Multiple Files of the Same Name in the META-INF folder of a JAR

I have the following issue:

I have multiple files of the same name in this single META-INF folder. I know that Android has packagingOptions to help solve this problem, but I do not know of any solutions for an executable JAR. Fortunately, the JAR runs fine by itself, but my problem extends to stopping other software that would also process that JAR file. I at least know that I can manually delete or rename files.

Thanks for your insight.