Getting ready to upgrade to latest version of Atahualpa.
Am now in version 3.4.6, with WP 3.2.1. I have juggledad's upgrading procedures post.

Had work done by a coder to add a database to my WP site, and the coder added 30+ database-related files (example: page-2417.php) to my atahualpa346 folder.
Here's the site: http://seriousgivers.org/

I know just about enough to be dangerous, so want to check before I make a mess of this:
** I'm thinking that I should move those non-theme files into a new folder, which would be a sub-folder of wp-content. Is that the best way?
** Once I've moved them, do I adjust the WP database so links to the moved files will work? If so, how?
Suggestions will be much appreciated.

Why not install atahualpa 3.6.7 in a separate folder called atahualpa367 - keep the original also, then make a copy of all those files and put them into the atahualpa367 folder and then you can switch back and forth between the versions.

Don't be surprised if you run into some issues depending on how he coded the files for you.

juggledad -
Thanks for the tip. It saved me a bunch of time.
Followed the upgrade instructions, activated the theme in 3.6.7 -- unfortunately, the layout is messed up badly.
I'm guessing there are a bunch of customizations that were done. I've identified several files that have later dates that the 3.4.6 files, and am guessing they're the culprits.
I have the original 3.4.6 versions. Is there a way to compare the contents of two files? Notepad ++?
Thanks again for any suggestions.

I'm on a mac and have a great tool for comparing files called TextWrangler. I'm sure there is something on the PC side that will do it too.

There were several files that were patched in 3.6.4 - you can find the patches(bug fix's) in the 'Old Version fixes and change logs' subforum of the 'New Versions, & Updating' forum

juggledad -
Thanks. It looks like Notepad++ has a compare feature.
Will keep at it.

This is exactly the scenario where a child theme would be helpful. An official guide to using child themes with Atahualpa would be very nice.

you don't need child themes since all the theme changes/options are stored in the DB
seems to me this is a case of a coder doing something with a tool they didn't understand and couldn't/wouldn't admit it.

Not all changes are stored in the database, most commonly not the images (header, favicon and the like). Also not any custom php changes. No offense, but even Atahualpa will never be able to cater to everyones specific need.

Keeping added and changed files in a child theme makes moving/diffing those files a lot less painful on upgrade.