[[forum/refresh_and_setup]] indicates some confusion between --setup
and -setup. Both work, but it's clearer if we stick to one in
documentation and code.
A 2012 commit to [[plugins/theme]] claims that "-setup" is required
and "--setup" won't work, but I cannot find any evidence in ikiwiki's
source code that this has ever been the case.
Turns out duplicate index files do not need to be stored when usedirs is in
use, just when it's not. Ikiwiki is quite consistent about using page/ when
usedirs is in use. (The only exception is the search plugin, which needs
fixing.)
This also includes significant code cleanup, removal of a incorrect special
case for empty files, and addition of a workaround for a bug in the amazon
perl module.