johnga:
The mystery is:
What exactly am I looking for? Once I compare my files, am I looking for something that is not in my files that should be, or am I looking for something that is in my files that shouldn't be. Is there an explanation of what this new security feature does and which files it involves so people that don't know a lot about coding stand a chance of finding where they went wrong?
New lines were added to the original files.
In some cases, existing lines were changed.
And, in your customized files, you have made some changes of some sort ... otherwise you wouldn't have copied those files into your custom template folder, right?
When comparing the files, you should see the differences highlighted.
You need to compare the files and integrate the "new" and/or "changed" stuff from the master files ... into your customized files.
One thing that makes it easier is to do a compare of the "old" master file vs your "old" customized file ... so you can clearly see the changes you have made. Then when you're merging the "new" master file contents into your customized file, you'll know whether the changes are affecting one of your intended customizations.
Things that are just "new" from the "new" file can be copied over into your custom file directly.
Things that are changed in the new file but also affect a customization you had made in your custom file, will require some careful re-customizing based on the new file contents.
In some cases (not likely with the files in this particular upgrade) some of your customized files may have to be dumped and the customization redone using the new version of the file. This isn't very common unless huge changes were required in the master file or if you did extensive customizations to the file for your own purposes. In these cases, comparing "old" default vs "old" customized will show you very quickly how you had changed your file, and give you a clue where to start.
You need to do this for all files on your site ... all the default files, as well as all your customized files.
It sounds a whole lot more complicated than it is. It takes a bit of time, but is generally fairly straightforward.
This is largely the same concept described in the upgrade documentation in the /docs/ folder of your site, and also in the FAQ area. Those docs contain a bit more information about the procedure, and also reference how to do the database side, which contains all your product/customer/order data.
And here I am off topic again :(