proguard-maven-plugin will obfuscate the primary artifact of your project, not the secondary artifact jar-with-dependencies that the maven-assembly-plugin generated.
You need to configure the plugin to obfuscate the jar-with-dependencies by specifying the injar attribute:
Specifies the input jar name (or wars, ears, zips) of the application to be processed.
<injar>${project.build.finalName}-jar-with-dependencies.jar</injar>
Now, there is also a problem in the order of execution of plugins in your POM: we need to make sure that the maven-assembly-plugin is executed before the proguard-maven-plugin. As such, it is best to define an explicit execution for the maven-assembly-plugin bound to the package phase instead of manually invoking it from the command line with assembly:single. This would be the configuration:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>assembly</id>
<goals>
<goal>single</goal>
</goals>
<phase>package</phase>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</execution>
</executions>
</plugin>
and then, you just need to make sure that the proguard-maven-plugin plugin configuration is after that in your POM.
Having done that, invoking Maven with mvn clean install will result in an obfuscated jar with dependencies.
To test with your actual POM, I added two repositories:
https://repo.spongepowered.org/maven to resolve the spongeapi dependency.http://maven.restlet.com to resolve the org.restlet.jse dependencies.
With those 2 dependencies, warnings were generated by ProGuard because the org.restlet.ext.jackson dependency utilizes com.sun.msv.* classes that are not on the buildpath. Since I figure that your code is currently working, it means those classes don't need to be included and that those warnings can be ignored. As such, I added the -dontwarn option so that ProGuard doesn't error when there is a warning.
The final POM for which I was able to successfully obfuscate the jar with dependencies is the following:
<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>com.mycompany</groupId>
<artifactId>myproduct</artifactId>
<version>1.0-SNAPSHOT</version>
<repositories>
<repository>
<id>spongepowered</id>
<url>https://repo.spongepowered.org/maven</url>
</repository>
<repository>
<id>restlet</id>
<url>http://maven.restlet.com</url>
</repository>
</repositories>
<properties>
<restlet-version>2.3.5</restlet-version>
</properties>
<build>
<resources>
<resource>
<directory>${project.basedir}/src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>templating-maven-plugin</artifactId>
<version>1.0-alpha-3</version>
<executions>
<execution>
<id>filter-src</id>
<goals>
<goal>filter-sources</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>assembly</id>
<goals>
<goal>single</goal>
</goals>
<phase>package</phase>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.github.wvengen</groupId>
<artifactId>proguard-maven-plugin</artifactId>
<version>2.0.8</version>
<executions>
<execution>
<phase>package</phase>
<goals><goal>proguard</goal></goals>
<configuration>
<injar>${project.build.finalName}-jar-with-dependencies.jar</injar> <!-- make sure to obfuscate the jar with dependencies -->
<proguardVersion>5.2</proguardVersion>
<options>
<option>-allowaccessmodification</option>
<option>-dontoptimize</option>
<option>-dontshrink</option>
<option>-dontnote</option>
<option>-dontwarn</option> <!-- added option to ignore com.sun missing classes -->
<option>-keepattributes Signature</option>
<option>-keep class com.mycompany.MyPlugin { *; }</option>
</options>
<libs>
<lib>${java.home}/lib/rt.jar</lib>
</libs>
<dependencies>
<dependency>
<groupId>net.sf.proguard</groupId>
<artifactId>proguard-base</artifactId>
<version>5.2</version>
<scope>runtime</scope>
</dependency>
</dependencies>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.spongepowered</groupId>
<artifactId>spongeapi</artifactId>
<version>3.0.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
</dependency>
<dependency>
<groupId>org.easytesting</groupId>
<artifactId>fest-assert-core</artifactId>
<version>2.0M8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>1.10.19</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.restlet.jse</groupId>
<artifactId>org.restlet</artifactId>
<version>${restlet-version}</version>
</dependency>
<dependency>
<groupId>org.restlet.jse</groupId>
<artifactId>org.restlet.ext.jackson</artifactId>
<version>${restlet-version}</version>
</dependency>
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
</dependency>
</dependencies>
</project>
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