It works quite well, and might be exactly what you want as far as publishing goes.
> end up in weird jams where Emacs has opened up 3+ panes (buffers), and I can’t figure how to even close/quit them
Typically 'q' will close Doom's popup windows (+popup/quit-window), otherwise you should be able use plain ol' Emacs 'C-x k' or Doom's '<leader> b k' (also 'b d') to kill a buffer.
If you actually want to keep the buffers, and you just want the windows out of the way, you can use winner-undo / winner-redo to cycle through past window configurations.
> bottom-up guide for personal information systems
AFAIK, this does not exist. But there is, I'm sure you've seen, a variety of independent users continually working out interesting new ways to process and link information using Emacs. For example, outside of bloggers in the Roam/Zettelkasten camp, you can always glean insights from John Kitchen's work [0][1], although it leans more towards research/academic use than PIM/PKM.
> my brother is writing a book - he’s not super technical but can get around
If it's technical/academic writing, you can honestly get astonishingly far just using org-mode's LaTeX export.
Definitely a lot of ways to go about this.
If you haven't already, I'd suggest checking out what the creator of org-roam does for publishing his own notes: https://github.com/jethrokuan/braindump
It works quite well, and might be exactly what you want as far as publishing goes.
> end up in weird jams where Emacs has opened up 3+ panes (buffers), and I can’t figure how to even close/quit them
Typically 'q' will close Doom's popup windows (+popup/quit-window), otherwise you should be able use plain ol' Emacs 'C-x k' or Doom's '<leader> b k' (also 'b d') to kill a buffer.
If you actually want to keep the buffers, and you just want the windows out of the way, you can use winner-undo / winner-redo to cycle through past window configurations.
> bottom-up guide for personal information systems
AFAIK, this does not exist. But there is, I'm sure you've seen, a variety of independent users continually working out interesting new ways to process and link information using Emacs. For example, outside of bloggers in the Roam/Zettelkasten camp, you can always glean insights from John Kitchen's work [0][1], although it leans more towards research/academic use than PIM/PKM.
> my brother is writing a book - he’s not super technical but can get around
If it's technical/academic writing, you can honestly get astonishingly far just using org-mode's LaTeX export.
[0] https://kitchingroup.cheme.cmu.edu/
[1] https://github.com/jkitchin