The short story is that this is not a good structure. A branch is not a 
good abstraction for keeping a certain part of the code separate from 
another. You're better off keeping the private code in a separate 
repository, and then integrate them at build- or runtime.

We've discussed a similar issue recently 
here: https://groups.google.com/d/msg/git-users/VlXh75VPVWU/7iv5R6AcfDkJ

On Monday, July 2, 2012 9:44:23 PM UTC+2, Japie wrote:
> Hi,
>  I have two branches in my project, A and B. A is the master branch and B 
> is from A but includes code which should never be public. 
>  When I write code that needs to go to both branches I create a new 
> branch from A, do the feature code, and then merge back into A and into B. 
> But some files from branch B, especially the build config files, which 
> includes extra directories, get changed back into the versions as in branch 
> A. What would the correct workflow for such a setup be?
>  regards

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