You can pass the wildcards to the program by running GenerateIndex index.html "*.ps" "*.pdf" "*.txt". (Ie. by quoting the wildcards. You can just as well use single quotes or backslashes.)
Also, you sound like it would be something bad. If so, I just wanted to notify you that so is not the case. It is enormously convenient for application developers to have wildcards expanded when the program starts.