(Issue540) Compatibility with PDFtk 2+

We'll need to upgrade PDFtk to version 2.01 to address issues with generating PDFs created with Keynote (and probably many other issues with processing PDFs).

While that is a deployment configuration change, these changes make our code work with that version (and is backward compatible with 1.44 / 1.45):

* Filter out non-pdf files (compatibility with 2.01)
* Sort pages by page number when splitting the document (spotted a potential bug here with pages being processed in weird order when the doc was over 250 pages)