sorry for the late reply.
A little bit of background. SSH stands for Secure SHell. At its core, it allows you to access a remote computer securely. Think of it as VPN on the fly. SSH is commonly used to on Linux/Unix systems to get remote access to the command line (like accessing the DOS prompt remotely). Windows systems do not have SSH natively, so you can download an open source program called PuTTY. PuTTY is a client for SSH as well as a program to access the serial port. It’s a very handy utility to have on your computer. To get PuTTY, go to http://www.chiark.greenend.org.uk/~sgtatham/putty/.
Look at the attached screencap. This is the way you set up the connection. In my case, the BBB was connected via the USB, and I was using the fixed IP address provided at factory - 192.168.7.2. You leave the port number at 22 (the default for SSH) and insure the connection type is SSH. That’s it! You click on the “Open” button. When you do that, you should see a slight delay, and on the very first time you connect via SSH, you will get a pop up window asking you to accept a key. The key looks like a massive MAC address (hexadecimal number). You accept that key, and then a second screen will open. You enter the user name (which would be root) and password (which is blank). After that, you get what looks like a DOS prompt - it may look like “root@beaglebone~#” This is the Linux equivalent of the “C:>” prompt.
It was through this prompt that I created the directory. The command to make the directory is:
mkdir /var/lib/cloud9 (then hit enter)
Once you have done this, reboot your Beagle Bone and your Cloud9 programming space will come back.
I hope this helps.