I'd imagine there is a 'new project from repo' option somewhere but I can't find it. Is there more to it than this, or am I missing something?
In Netbeans if you have a file as your active window then it will only commit that file. To commit multiple modified files right click on the name of the project in the Project Window (usually on the left of the screen--you can also go to "Window" in the menu and activate it there), select Git, and then select commit.
Use the Team menu, select "Git" > "Clone..."
Once the repo has been cloned into a local folder, NetBeans will give you the option to open the project.
Trying to create a project and then clone into it fails because the target folder is not completely empty.
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