On our network, users connect to a central server to use ArcGIS, so ArcGIS isn't newly installed for each user, but each server user running ArcGIS for the first time would normally get an empty list of folder connections.
In older versions of Windows, we used to manage this by copying the Esri user profile from a user who had folder connections set up in the desired way to the "Default" user profile. The key file was ArcCatalog.gx, which resided in %APPDATA%\Esri\DesktopN.N\ArcCatalog. Users starting ArcGIS for the first time would have the default user profile copied to their own user profile automatically by Windows. Unfortunately, later versions of Windows (8, 2012, 10, 2016) don't use the default user profile anymore. I'm at a loss as to how to accomplish my task under these newer versions, but this idea could help in both the shared server case and the separate installations case.
There is a way to share Folder connections: How To: Share folder connections in ArcCatalog with other machines
But if I use this way, I overwrite the existing User settings, it would be fine, if there is the possibility to have "System-Folder Connections" and "User Folder Connections" like the "Toolboxes"
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