How can I use git to help me merge a patch with the new directory structure

[Carl Sorensen]

As you're aware, I've been working on a patch for autobeaming.

It affects c++, scheme, and documentation files.

Now I want to apply the patch to master.  But the problem is that all of the
documentation files have moved to Documentation/ISOLANG/notation  instead of
Documentation/ISOLANG/user

So this seems to break any means of making my patch apply.

Any git gurus out there who have an idea of how I can do this without having
to manually apply patches made between the files in the different
directories?

Any help would be appreciated; right now I feel like all of my work on
autobeaming is in shambles and I'm going to have to do it all over again.

Thanks,

Carl