Better update routine?

One possible project structure:
- application ... for all *your* logic
- ci3 ... the CodeIgniter3 download/composer/whatever
- public ... your public facing document root

With a new app, copy public & application from "ci3" to your project root, as a starting point for your app,

*index.php* from CI would go inside "public", and would have to be modified so that system="../ci3/system" and application="../application"

Configure your web server or virtual host to use your project's "public" folder as document root.

Whenever a new version of CI comes out, replace your "ci3" folder (clone/download/composer/whatever).
You then need to check "ci3/index.php" to see if any changes need to made to your "public/index.php".
You also need to check your "application/..." files to see if there are changes in "ci3/application/..." - those are likely to be mostly (or even only) in the "config" subfolder.

No constant merging, just checking on new release.
Your application is intact & not clobbered by an update, nor is your public folder.

Works for me.

Thanks for the input. But this still does not eliminate the manual comparison of config files in the application folder when updating. I think I'll see if I can find an application that can automatically check two directories against each other (just like git does) and then let me decide what to do when files are different ... wonder whether this will do: www.sublimerge.com (or something the like).