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You essentially already answer your own question: indexes are more than just a reference to the words in a text. Apart from creating relationships an index
can hide non-essential use of a word, and have definitions be different from normal use of a word. This requires interpretation by the author, something a search does not do.

I used LaTeX and its index generating capabilities when writing my thesis and the references to defining occurrences showed differently (italics) from the normal entries. Of course the software also helped by showing ranges of pages where a word was marked for indexing, which is also something a search engine seldom indicates (it might highlight all occurrences on a page, but that is not the same as knowing that a term is used in 10 consecutive pages).


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