Right now with CDK 2.1 when you have a manual cdk install (i.e. using cdk.zip and then adding the vagrant box yourself), there will be no .cdk marker, so Runtime Detection will not work.

The only case where Runtime Detection will work is when you use the (as of now Windows-only) suite installer. At that point Runtime Detection will do its thing silently without you noticing.

The way I see it there are two options:
a) Create and upstream issue with CDK and ask them to include a basic .cdk in their zip
b) Make the runtime detection work without .cdk