Currently the archive report for each JAR file lists its locations and their version number; or lack of same.
The idea is to include an 'Action' report where the tool reports various actions that the developer need to look at (see https://jira.jboss.org/jira/browse/TTALE-28).
First on the list is the issue you talk about -- Eliminate JAR files with different version identifier (https://jira.jboss.org/jira/browse/TTALE-29).
Feel free to open a thread with these issue identifiers to discuss the design and implementation of this functionality.
This has been implemented - 1.0.Beta2 will have this functionality