C:\mbed\xxx>yt build
warning: dependencies of mbed-thread-example are pegged by yotta-shrinkwrap.json
warning: dependencies of mbed-thread-example are pegged by yotta-shrinkwrap.json
info: generate for target: ...
warning: nothing to build!
This happens because the module.json (and shrinkwrap) is parsed separately by the build and install steps, and this message is emitted when the file is parsed, but you're right that it shouldn't be.
yotta version 0.13.0