We have a build script for installing and building Cordova from source control that begins with the line:
cordova create bin com.example.domain APPNAME --link-to=www
Where www is our existing app code (html, css, js etc.)
We've been running this build script on new deployments just fine for 6 months or so, and its behaviour until this version has been to create a simlink in the newly-created 'bin' folder to our existing app in 'www'; however, as of 6.3.0 this is no longer working. The command creates the bin folder, but it only contains the default 'Hello Cordova' application.
--copy-from still seems to be working (although is marked as deprecated), so we can work around this issue, but it's not appropriate for our deployment and development process.