Answer by Mohamed Mufeed for How to apply same set of changes to different repos using git?

After a bit of struggle I have managed to work it out. For future reference for any body having the same issue I am posting my solution here

first create the patch (thanks to Mureinik's answer)

git format-patch --ignore-space-change -1 <cimmit_hash>

then apply the patch using the unix patch utility instead of git am

 patch -p1 --binary --merge -l < ../path/to/your/patch/file

This will get you to a point where you can manage manually.