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my application needs multiple jars to work. Since it is a desktop application i can not hold the user responsible of installing. So in my build script i unzip the jars content in to my build directory delete manifest files, compile my software and jar it again. Everything works as it should my question is are there any long term side effects to this process?
In the past, there were JARs with weird content (like the DB2 driver which contains
com.ibmandcom.IBM; after decompressing in a Windows filesystem, those two packages would be merged).The only issue you need to be aware of are signed jars and other files in META-INF which might have the same name in multiple source JARs.
A simple solution for all these issues is to use One-JAR. It allows to wrap several JARs into one without unpacking them, first. And read this answer: Easiest way to merge a release into one JAR file