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We set up an Amazon EC2 instance and managed to WinSCP into it by setting up WinSSHD on the server.

As WinSSHD is commercial, we were looking for a free alternative and opted to try OpenSSH, which I have always heard good things about.

After installing Cygwin with OpenSSH and starting up OpenSSH from the Cygwin console, I attempted to WinSCP into the server from my computer, and got access to /root that contains files like Cygwin.bat and such.

I was wondering if I had done something wrong during the setup, or if I have to change the sshd_config file for it to work.

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You haven't setup a standard user. As such, you're connecting with root. Consider adding a regular user and specifying that users login credentials when connecting.

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