Update documentation links.

Where possible (mostly with the Nikoli links), they've been updated to their
modern locations.  At least one link had to become a Wayback Machine link;
I didn't bother making the floodit.appspot.com link a Wayback one because
there's no content there without the backing of Google App Engine.  There
are other implementations online nowadays, of course, but I didn't want to
change the meaning of the text if at all possible.  In addition, I added
Flash warnings for the Nikoli pages that now use Flash for instructions.