I have the following dependency:
compile 'axis:axis-jaxrpc:1.4'
If you look at the POM file for that library, it has:
<relocation>
<groupId>org.apache.axis</groupId>
</relocation>
The result is the jar file getting added to the .classpath file twice. If I change my dependency to
compile 'org.apache.axis:axis-jaxrpc:1.4'
then the problem goes away.