FWIW, a user defined folder structure is our next Sigil project (in other words stop moving everything to fit our structure). We will branch to start work on it immediately after the next release.
As for multi-lingual spell checking, that is actually not hard if it is done by a spellcheck modal dialog and not trying to do it while typing. The "do it while typing" is in fact very hard to do as the tag that indicates the language may be far away from the text being checked. The modal dialog spell checker might be a good project for a plugin developer.
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