build.gradle

apply plugin: 'java'

repositories {
    mavenCentral()
}

dependencies {
    testCompile 'junit:junit:4.+'
}

sourceSets {
    main {
        java {
            srcDir '.'
        }
    }
}

test {
    testLogging {
        events 'passed', 'skipped', 'failed', 'standardOut', 'standardError'
    }
}

jar {
    manifest {
        attributes 'Main-Class': 'Selfupdate'
    }
}

Selfupdate.java

import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;

public class Selfupdate {
    public static void main(final String[] args) throws URISyntaxException, IOException {
        final URI uri = Selfupdate.class.getProtectionDomain().getCodeSource().getLocation().toURI();
        final Path oldPath = Paths.get(uri);
        final Path newPath = oldPath.resolveSibling(oldPath.getFileName().toString() + ".renamed");
        Files.move(oldPath, newPath);
        /*
        final File oldFile = new File(uri);
        final File newFile = new File(Paths.get(uri).toString() + ".renamed");
        oldFile.renameTo(newFile);
        */
    }
}