Para executar o maven-shade-plugin, eu tenho que usar o método descritoaqui devido a dependências assinadas, como mostrado aqui:

<plugin>
    <artifactId>maven-shade-plugin</artifactId>
    <executions>
        <execution>
            <phase>package</phase>
            <goals><goal>shade</goal></goals>
            <configuration>
                <filters>
                    <filter>
                        <!-- filter out signature files from signed dependencies, else repackaging fails with security ex -->
                        <artifact>*:*</artifact>
                        <excludes>
                            <exclude>META-INF/*.SF</exclude>
                            <exclude>META-INF/*.DSA</exclude>
                            <exclude>META-INF/*.RSA</exclude>
                        </excludes>
                    </filter>
                </filters>
            </configuration>
        </execution>
    </executions>
</plugin>

Pergunta: Como posso saberqual JAR causou falha no plug-in? Não parece ser o mais mencionado recentemente.

Cauda da saída de depuração:

[DEBUG] We have a duplicate org/jdom2/xpath/util/AbstractXPathCompiled.class in C:\Users\me\aaaa-1.11.0-SNAPSHOT.jar
[DEBUG] We have a duplicate org/jdom2/xpath/util/XPathDiagnosticImpl.class in C:\Users\me\aaaa-1.11.0-SNAPSHOT.jar
[DEBUG] Processing JAR C:\Users\me\bbbb-1.11.0-SNAPSHOT.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Retrievers JAR ................................ FAILURE [  9.581 s]
[INFO] Retrievers .................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 10.208 s
[INFO] Finished at: 2015-05-12T14:20:54-05:00
[INFO] Final Memory: 100M/726M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-shade-plugin:2.3:shade (default) on project aaa-retrievers-jar: Error creating shaded jar: Invalid signature file digest for Manifest main attributes -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-shade-plugin:2.3:shade (default) on project aaa-retrievers-jar: Error creating shaded jar: Invalid signature file digest for Manifest main attributes
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:216)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuild,er.java:108)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:76)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:116)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:361)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:155)
    at org.apache.maven.cli.MavenCli.execute(MavenCli.java:584)
    at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:213)
    at org.apache.maven.cli.MavenCli.main(MavenCli.java:157)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:483)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException: Error creating shaded jar: Invalid signature file digest for Manifest main attributes
    at org.apache.maven.plugins.shade.mojo.ShadeMojo.execute(ShadeMojo.java:566)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:133)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
    ... 19 more
Caused by: java.lang.SecurityException: Invalid signature file digest for Manifest main attributes
    at sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:284)
    at sun.security.util.SignatureFileVerifier.process(SignatureFileVerifier.java:238)
    at java.util.jar.JarVerifier.processEntry(JarVerifier.java:316)
    at java.util.jar.JarVerifier.update(JarVerifier.java:228)
    at java.util.jar.JarFile.initializeVerifier(JarFile.java:383)
    at java.util.jar.JarFile.getInputStream(JarFile.java:450)
    at org.apache.maven.plugins.shade.DefaultShader.shade(DefaultShader.java:147)
    at org.apache.maven.plugins.shade.mojo.ShadeMojo.execute(ShadeMojo.java:471)
    ... 21 more
[ERROR] 
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException