Seeing as the Clinton's are the most untrustworthy people on this planet, it is more then likely the original Thesis was replaced by one more palatable to the general population. Maybe the ink or paper on what is purported to be her Thesis can be analyzed to determine its age. By FReeper Eagles Talon IV
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If Hillary did replace the original in the college archives, there might be other originals out there.
The Library of Congress should be checked to see if they might have archived the original.
Also to be checked is the institution (library or college) that stores the collection of Alinsky's papers and books.
Alinsky must have made arrangements to donate his aftereffects and papers upon his death. (Just as an example, Princeton University stores the papers of ACLU founder, Roger Baldwin).
Thanks for the ping! Hillary's book includes a few comments on the thesis, IIRC.