Upgrading to El Capitan

That would only effect new users, no? What kind of environment are you dealing with where you need the contents of that folder to be intact? A lab? Shared computers? You should really look at what you're putting in User Template and see if you can make use of custom config profiles where possible and/or scripts and launch agents where it makes sense.

I individually package any files I add to the User Template folder. When I run an in-place upgrade, I have a policy that re-distributes/re-installs the packages that go into the User Template after the upgrade has completed.

But I agree with @bpavlov - you should look to see if configuration profiles and scripts can reduce what you place in there. I'm down to only a handful of settings that are easier to drop into the User Template folder than to script it out at the moment due to time constraints.

~Ted

Correct, this is only affecting new users. It is in labs at our college and we clear out the AD profiles between semesters. Potentially, I would like to eliminate using the user template as much as possible. Personally though, I have just not done much with custom config profiles.

When it comes to custom config profiles and scripting the settings. Are you saying when I need to customize the home settings for browsers or specific settings for applications, I should/could use the associated .plists in custom config profiles? I ask because I have not done that in the past. I have always wrapped the needed settings into the package of the application and installed using FEU and FUT.

Mick

Not guaranteed to work for all apps, but yes some apps can have their settings managed via custom config profile. You would basically look at the plist file on the computer for that particular and look at settings you want to manage. You should only have the preferences that you want managed in that plist so as to avoid managing settings that you don't want managed which basically means you will be left with a pretty bare bones plist. There are already OS X payloads in config profiles which might let you do certain things as well for Safari. Google Chrome has their own custom config profile options as well that you can use. Do a search on JAMF Nation for previous threads where that's discussed. Anything questions regarding a specific app or setting, feel free to ask.

By the way, you can create a custom profile by creating a new config profile and selecting the custom payload option and uploading your PLIST. Or if you've got a .mobileconfig file already generated (could have been done with Profile Manager, a tool like MCXtoProfile, or any other mechanism that lets you generated config profiles) then you can upload it by clicking on the Configuration Profiles page and click on "Upload".