Worklight does not provide this ability. IMO this is because what you're asking for is not inline with the thinking and intended usage of the Direct Update feature.
Direct Update is meant as a way to quickly provide fixes after having already released an app version to the store, for example in cases such as:
- discovery of minor or major UI or logic bugs you've found in the app, or
- for closing security holes that have been found
This is all happening to the same app version (lets say 3.0.1). Consider these as 3.0.1.build releases. or something.
It is not meant as a way of releasing new versions of the app. For this purpose use the conventional and appropriate way of releasing new app versions.
If you want to change the app version (which should coincide with a new app release), then you need to increase it in application-descriptor.xml
(and other Worklight-related tasks), create a new binary and upload it to store, which users are then able to update and will see the new version number (lets say 3.0.2).