Bouncy Castle unsigned entries Error running Jar-with-dependencies using Maven

Question

I am currently experiencing a problem trying to run an executable jar that used bouncy castle for decryption. Using maven, I create a jar-with-dependencies that upon running throws

java.util.jar.JarException: file: FileDecrypter-1.0-jar-with-dependencies.jar 
has unsigned entries - org/apache/commons/io/ByteOrderMark.class

Of course I researched this issue and found "Invalid signature file" when attempting to run a .jar but I'm not creating an uber-jar neither am I using a manifest file to create my jar.

My pom.xml:

<project xmlns="http://maven.apache.org/POM/4.0.0" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 
http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>FileDecrypter</groupId>
<artifactId>FileDecrypter</artifactId>
<version>1.0</version>

<dependencies>
<dependency>
    <groupId>commons-io</groupId>
    <artifactId>commons-io</artifactId>
    <version>2.4</version>
</dependency>
<dependency>
    <groupId>org.apache.commons</groupId>
    <artifactId>commons-vfs2</artifactId>
    <version>2.0</version>
</dependency>
<dependency>
    <groupId>commons-net</groupId>
    <artifactId>commons-net</artifactId>
    <version>3.3</version>
</dependency>
<dependency>
    <groupId>org.apache.logging.log4j</groupId>
    <artifactId>log4j-api</artifactId>
    <version>2.2</version>
</dependency>
<dependency>
    <groupId>org.apache.logging.log4j</groupId>
    <artifactId>log4j-core</artifactId>
    <version>2.2</version>
</dependency>
<dependency>
    <groupId>org.bouncycastle</groupId>
    <artifactId>bcprov-jdk15on</artifactId>
    <version>1.48</version>
</dependency>
<dependency>
    <groupId>org.bouncycastle</groupId>
    <artifactId>bcpg-jdk15on</artifactId>
    <version>1.48</version>
</dependency>
</dependencies>

<build>
<sourceDirectory>src</sourceDirectory>
 <resources>
  <resource>
    <directory>src</directory>
    <excludes>
      <exclude>**/*.java</exclude>
    </excludes>
  </resource>
 </resources>

 <plugins>
  <!-- download source code in Eclipse, best practice -->
 <plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-eclipse-plugin</artifactId>
    <version>2.9</version>
    <configuration>
        <downloadSources>true</downloadSources>
        <downloadJavadocs>false</downloadJavadocs>
    </configuration>
</plugin>

 <!-- Make this jar executable -->
<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-jar-plugin</artifactId>
    <version>2.6</version>
    <configuration>
        <excludes>
            <exclude>**/log4j.properties</exclude>
        </excludes>
        <archive>
            <manifest>
                <addClasspath>true</addClasspath>
                <mainClass>com.mps.main.DecryptInput</mainClass>
                <classpathPrefix>dependency-jars/</classpathPrefix>
            </manifest>
        </archive>
    </configuration>
</plugin>

<!-- Copy project dependency -->
<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-dependency-plugin</artifactId>
    <version>2.5.1</version>
    <executions>
        <execution>
            <id>copy-dependencies</id>
            <phase>package</phase>
            <goals>
                <goal>copy-dependencies</goal>
            </goals>
            <configuration>
                <!-- exclude junit, we need runtime dependency only -->
                <includeScope>runtime</includeScope>
                <outputDirectory>${project.build.directory}/dependency-  
jars/</outputDirectory>
            </configuration>
        </execution>
    </executions>
</plugin>

<!-- set jdk compiler -->
<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-compiler-plugin</artifactId>
    <version>3.3</version>
    <configuration>
      <verbose>true</verbose>
      <fork>true</fork>
      <executable>${JAVA_1_7_HOME}</executable>
      <compilerVersion>1.7</compilerVersion>
    </configuration>
</plugin>

 <!-- Maven Assembly Plugin -->
<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-assembly-plugin</artifactId>
    <version>2.4.1</version>
    <configuration>
        <!-- get all project dependencies -->
        <descriptorRefs>
            <descriptorRef>jar-with-dependencies</descriptorRef>
        </descriptorRefs>
        <!-- MainClass in mainfest make a executable jar -->
        <archive>
          <manifest>
            <mainClass>com.mps.main.DecryptInput</mainClass>
          </manifest>
        </archive>

    </configuration>
    <executions>
      <execution>
        <id>make-assembly</id>
                                  <!-- bind to the packaging phase -->
        <phase>package</phase> 
        <goals>
            <goal>single</goal>
        </goals>
      </execution>
    </executions>
</plugin>
</plugins>
</build>
</project>

Answer 1

I finally got it to work, although I was approaching the problem in the wrong way. Using the following code in my pom.xml, I was able to create a jar containing a manifest file that pointed to my dependencies:

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.5.1</version>
<executions>
    <execution>
        <id>copy-dependencies</id>
        <phase>package</phase>
        <goals>
            <goal>copy-dependencies</goal>
        </goals>
        <configuration>
            <!-- exclude junit, we need runtime dependency only -->
            <includeScope>runtime</includeScope>
            <outputDirectory>${project.build.directory}/dependency-  
jars/</outputDirectory>
        </configuration>
    </execution>
</executions>
</plugin>

Using my pom.xml and running "mvn package" in command-line while my present working directory is my current project workspace, a folder named "target" is created that contains my jar file "FileDecrypter.jar" and a folder with all of my jars named "dependency-jars". The manifest file inside of my execute jar points to the dependency-jar folder, which allows my bouncy-castle jars to remain signed.