Much-Assembly-Required/Server/pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<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>


    <build>

        <plugins>
            <plugin>
                <artifactId>maven-resources-plugin</artifactId>
                <version>3.0.2</version>
                <executions>
                    <execution>
                        <id>default-resources</id>
                        <!-- here the phase you need -->
                        <phase>prepare-package</phase>
                        <goals>
                            <goal>resources</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>../target/</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>../Server/src/main/resources</directory>
                                    <filtering>true</filtering>
                                    <includes>
                                        <include>config.properties</include>
                                    </includes>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <version>3.6.2</version>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <configuration>
                    <source>1.8</source>
                    <target>1.8</target>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>copy-dependencies</id>
                        <phase>prepare-package</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>../target/libs</outputDirectory>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>3.0.2</version>
                <configuration>
                    <outputDirectory>../target</outputDirectory>
                    <archive>
                        <manifest>
                            <mainClass>net.simon987.server.Main</mainClass>
                            <addClasspath>true</addClasspath>
                            <classpathPrefix>libs/</classpathPrefix>
                        </manifest>
                    </archive>
                </configuration>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.7.2</version>
                <configuration>
                    <workingDirectory>./src/main/resources</workingDirectory>
                </configuration>
            </plugin>
        </plugins>
    </build>

    <groupId>net.simon987.server</groupId>
    <artifactId>server</artifactId>
    <version>1.4a</version>

    <dependencies>
        <dependency>
            <groupId>org.java-websocket</groupId>
            <artifactId>Java-WebSocket</artifactId>
            <version>1.3.6</version>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.12</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>mysql</groupId>
            <artifactId>mysql-connector-java</artifactId>
            <version>5.1.42</version>
        </dependency>
        <dependency>
            <groupId>com.googlecode.json-simple</groupId>
            <artifactId>json-simple</artifactId>
            <version>1.1.1</version>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-text</artifactId>
            <version>1.2</version>
        </dependency>
        <dependency>
            <groupId>org.mongodb</groupId>
            <artifactId>mongo-java-driver</artifactId>
            <version>2.10.1</version>
        </dependency>

    </dependencies>

    <properties>
        <!-- explicitly set build encoding so not altered by build platform defaults -->
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

</project>