Use [GNU Stow](https://www.gnu.org/software/stow/) (`apt install stow`, etc.). The repo has a `.stowrc` which should target your home directory as the installation directory, but in some cases the `~` may not be evaluated and you'll have to specify `--target="$HOME"`.
Most of my git configuration lives in `~/.config/git/personal.gitconfig`, which is `include`d from `~/.gitconfig`. I do this to separate system-specific configuration that may be set by automated tools (i.e. the Github CLI setting up credential managers for guthub.com and gist.github.com) from my personal, cross-platform configuration (e.g. my identity and aliases).
Keep configuration that should be synced between computers in the `personal.gitconfig` file, and after cloning the repository, consider telling Git to ignore local changes to the main `.gitconfig` file: