Git: Two initial commits

You need to create an orphan branch:

git checkout --orphan <branch>

git checkout has an option for exactly such use case: --orphan.

From the Git manual:

--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.

Also, the man says explicitly:

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.

Apart from using the checkout --orphan method, you can as well create a separate repository in your other code base, make the initial commit, and then push to the other repository (or from the other repository pull from this one)

cd old-code
git init
git add .
git commit -m 'Initial commit of historical codebase'
git push ../path/to/current/code/repository master:historical

After that you can remove the repository again (rm -rf old-code/.git) if you don't need it (but it shouldn't hurt)