Two days ago I downloaded and installed the latest Kicad. While doing so I noticed that part libaries were a separate download. So I installed Git, and cloned the libaries into the directory: “C:\Kicad User Libraries\Git”.
Then I ran Kicad and found that the Kicad installation already included a part library which is located at: “C:\Program Files\KiCad\share\kicad”
Do these libraries contain the same part data? If not, what are the best practices for using them together?
Should Git have been used to synchronize the data at “C:\Program Files\KiCad\share\kicad” instead of cloning to as new directory?
Yes, but the libraries are developed through git, and if you want to keep up to date with all possible changes, you have to download or update them separately. This doesn’t matter much for v5.1 because all actual development, i.e. adding new parts, is happening in 5.99 branch which isn’t compatible with 5.1. You would hardly gain anything by updating 5.1 libraries through git. If there are bugfixes (I don’t know if there are any for 5.1), they would come with new KiCad bugfix releases in the 5.1.x Windows installer.
In general you don’t have to manage the libraries separately on Windows unless you have some specific need. Just use the ones which come with the installer.