This issue will occur if you have installed VS to your non-system drive.
In that case you can workaround it by copying and merging the contents of the "~\Program Files\Microsoft Visual Studio 14.0\Common7\Ide\CommonExtensions\Microsoft\WebClient"
folder from the standard install location on the system drive to your custom location, and then running "devenv /setup" from an elevated VS developer command prompt. This bug will be fixed in the next public release.
The issue will also occur if you have upgraded to CTP6 directly from CTP5, without first uninstalling CTP5.
In that case the workaround is:
1. Go to Control Panel, choose Repair on Tools for Apache Cordova MSI.
- Verify that C:\Program Files (x86)\Microsoft Visual Studio 14.0\Common7\IDE\ProjectTemplates\JavaScript\Apache Cordova Apps\1033\blankCordovaJS is populated.
- From elevated developer command prompts run devenv /setup
Open VS and your Cordova project template is back.