Installation profile warns about embedded repository

Problem/Motivation

I followed the Option B installation instructions here: https://www.drupal.org/docs/contributed-modules/intercept/installation-g... →

After installing Intercept, we got a working site, so we needed to commit our work and push to Pantheon.
- Installed Intercept according to Option B instructions.
- Then we did `git init` so we could do a commit.
- Then we did `git add .` and got the warning below about embedded repository.

warning: adding embedded git repository: web/modules/contrib/intercept
hint: You've added another git repository inside your current repository.
hint: Clones of the outer repository will not contain the contents of
hint: the embedded repository and will not know how to obtain it.
hint: If you meant to add a submodule, use:
hint:
hint: git submodule add web/modules/contrib/intercept
hint:
hint: If you added this path by mistake, you can remove it from the
hint: index with:
hint:
hint: git rm --cached web/modules/contrib/intercept
hint:
hint: See "git help submodule" for more information.
warning: adding embedded git repository: web/modules/contrib/tally
warning: adding embedded git repository: web/profiles/contrib/intercept_profile
warning: adding embedded git repository: web/themes/contrib/intercept_base

We weren't sure how to add the intercept module to our commit. Do we add it and ignore the warning above? Creating your own repo wasn't part of the documentation.

Thanks!