doc: fix brackets for optional parameters

Documentation incorrectly used bracket notation for optional parameters.
This caused inconsistencies in usage because of examples like the
following:

    fs.write(fd, data[, position[, encoding]], callback)

This simply fixes all uses of bracket notation in documentation.

Signed-off-by: Trevor Norris <trev.norris@gmail.com>
Reviewed-by: Fedor Indutny <fedor@indutny.com>