Not overwriting a .git when I build a distill website

So I have two folders, lets call them

+== distill_project
+== public_site

The reason to do it this way is so I can have a public repository with my site, and a private repository with the .R files of my site. The problem is that every time I built the site, distill then proceeds to destroy the public_site .git, and it breaks my repository.

Is there any way that I can build the site without destroying the .git folder?

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