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I was thinking of some sort of vim extension that had a windows explorer tree on the side of the screen (for weaving through folders/text files).
One thing I did that saved my a: daily backups. My hard disk actually died 3 days before my deadline. These days I would also use Dropbox.
I'm not going to pretend I know much about the implications of storing huge binary files in SVN, but at least they were in VC.
The main benefit to me of this was not backup (although that was highly useful!) but in the fact that I could write it up in the Uni office, at home or on my laptop on holiday. Just don't forget to SVN commit every now and then :-)
For each of these structures, I use:
/ - top level have Latex files
/images - OmniGraffle figure files and exported vector PDFs
/code - code snippets that are automatically included and formatted using Latex commands
NERD_tree
minibufexplorer
command-t
good choices not only for books but also for coding.
The two main approaches are to have the whole book in one big file or one chapter per file. I think that having one chapter per file is more flexible and that's the way I'd do today.
Another thing to keep in mind is if your book is going to have source code. Is it going to be highlighted? If so, in color or grayscale? Do you want to have a way to test automatically every code snippet so you don't ship the book with broken code examples?
Also, do you have images that need to be converted, say from inkscape to png or eps? Usually I use a makefile for things like that.