Git packages can be added via using their git link, this is the url ending in .git, and not the url of the repository page.
Sometimes these packages are hosted on OpenUPM, in these cases you can follow these steps to easily add and maintain packages to your project.
As of 2019.3.4.f1 (and 2020.1.a21) git urls for packages supports subfolders.
To update a git package with new changes, remove the lock from the packages-lock.json file.
You can find this file in your Packages folder at the root of your project. The lock is the block of json that relates to your package.
If you don't have a packages-lock.json file, then the manifest.json file should contain the lock near the bottom of the json.
Unity, huh, how?