The PDF_Include extension that you are using has a bug. I took some time today to look at this today and updated the code. You should update your code and try again: https://www.mediawiki.org/wiki/Extension:PDF_Include
Thanks, Mark. I see you did a lot, and now it works. At least, it allows to save the page with a PDF image and shows the pic. I made the preliminary test at http://mizugadro.mydns.jp/h/index.php/Testpdf
There is still a strange thing: if the PDF figure is loaded at the page, then it intercepts the keys "command,+" and "command,-" ; now, the zooming-in and zooming-out apply only to the PDF figures. However, the buttons "View","Bigger" and "View","Smaller" at the Macintosh menu bar seem to work as previously.
At the Linux brousers, the analogies, I suspect, are "control,+" and "control,-"; so, perhaps, you can reproduce the effect.
Such a mode (if one knows about this) could be useful to see details of the complicated figures, without to change the scaling of the description in the text. however, such a behavior looks unexpected; is it intentional? I suggest that you keep this option; althopugh I doubt if it should be default.
Is it possible to make the <pdf> program to get the data about sizes of the PDF figure from the included file?
I read, you suggest 400px as default size of the figure... Is it possible to ask the <pdf> to scale the figure to fit the frame indicated, as a default?
I think, this would correspond to the wiki style of loading of figures in other formats.