I want to develop an application that will manage users and permissions on Sharepoint. I don't want to add apps or parts to Sharepoint, just manage users and permissions. Here are my questions:
Thank you for any assistance you can give me.
If you're using SharePoint online,you could use SharePoint CSOM api for such requirement.
This can be done in several different solutions(PowerShell/client side app/Azure app etc.). Suppose you develop a cosole/winform application, you just need Visual Studio and install CSOM in your server.
https://www.nuget.org/packages/Microsoft.SharePointOnline.CSOM