I got this note a while back. It’s a great question and now I’m finally able to address it!
“It’s been about a year since your interview article about using Linux and Open Source for writing and publishing. Is there any chance you might consider a follow-on piece that talks about what has happened, what you have learned, and such during the past year? Also, much of the webliography that addresses Linux, Open Source and writing talks about “I have content. Let’s package it into the wild.” Talk about the front-end work flow: “I have facts. Let’s create content.” Notes, references, etc.“
As you can see, the answer to how I handle front-end workflow is paper. When I’m working on more scholarly work, I still print out articles and mark them up. In fact, I’ll often type an outline, print it, and then write on it as I work. There’s just something about the pen on a page that makes it easier for me to connect ideas. From the outline, I just type into a text editor. Any parts or pieces I feel I’m missing get flagged in the text as a note to myself. And any sections that need additional research get put into Remember the Milk for follow-up. I also use RTM to track ideas I want to integrate into an active piece. I use Google Keep to track ideas for pieces before I start writing, but once I’m writing, I don’t really use it. In fact, I usually just copy-and-paste my Google Keep notes into a text file and just work from the text file.