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>
    <groupId>edu.stonybrook.bmi</groupId>
    <artifactId>Nanoborb</artifactId>
    <version>1.5.0</version>
    <packaging>jar</packaging>
    <dependencies>
        <dependency>
            <groupId>com.ebremer</groupId>
            <artifactId>ImageBox</artifactId>
            <version>1.1.1</version>
            <type>jar</type>
        </dependency>
        <dependency>
            <groupId>jcef</groupId>
            <artifactId>jcef</artifactId>
            <version>1.0</version>
            <type>jar</type>
        </dependency>
    </dependencies>
    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <maven.compiler.source>1.8</maven.compiler.source>
        <maven.compiler.target>1.8</maven.compiler.target>
    </properties>
    <build>
        <resources>
            <resource>
                <directory>files/</directory>
                    <includes>
                        <include>**/*.js</include>
                        <include>**/*.html</include>
                        <include>**/*.svs</include>
                        <include>**/*.png</include>
                    </includes>
                </resource>             
            </resources>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>2.4.3</version>
                <configuration>
                    <shadedArtifactAttached>false</shadedArtifactAttached>
                    <transformers>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                            <mainClass>edu.stonybrook.bmi.nanoborb.MainFrame</mainClass>
                        </transformer>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer" />
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
                            <addHeader>false</addHeader>
                        </transformer>
                    </transformers>
                <filters>
                    <filter>
                        <artifact>*:*</artifact>
                        <excludes>
                            <!-- Some jars are signed but shading breaks that.
                                Don't include signing files.
                            -->
                            <exclude>META-INF/*.SF</exclude>
                            <exclude>META-INF/*.DSA</exclude>
                            <exclude>META-INF/*.RSA</exclude>
                        </excludes>
                    </filter>
                </filters>
                </configuration>
                <executions>
                    <execution>
                    <phase>package</phase>
                    <!--<phase /><!- - Switch off -->
                    <goals>
                        <goal>shade</goal>
                    </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.22.2</version>
                <configuration>
                    <systemPropertyVariables>
                        <propertyName>java.library.path</propertyName>
                        <buildDirectory>lib/win64</buildDirectory>
                    </systemPropertyVariables>
                </configuration>
            </plugin>
        </plugins>
    </build>
</project>