OK I fixed this myself! I recalled doing this a few days ago (before I was dragged away and VM rebooted) : technet.microsoft.com/.../gg188575.aspx I'd unchecked HTTP and checked HTTPS and left it in that state. Even though we could access the CRM from browsers the plugin reg tool was failing. I'd even checked SSL in the reg tool to no avail. Going back to deployment manager and reverting the HTTPS to HTTP, worked and I can now see assemblies etc in the reg-tool!
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