I use Atahualpa for several sites, and I'm running the latest -- 3.7.13. I note the following change:
* Until now, when I uploaded a PDF file to my Media folder and then linked to it from within either a page or a post, clicking on that link took me (and my visitors) directly to the PDF. This required no settings, but worked as default.
* With the latest release, those links now take me to a page within the blog where the link appears, with its filename. Clicking on that link then takes me to the PDF file.
So why have you chosen to revise this in such a way as to intrude an additional step into PDF retrieval?
I've attached a screenshot so you can see what I mean.
Here's a link to the page of my blog that includes the link to the pdf: <http://www.nearbycafe.com/artandphoto/photocritic/about-a-d-coleman/adc-in-print-and-pixels/recent-publications/>
And here's a link to the result of clicking on that link:
<http://www.nearbycafe.com/artandphoto/photocritic/?attachment_id=19825>