Jar creation for custom message using a subfolder

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Hi,

I am using ROS Kinetic on Ubuntu 16 to generate jar files for custom messages using genjava. Everytime I catkin_make, ROS will automatically build the packages and generate JAR artifacts for them which I can use in Java. If I simply create the ROS package and drop the msg folder with the custom msg without a subfolder it compiles just fine and creates the respective jar files. An example of this directory structure is:

catkin_ws/src/package A/msg/customMsg.msg

If I try to add a subfolder and the msg folder in it like so:

catkin_ws/src/package A/subfolder/msg/customMsg.msg

catkin_make fails at 100% with the jar generation portion giving the following message:

Failed to capture fingerprint of input files for task ':jar' property 'rootSpec$2$1' during up-to-date check "Could not copy MANIFEST.MF to "home/exampleUser/catkin_ws/build/examplePackage/java/examplePackage/build/tmp/jar/MANIFEST.MF'

I have already modified the CMakeLists.txt to include the subfolder by using the DIRECTORY tag inside add_message_files() otherwise the build fails a lot earlier.

What am I missing here? Any help is greatly appreciated.