Whenever I make changes to artifacts in my pom.xml that are different than those initially populated by Roo, any command executed in the Roo shell that relies on those artifacts will reset them to values that Roo likes, but which may be incompatible with my application.
For example, I have upgrade Spring-Data to v1.4.1.RELEASE. However, if I create a new repository via the Roo shell, Roo will overwrite my version to v1.2.0.RELEASE.
This is problematic, especially if/when my code relies on newer constructs not available in the older versions as referenced by Roo.
I have noticed this occurring with Spring-Data as well as javax.validation.validation-api, although I presume that it occurs with other libs as well.