#1261: Redo how we iterate over files.

Previously, the update was missing over 1000 files, which is probably a result of the moving target we were trying to hit. To handle it, I got all the fids we would need to update at the start and stored them in the sandbox. This gave us a non-moving target, so each pass could carve out a chunk of this dataset and process it.
Ballar theme: show white version of os powered by logo in footer
Merge branch 'SCHOLAR-3-0' of github.com:openscholar/openscholar into SCHOLAR-3-0
#1262: Use different end trail character when forming original filename

I was using a period for, so it was searching for _0. Well, it turns out someone was using that legitimately. YourCast_0.9.3, for instance. So I switched it to triple |||. There's no way someone is using _0||| for a legitimate file name.
#1261: If the filename is an actual filename, the filename in the uri should match it.
add box reaction to os_faq; correct box setting #811
#1261: If the filename is an actual filename, the filename in the uri should match it.
#1261: Add union to catch files that are attached to group nodes but have no spaces info.
#1261: Drupal doesn't support UNION and ORDER BY in the same query. Move the sorting into PHP.
Bunchy theme bug: fix nav bar negative top margin
Found a small issue where new users weren't getting their IDs hashed after the update hook was run, this will fix the issue.  #110
#1261:  Remove ambiguous column ref
#1261: Remove other ambiguous clause.
#1261: Write updated body data to the correct node.
#1261: Better handling of different files with the same name.
Remove biblio list caching
Merge in last of the 3.0 bugfixes into 3.1
Merge branch 'SCHOLAR-3.1' of github.com:openscholar/openscholar into SCHOLAR-3.1