I've done some reading on this but figured a specific post might be helpful.
Let's say I'm using FuelPHP framework on some custom projects, and those guys release a new update to the framework. My project already has a GIT repository of the project with all my custom scripts/views/libraries, etc.
Can I add the updated framework as a remote, and pull from it? Will it update the framework files without screwing up all of the custom work I did building the app? I'm trying to take my use of GIT to the next level, making it easy to update frameworks and deploy to my servers.
I'd take a look at using Git Submodules. That way, you can use Fuel almost as it's own repository, that can be updated and pulled independent from the rest of your structure.