I use DevonThink to keep all the files related to the book, basically trying to cargo-cult Steven Johnson. It’s a Mac app that’s, on its surface, a very rich, more easily-controlled Finder. DevonThink allows me to drag in text documents, images, videos, notes, snippets from other books, websites (saved locally in their entirety), and PDFs (with an option to run optical character recognition if necessary). I can then categorize all the documents as I see fit, put them in different folders, and cross-link. The app also offers full text search on the entire database.
It also has scripting capabilities — although it uses AppleScript, which is far from ideal. Steven Johnson used it to suggest connections between things, although I haven’t done much of that. More importantly for me, the app is still under active development, and everything can be dragged out as easily as dragged into it.
The book database is currently at over 274GB, and below is a list of folders in it (both as of January 2018). If there’s anything here that might be interesting to you, please let me know. I don’t mind sharing. There are so many books that could be written from this alone; mine doesn’t have to be the only one.