I have a customized fork of CodeIgniter that I use as a standard baseline for several projects. Recently, I've made significant improvements in this repo that I want to use to update the client projects that use it. What I can't seem to figure out is how to pull in the changes to a client project.

So I have:

Baseline:
A--B--C--D--E

Client cloned @ C
C'--D'--E'

And I want to update the client repo to E from the Baseline project.

I've tried rebase, and it has erased the files not present in the baseline project (views and such), and creates a bunch of conflicts that really don't need to be conflicts with things like the default HTML5 boilerplate that I use.

Is there an option for rebase that I should be using? Is there a different way to approach it? Do I need a bunch of .gitignores for the content directories?