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My version of Haddock does not accept some infix operators like (#)

In fact it does, but you have to add spaces between parentheses and the infix symbols sometimes: ( # ).

How do I get hyperlinks to definitions in e.g. Haskell98?

You must have the relevant documentation installed e.g. ghc-doc. Then you can say e.g.:

    -odir=haddock --html

or much easier just use cabal:

./Setup haddock