How to assembly a project after using proguard-maven-plugin - java

I am trying to add an obfuscation step while packaging my app. I supposed that I had to insert the Proguard plugin between the compiler plugin and the assembly (the assembly just put all of my app and dependencies into one single jar).
<build>
<finalName>myApp</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.2</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>com.github.wvengen</groupId>
<artifactId>proguard-maven-plugin</artifactId>
<version>2.0.11</version>
<executions>
<execution>
<id>obfuscation-packaging</id>
<phase>package</phase>
<goals>
<goal>proguard</goal>
</goals>
<configuration>
<proguardVersion>5.2</proguardVersion>
<obfuscate>true</obfuscate>
<attach>true</attach>
<appendClassifier>false</appendClassifier>
<addMavenDescriptor>true</addMavenDescriptor>
<injar>${project.build.finalName}.jar</injar>
<outjar>${project.build.finalName}.jar</outjar>
<injarNotExistsSkip>true</injarNotExistsSkip>
<libs>
<lib>${java.home}/lib/rt.jar</lib>
</libs>
<options>
...
</options>
</configuration>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>net.sf.proguard</groupId>
<artifactId>proguard-base</artifactId>
<version>5.2</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.4</version>
<executions>
<execution>
<id>create-executable-jar</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptors>
<descriptor>assembly.xml</descriptor>
</descriptors>
<archive>
<manifest>
<mainClass>myApp.Main</mainClass>
</manifest>
</archive>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
The compiling works fine, so does the obfuscation, but the assembly seems to be made with the normal jar, not the obfuscated one.
Here is my assembly.xml if needed:
<?xml version="1.0" encoding="UTF-8"?>
<assembly>
<id>with-dep</id>
<formats>
<format>jar</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<dependencySets>
<dependencySet>
<!-- unpack les dépendances avant de les inclures dans le jar final de l'application -->
<unpack>true</unpack>
<scope>runtime</scope>
<useProjectArtifact>false</useProjectArtifact>
</dependencySet>
</dependencySets>
<fileSets>
<fileSet>
<directory>${project.build.outputDirectory}</directory>
<outputDirectory></outputDirectory>
</fileSet>
</fileSets>
</assembly>
In the end, myApp.jar is obfuscated, but myApp-with-dep.jar is not...
I also precise that I'm not quite sure about the configuration of my proguard plugin. If you see something weird, say it.
Thanks for your time.


I solved it by abandoning maven assembly plugin to shade plugin. Hope it might help someone.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.2</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<!--Obfuscation-->
<plugin>
<groupId>com.github.wvengen</groupId>
<artifactId>proguard-maven-plugin</artifactId>
<version>2.0.13</version>
<executions>
<execution>
<id>obfuscation-packaging</id>
<phase>package</phase>
<goals>
<goal>proguard</goal>
</goals>
<configuration>
<proguardVersion>5.2</proguardVersion>
<obfuscate>true</obfuscate>
<addMavenDescriptor>true</addMavenDescriptor>
<injar>${project.build.finalName}.jar</injar>
<outjar>${project.build.finalName}.jar</outjar>
<mappingFileName>proguard_map.txt</mappingFileName>
<seedFileName>proguard_seed.txt</seedFileName>
<libs>
<lib>${java.home}/lib/rt.jar</lib>
</libs>
<options>
...
</options>
</configuration>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>net.sf.proguard</groupId>
<artifactId>proguard-base</artifactId>
<version>5.2</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>xxx.Main</mainClass>
</transformer>
</transformers>
<filters>
<filter>
<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>

Related

"java.lang.ClassCastException" error while running scalatest through maven

I run my test cases successfully through Intellij.
But I got the "java.lang.ClassCastException" error when I run scalatest through "mvn test" command.
It's really weird. The reason might be that my scala program calls java program because some of the pure scala test cases don't have this kind of error.
Does someone know how to fix this issue?
Cause: java.lang.ClassCastException: cannot assign instance of scala.collection.immutable.List$SerializationProxy to field org.apache.spark.rdd.RDD.org$apache$spark$rdd$RDD$$dependencies_ of type scala.collection.Seq in instance of org.apache.spark.rdd.MapPartitionsRDD at java.io.ObjectStreamClass$FieldReflector.setObjFieldValues(ObjectStreamClass.java:2287) at java.io.ObjectStreamClass.setObjFieldValues(ObjectStreamClass.java:1417) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2293) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2211) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2069) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1573) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2287) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2211) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2069) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1573) ...
Also here is the part of my pom.xml
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.7</version>
</plugin>
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<version>1.0</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<configuration>
<reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
<junitxml>.</junitxml>
<filereports>WDF TestSuite.txt</filereports>
</configuration>
<executions>
<execution>
<id>test</id>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>compile</goal>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<configuration>
<keepDependenciesWithProvidedScope>true</keepDependenciesWithProvidedScope>
<createDependencyReducedPom>true</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<executions>
<execution>
<id>log4j-plugin-processor</id>
<goals>
<goal>compile</goal>
</goals>
<phase>process-classes</phase>
<configuration>
<proc>only</proc>
<annotationProcessors>
<annotationProcessor>
org.apache.logging.log4j.core.config.plugins.processor.PluginProcessor
</annotationProcessor>
</annotationProcessors>
<source>8</source>
<target>8</target>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>```

Invalid signature file digest for Manifest main attributes while running jar

I am trying to run the jar file of my project. I am working on STS. a But every time i am trying to run my jar file its giving me exception like Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.SecurityException: Invalid signature file digest for Manifest main attributes
my pom.xml is
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.3</version>
<executions>
<!-- <execution> <id>copy-dependencies</id> <phase>prepare-package</phase>
<goals> <goal>copy-dependencies</goal> </goals> <configuration> <outputDirectory>
${project.build.directory}/${environment}/dependencies ${project.build.directory}/dependency-jars/
</outputDirectory> <overWriteReleases>false</overWriteReleases> <overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer> <includeScope>runtime</includeScope>
</configuration> </execution> -->
<execution>
<id>unpack-dependencies</id>
<phase>package</phase>
<goals>
<goal>unpack-dependencies</goal>
</goals>
<!-- <configuration> <excludeScope>system</excludeScope> <excludes>META-INF/*.SF</excludes>
<excludes>META-INF/*.DSA</excludes> <excludes>META-INF/*.RSA</excludes> <excludeGroupIds>junit,org.mockito,org.hamcrest</excludeGroupIds>
<outputDirectory>${project.build.directory}/dependency-jars/</outputDirectory>
</configuration> -->
<configuration>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<!-- Additional configuration. -->
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.5</version>
<executions>
<execution>
<id>copy-resources</id>
<!-- here the phase you need -->
<phase>validate</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/resources
</outputDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<mainClass>com.emo.process.EmoBatchProcess</mainClass>
<classpathPrefix>dependency-jars/</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>1.4</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>EMOBatchProcess</finalName>
<outputDirectory>${basedir}/target/LOCAL</outputDirectory>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>all</shadedClassifierName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>

How to add other directory while making zip archive using maven package command?

I have below project maven project :
I would like to add resource and scenarios directory in zip created by mvn package command.
I have added zip.xml assembly and required plugin in pom.xml:
src/main/assembly/zip.xml
<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
<id>zip</id>
<formats>
<format>zip</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<fileSets>
<fileSet>
<directory>${project.build.directory}</directory>
<outputDirectory>./</outputDirectory>
<includes>
<include>*.jar</include>
</includes>
</fileSet>
<fileSet>
<directory>${project.build.directory}</directory>
<outputDirectory>./</outputDirectory>
<includes>
<include>/dependency-jars/</include>
</includes>
</fileSet>
</fileSets>
</assembly>
And this is pom.xml:
<packaging>jar</packaging>
<dependencies>
.....
</dependencies>
<build>
<testResources>
<testResource>
<directory>${project.basedir}/config</directory>
</testResource>
</testResources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<compilerVersion>${sourceVersion}</compilerVersion>
<source>${sourceVersion}</source>
<target>${targetVersion}</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/dependency-jars/</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<goals>
<goal>test-jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.5.4</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<finalName>zip-with-dependencies</finalName>
<appendAssemblyId>false</appendAssemblyId>
<descriptors>
<descriptor>src/main/assembly/zip.xml</descriptor>
</descriptors>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>aspectj-maven-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>test-compile</id>
<goals>
<goal>test-compile</goal>
</goals>
</execution>
</executions>
<configuration>
<source>${sourceVersion}</source>
<target>${targetVersion}</target>
<showWeaveInfo>true</showWeaveInfo>
<complianceLevel>${sourceVersion}</complianceLevel>
<aspectLibraries>
<aspectLibrary>
<groupId>com.qmetry</groupId>
<artifactId>qaf</artifactId>
</aspectLibrary>
</aspectLibraries>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.9</version>
<configuration>
<suiteXmlFiles>
<suiteXmlFile>${testSuiteFile}</suiteXmlFile>
</suiteXmlFiles>
<reportsDirectory>${test.results.dir}/${run.time}</reportsDirectory>
<systemPropertyVariables>
<org.uncommons.reportng.xml-dialect>testng</org.uncommons.reportng.xml-dialect>
<org.uncommons.reportng.escape-output>false</org.uncommons.reportng.escape-output>
<log4j.configuration>file:///${resource.dir}/log4j.properties</log4j.configuration>
<outputDir>${output.dir}</outputDir>
<test.results.dir>${output.dir}/html</test.results.dir>
<json.report.root.dir>${test.results.dir}</json.report.root.dir>
<json.report.dir>${output.dir}/json</json.report.dir>
<selenium.screenshots.dir>${output.dir}/img</selenium.screenshots.dir>
<selenium.screenshots.relative.path>../img</selenium.screenshots.relative.path>
</systemPropertyVariables>
</configuration>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.codehaus.mojo</groupId>
<artifactId>aspectj-maven-plugin</artifactId>
<versionRange>[1.0,)</versionRange>
<goals>
<goal>test-compile</goal>
<goal>compile</goal>
</goals>
</pluginExecutionFilter>
<action>
<execute />
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
Any help would be great appreciated. Thanks

I figured it out. We can use <testResources> in pom.xml to add required directory. e.g.
<testResources>
<testResource>
<directory>${project.basedir}/resources</directory>
</testResource>
</testResources>

.exe is not created when using launch4j and maven

I'm trying to create an exe file for my JAVA project using launch4j and Maven.
Here is my pom.xml
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.0</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.4</version>
<configuration>
<descriptorRefs>
<descriptortRef>jar-with-dependencies</descriptortRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>dev.main.App</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>1.7.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
<configuration>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>shaded</shadedClassifierName>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>dev.main.App</mainClass>
</transformer>
</transformers>
</configuration>
</plugin>
<plugin>
<groupId>com.akathist.maven.plugins.launch4j</groupId>
<artifactId>launch4j-maven-plugin</artifactId>
<version>1.5.1</version>
<executions>
<execution>
<id>l4j-clui</id>
<phase>package</phase>
<goals>
<goal>launch4j</goal>
</goals>
<configuration>
<headerType>console</headerType>
<jar>${project.build.directory}/target/App-jar-with-dependencies.jar</jar>
<outfile>${project.build.directory}/target/App.exe</outfile>
<downloadUrl>http://java.com/download</downloadUrl>
<classPath>
<mainClass>dev.main.App</mainClass>
</classPath>
<jre>
<minVersion>1.6.0</minVersion>
<jdkPreference>preferJre</jdkPreference>
</jre>
<versionInfo>
<fileVersion>1.0.0.0</fileVersion>
<txtFileVersion>${project.version}</txtFileVersion>
<fileDescription>${project.name}</fileDescription>
<copyright>C</copyright>
<productVersion>1.0.0.0</productVersion>
<txtProductVersion>1.0.0.0</txtProductVersion>
<productName>${project.name}</productName>
<internalName>AppName</internalName>
<originalFilename>App.exe</originalFilename>
</versionInfo>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
I run : mvn clean compile assembly:single to create my jar app with all Maven dependencies.
To create the .exe I do : mvn package but nothing is created under target folder.
Am I missing a goal or a configuration ?
Ismail

Well, I'm not an expert on maven, but the <pluginManagement> tag looks fishy to me. When I get the Maven POM documentation right, you want a plain <plugins> Element.

Maven, Jar does not contain the MAIN project jar

I am using maven to build my project. I wanted to create assembly jar including some of the dependencies, so I wrote my custom assembly descriptor.
POM.XML
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.guavus.exporter.Exporter</mainClass>
</manifest>
</archive>
<descriptors>
<descriptor>/Users/archit.thakur/Documents/Code_dev_cdn_mapreduce/exporter/src/main/assembly/configurator.xml</descriptor>
<!-- <descriptorRef>jar-with-dependencies</descriptorRef> -->
</descriptors>
<finalName>Exporter-${project.version}</finalName>
<appendAssemblyId>false</appendAssemblyId>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.1</version>
<executions>
<execution>
<id>default-jar</id>
<phase>none</phase>
</execution>
</executions>
</plugin>
ASSEMBLY DESCRIPTOR :
<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
<id>dep</id>
<formats>
<format>jar</format>
</formats>
<dependencySets>
<dependencySet>
<outputDirectory>${project.artifactId}</outputDirectory>
<unpack>true</unpack>
<useProjectArtifact>true</useProjectArtifact>
<includes>
<include>log4j:log4j</include>
<include>org.slf4j:slf4j-api</include>
<include>ch.qos.logback:logback-access</include>
<include>ch.qos.logback:logback-classic</include>
<include>ch.qos.logback:logback-core</include>
</includes>
</dependencySet>
</dependencySets>
</assembly>
The problem is, now it is creating jar only having dependency jars. and not making jar out of my code and including it in the final jar.

Try to use the Shade plugin :
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>1.2.2</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>com.app.MyMainClass</mainClass>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.eclipse.swt.win32.win32:x86</artifact>
<excludes>
<exclude>META-INF/eclipse.inf</exclude>
<exclude>META-INF/ECLIPSE.RSA</exclude>
<exclude>META-INF/ECLIPSE.SF</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
<configuration>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
</plugin>
</plugins>
<resources>
<resource>
<directory>src/main/resources</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
</build>

<fileset>...my classes... </fileset>
Adding the tag in the assembly configurator/descriptor resolved the issue.
Thanks to this comment:
Maybe try adding a fileSet for everything in the target/classes directory? (Don't remember the POM variable reference offhand sorry...) – Charlie Jan 22 at 7:21

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