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Add:

%!preproc: '\\[(.*?)\\]' ' INDEX='
%!preproc: '\\[(.*?)\\]' ' INDEX='
%!postproc: 'INDEX=' 'doku.php?id='

in the header of any page you need to use the wiki inner links (double [)

(check the source of this document to see the correct syntax, the wiki might mangle some symbols)