Either version 2.2.2 of the Assembly plugin has a regression or the issue has not been fixed. I am currently creating zip files from the assembly that contains duplicate jar files.
Some background : I am using the assembly to create a zip file of an application. Why Zip ? because the application requires multiple configuration files and spans larger than just Java so I cannot use a uber Jar (I would prefer that but technical limitations out of my control force me otherwise).
This package is built correctly.
To make life simpler I made it possible to extend this package with a project that can add extra classes (plugins and such) and configuration from a standard layout in the project that gets picked up by the assembly and merged with the previous vanilla package. the end result is a fully assembled zip file with all the customized parts in the right place.
Now, behaviour changed across version wheras previously I would overwrite the original package with the content of the new one, now I have to start from the overrides and complete withe the original files. Easily fixed through changing the order I declared the filesets in the assembly. When using filesets strictly nothing gets added twice, though the replace was changed to skip which is a bit counter intuitive.
Since I extend some parts of the original system, I will share some dependencies with this one. These dependencies are already present in the original package and get added through a file set (I get the package and unzip it in a temporary folder where I integrate it`s content inthe assembly through a fileset).
I also add the dependencies of the new customized project, and these get added twice.
I think there is a regression here when filesets and dependencysets interact where if files are present in both they get added twice in the zip file. Now I would re-open this current task but it seems I cannot so I will open a sub task instead.