Minijar release
A new version (1.0-alpha-3) of minijar is available. For sure the biggest improvement is that (with the new vafer.org dependency release) the relocation now works for resources and reflection, too. It wraps the calls and pipes them through a static method to point them to the new location. This much superior to static rewriting of strings. Other than that more options (e.g. includes/excludes) are now available and the documentation has been improved.
...
<build>
<plugins>
<plugin>
<artifactId>minijar-maven-plugin</artifactId>
<groupId>org.codehaus.mojo</groupId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>ueberjar</goal>
</goals>
<configuration>
<stripUnusedClasses>false</stripUnusedClasses>
<includeDependencies>
<param>org.vafer:dependency</param>
</includeDependencies>
<includeDependenciesInRelocation>
<param>org.vafer:dependency</param>
</includeDependenciesInRelocation>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
...
Give it a try an let me know how it works for you!