Empty directories in jar

What steps will reproduce the problem?
1. Create a jar with say google guava (com.google.*) and your code 
(com.myproject.*)
2. Create rule to move guava into your namespace:
rule pattern: "com.google.**", result: "com.myproject.libs.com.google.@1"

What is the expected output? What do you see instead?
Expected :
1. The resulting jar does have the class files moved into appropriate folders 
(under com/myproject/libs/com/google/)
YES.
2. Empty folders of guava deleted from the jar
eg -(com/google/), (com/google/common)
NO.

Actual:
The folders from all the moved classes remain in the jar.

What version of the product are you using? On what operating system?
JarJar 1.3. Windows 8. Gradle

Please provide any additional information below.
Noticed on previous versions of jarjar too.

Original issue reported on code.google.com by prashant...@gmail.com on 3 Mar 2013 at 9:11

runt18 / jarjar

Empty directories in jar #60