As usual I'm late to the party but I find uses for both a
single large org file as well as multiple small ones.

-For knowledge capture, I prefer the quick action of small
 files, one file per capture instance.  I use a personally
 written system called 'scraps' (with many similarities to
 'denote' or 'howm' etc.) which quickly captures one 'scrap'
 of information to a single (generally small) file.  I recall
 information later with deadgrep or similar fast tools.

-But for my fiction writing, including full length novels, it
 is always one file per project.  I don't want to have to deal
 with identifying multiple files (like a file per chapter or
 scene or whatever).  Org-mode makes this work easily; my
 research notes are in the same file.  It is all very portable
 and easy to manage with a dead simple version control system
 like the venerable RCS.  As long as I don't use things like
 flyspell or live word count, performance is more than fast
 enough even on old slow computers.  Another benefit is easily
 exporting everything at once (with :export: and :noexport:
 tagging) to LaTeX or odt.
 
-- 
Bob Newell
Honolulu, Hawai`i

- Via GNU-Linux/Emacs/Gnus/BBDB

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