Are faculty job applications evaluated on a computer or on a paper?
We've had a variety of practices. Some of it depends on the computer literacy of the admin assistant doing the application file processing. We've had cases of electronic material (PDFs) being printed out and then rescanned back in as the staff person did not know how to collate multiple PDFs into a single document.

[HEAD PALM] Sigh...

To be entirely fair, some of our faculty are also very visual-tactile and will prefer print out the dossier and read it there, rather than online. 

In other words, you can't assume anything about how the files will be handled. You should be explicit in the URLs. If you have media files on disk or thumb drive (photographs, video, source code, simulations, etc.), then you should also post a visible link to an archive location.