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http://jira.codehaus.org/browse/MASSEMBLY-416?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=179578#action_179578
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Grzegorz Slowikowski commented on MASSEMBLY-416:
------------------------------------------------

I found the error. It is still present in the just released version of assembly 
plugin.
the problem is in plexus-archiver library.

Assembly is being built from two sources: 
"target/massembly-416-1.0-SNAPSHOT.jar" and "target/classes" directory.

org.codehaus.plexus.archiver.AbstractArchiver contains "seenEntries" HashSet
The keys added there from "target/massembly-416-1.0-SNAPSHOT.jar" are:
META-INF/
META-INF/MANIFEST-MF
test/
test/App.class
META-INF/maven/
META-INF/maven/test/
META-INF/maven/test/massembly-416/
META-INF/maven/test/massembly-416/pom.xml
META-INF/maven/test/massembly-416/pom.properties
and the keys added there from "target/classes" are:
test <-- without trailing slash
test\\App.class <-- with double backslash instead of single slash

As you can see the second ones are not normalized (AbstractArchiver line 495 - 
no normalization, but there should be something like in AbstractZipArchiver 
lines 410 and 419; in other words the name should be normalized before adding 
it as a key to "seenEntries" HashSet).

Do you need more details? The logs don't tell the truth, because the names 
there are after normalization and don't match with the keys in "seenEntries".

Btw, why the contents of  "classes" dir is added to the assembly? If you add 
the contents of the jar file and you have some shading for example the class 
files shouldn't be added to the assembly. Adding them could make sense only if 
you create the assembly before "package" phase, but this does not make sense to 
me.

> outputDirectory default value in fileSet seems changed; now seems to use 
> directory name of fileSet sourcedir
> ------------------------------------------------------------------------------------------------------------
>
>                 Key: MASSEMBLY-416
>                 URL: http://jira.codehaus.org/browse/MASSEMBLY-416
>             Project: Maven 2.x Assembly Plugin
>          Issue Type: Bug
>    Affects Versions: 2.2-beta-3
>            Reporter: John Casey
>            Assignee: John Casey
>            Priority: Blocker
>             Fix For: 2.2-beta-4
>
>         Attachments: massembly-416-1.0-SNAPSHOT-jar-with-dependencies.jar, 
> massembly-416-2.jar, massembly-416-jar-listing.txt, massembly-416.zip
>
>
> From Grzegorz Slowikowski on the d...@maven mailing list ([VOTE] 
> maven-assembly-plugin 2.2-beta-4 thread):
> {noformat}
> Hi
> With this configuration:
>    <pluginRepositories>
>        <pluginRepository>
>            <id>maven-staging-031</id>
>            <name>maven-staging-031</name>
>            
> <url>https://repository.apache.org/content/repositories/maven-staging-031</url>
>        </pluginRepository>
>    </pluginRepositories>
>    <build>
>        <plugins>
>            <plugin>
>                <groupId>org.apache.maven.plugins</groupId>
>                <artifactId>maven-assembly-plugin</artifactId>
>                <version>2.2-beta-4</version>
>                <configuration>
>                    <descriptorRefs>
>                        <descriptorRef>jar-with-dependencies</descriptorRef>
>                    </descriptorRefs>
>                </configuration>
>                <executions>
>                    <execution>
>                        <id>make-assembly</id>
>                        <phase>package</phase>
>                        <goals>
>                            <goal>single</goal>
>                        </goals>
>                    </execution>
>                </executions>
>            </plugin>
>        </plugins>
>    </build>
> I have "target" folder/package inside jar-with-dependencies archive which 
> contains copies of my project classes (they are in the normal
> package structure within this archive too).
> ...
> {noformat}

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