The new version does not honor my setting to not use the staging area. If I set the preference to not use the staging area, once I add a file to my git repository, the staging area is turned back on and I can't change the preference again until the files have been committed.
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Sorry, from the next version we won't automatically flip to staging mode when added or removed files are in the index. We added the automatic flip in 1.9.1 to reduce confusion for people viewing repos which already had staged changes but of course you can add/remove without using staging (conceptually).