The default will be as I described above. Getting Sigil to index anything else is a simple as temporarily toggling that file's semantic off until the index is built, then re-enabling it. So by a simple right-click on the file in the BookBrowser and selecting Add Semantics you can control if footnotes or appendices or whatever will be indexed.
As for Spellchecking, the results are not added to the book and you can spellcheck by file, or as you type, or all xhtml files, so this should not be an issue.
Thanks.
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