I ran into this problem today after I needed to change the CRM URL on the Dev Server I am working with CRM 2015 on.
I had previously created both a Plugin project and a Web Resources project and used the CRM Explorer to browse these to extract items, setup new Plugin Steps, etc.
I was tweakign the CRM Dev server and discovered that I needed to modify the URL for the server in the Deployment Manager.
After doing so, my Visual Studio project stopped working correctly, and the CRM explorer would throw an error about
“No Organization has been specified“
Did some searching and came across this forum post.
I figured it out: informations about CRM Server are stored in *.suo file. I just deleted this file, opened my solution in VS and entered all informations for CRM Server connection. The suo file was regenerated automatically and I can work now with my CRM solution
The answer was the *.suo file in the same directory as the VS solution file. While the solution is closed, just delete or rename that file. When you re-load Visual Studio next time, you may still see the error, but you can then reconnect to the new CRM server or URL.