I'm not completely happy with my setup, but that's what I have so far:
Tags to mark the type (novel, short, omnibus, collection, anthology): easily accessed from tag browser or searching tags-omnibus
You can assign a color to any column, so for example tag 'short' makes the title blue, tag 'novel' makes it teal...
ToC in the Comments field: so if I type name of the story into search, I'll get the book with the story - doesn't work well, for 'Who Goes There' I get 42 books, even novels. Still better than thousands. I'm sure some search wizard could get it pinned.
Custom column In: For a short story, I can list all collections and anthologies there (Or omnibus name, if I have a novel in there too). I thought about splitting Epubs but it's too much work, empty book is easier. But one collection can give birth to 20 empty books...no thanks. My library is growing fast enough without artificial help.
So mostly that column=Title, but sometimes there's two titles. Don't know how to search for the novels/stories that appear in several books. For example I have 2 collections by E.R. Burroughs and I want the search for 'Chessmen of Mars' to find them both.
I don't think I have lots of books with duplicated stories, but I have no idea how to find them either. For all I know some story could be in every second anthology.
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