Okay, I have gone over the set of possible epub2 guide types and epub3 landmarks (ie. semantics) and can see that by default we should be only indexing files with no semantics set at all OR that have the following semantic types:
Quote:
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"text", "bodymatter", "chapter", "conclusion", "division", "epilogue", "introduction", "part", "preamble", "subchapter", "prologue", "volume"
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All of the other semantic types in both epub2 and epub3 represent front matter, back matter, notes/footnotes, appendices, toc/indexes, etc and these should not be indexed by default.
If an author decides they want to index one of these files, they they can simply toggle off the semantics before running the index generator and then toggle it back on.
That should give the user more control over what gets indexed and what does not at the file level and follows the guidelines provided by the MIT Press for generating indexes.
I will commit that change now so that it will be available in the next release.