Purging all the files doesn't get rid of the history. You need to create a branch that has no history first, and the add your config files. These days git checkout has a --orphan option that makes a branch with no history. Here's the information on the --orphan option:
--orphan <new_branch>
Create a new orphan branch, named <new_branch>, started from <start_point> and switch to it. The first commit made on this new branch will have no parents and it will be the root of a new history totally disconnected from all the other branches and commits.
The index and the working tree are adjusted as if you had previously run "git checkout <start_point>". This allows you to start a new history that records a set of paths similar to <start_point> by easily running "git commit -a" to make the root commit.
This can be useful when you want to publish the tree from a commit without exposing its full history. You might want to do this to publish an open source branch of a project whose current tree is "clean", but whose full history contains proprietary or otherwise encumbered bits of code.
If you want to start a disconnected history that records a set of paths that is totally different from the one of <start_point>, then you should clear the index and the working tree right after creating the orphan branch by running "git rm -rf ." from the top level of the working tree. Afterwards you will be ready to prepare your new files, repopulating the working tree, by copying them from elsewhere, extracting a tarball, etc.
Here's a link to the documentation for checkout. You can also run git help checkout as well.
Once you've created your branch without history, then when you push it to the server, it won't have that history either. FWIW, it helps me to think of git push as "make the remote branch look the same as my local one". So if you have history, and push, it will have history. If you don't, then the pushed branch won't.
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