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https://jira.codehaus.org/browse/MASSEMBLY-285?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=288091#comment-288091
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Eric Daigneault commented on MASSEMBLY-285:
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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.

BUT....

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.
                
> regression: duplicate files added to the assembly
> -------------------------------------------------
>
>                 Key: MASSEMBLY-285
>                 URL: https://jira.codehaus.org/browse/MASSEMBLY-285
>             Project: Maven 2.x Assembly Plugin
>          Issue Type: Bug
>    Affects Versions: 2.2-beta-1
>            Reporter: Brett Porter
>            Assignee: John Casey
>            Priority: Blocker
>             Fix For: 2.2-beta-3
>
>
> I found that it was possible to add a file twice to the assembly through 
> different filesets (a zip file) so that when it extracted it prompted for 
> overwrite.
> It should error out or collapse the entries (as 2.1 did).

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