It's just the process of organizing your ideas in a logical order. At the start, I have a bunch of ideas and I do my best to organize them into an outline. Bu

It's just the process of organizing your ideas in a logical order. At the start, I have a bunch of ideas and I do my best to organize them into an outline. But as I begin writing and continue my research, I realize that some of my ideas suck, or I have new, better ideas, or I see a better way to share my ideas with the reader, so I need to constantly reorganize my document. I don't know if this process is a sign that I'm an amateur writer or not, but Scrivener makes document organization incredibly simple compared to writing in a normal text editor. It also enables me to keep my notes sorted without interfering with the prose. By the way, updating all the references is very easy using Bookdown and a bibtex bibliography.