs around, etc. But I guess these folks find that having to manipulate the software distracts them from the creative flow of writing. If it works for you, than fine.