[1.8] Help needed with gradle and shadowJar

For a 1.8 mod i'm making I need to use sqlite

Now I have found a nice standalone jar https://bitbucket.org/xerial/sqlite-jdbc/downloads(the 1.8.6 one, the 1.8.7 is bugged on unix)

I spent a long time with http://www.minecraftforge.net/forum/index.php?topic=18864.0 and fiddling around with a build.gradle and now i'm at a point where I actually have the sqlite jar included in my mod jar, and forge starts up with it(took me long enough to get this far, 2 hours at least)

But then, the feeling of triumph faded...

net.minecraft.launchwrapper.Launch.main(Launch.java:28)
Caused by: java.lang.NoClassDefFoundError: org/sqlite/core/NativeDB

Darn, the references dont line up anymore. So I'm guessing i'm missing a shadowjar reference somewhere where its supposed to rewrite my classes to reference the new classpaths, only I cant figure out which option to enable in my build.gradle to set shadow jar to rewrite my jar.

My current build.grade

buildscript {
    repositories {
        mavenCentral()
        maven {
            name = "forge"
            url = "http://files.minecraftforge.net/maven"
        }
        maven {
            name = "sonatype"
            url = "https://oss.sonatype.org/content/repositories/snapshots/"
        }
        maven {
            name = "shadow"
            url "https://plugins.gradle.org/m2/"
        }
    }
    dependencies {
        classpath 'net.minecraftforge.gradle:ForgeGradle:1.2-SNAPSHOT'
        classpath "com.github.jengelman.gradle.plugins:shadow:1.2.1"
    }
}
apply plugin: 'java' // or 'groovy'. Must be explicitly applied
apply plugin: 'com.github.johnrengelman.shadow'
shadowJar {
    relocate 'org.sqlite','tschallacka.whotookmycookies.org.sqlite'
}

apply plugin: 'forge'

version = "0.0.0.1"
group= "tschallacka.whotookmycookies.WhoTookMyCookies" // http://maven.apache.org/guides/mini/guide-naming-conventions.html
archivesBaseName = "WhoTookMyCookies"

minecraft {
    version = "1.8-11.14.1.1375"
    runDir = "eclipse"
    
    // the mappings can be changed at any time, and must be in the following format.
    // snapshot_YYYYMMDD   snapshot are built nightly.
    // stable_#            stables are built at the discretion of the MCP team.
    // Use non-default mappings at your own risk. they may not allways work.
    // simply re-run your setup task after changing the mappings to update your workspace.
    mappings = "snapshot_20141130"
}

processResources
{
    // this will ensure that this task is redone when the versions change.
    inputs.property "version", project.version
    inputs.property "mcversion", project.minecraft.version

    // replace stuff in mcmod.info, nothing else
    from(sourceSets.main.resources.srcDirs) {
        include 'mcmod.info'
                
        // replace version and mcversion
        expand 'version':project.version, 'mcversion':project.minecraft.version
    }
        
    // copy everything else, thats not the mcmod.info
    from(sourceSets.main.resources.srcDirs) {
        exclude 'mcmod.info'
    }
}
// Include external libs in compilation and jar
configurations {
    external
    compile.extendsFrom external
}
dependencies {
    // you may put jars on which you depend on in ./libs
    // or you may define them like so..
    //compile "some.group:artifact:version:classifier"
    //compile "some.group:artifact:version"
      
    // real examples
    //compile 'com.mod-buildcraft:buildcraft:6.0.8:dev'  // adds buildcraft to the dev env
    //compile 'com.googlecode.efficient-java-matrix-library:ejml:0.24' // adds ejml to the dev env

    // for more info...
    // http://www.gradle.org/docs/current/userguide/artifact_dependencies_tutorial.html
    // http://www.gradle.org/docs/current/userguide/dependency_management.html

}

jar {
    from { configurations.external.collect { it.isDirectory() ? it : zipTree(it) } }
}

// Let Shadow do its thing
build.dependsOn shadowJar

Anyone here have experience with shadowJar and how to set it up so it rewrites my classes to reference the correct classes?

Also, how can I tell it to overwrite my obfuscated classes instead of the deobfuscated classes. Because it does its magic on the deobfuscated classes.

The mod file(it crashes on the dirt printing, comment that out to get the noclassdeffound error)

package tschallacka.whotookmycookies;

import net.minecraft.init.Blocks;
import net.minecraftforge.fml.common.Mod;
import net.minecraftforge.fml.common.Mod.EventHandler;
import net.minecraftforge.fml.common.event.FMLInitializationEvent;
import java.sql.*;

@Mod(modid = WhoTookMyCookies.MODID, version = WhoTookMyCookies.VERSION)
public class WhoTookMyCookies
{
    public static final String MODID = "WhoTookMyCookies";
    public static final String VERSION = "0.0.0.1";

    @EventHandler
    public void init(FMLInitializationEvent event)
    {
    	// some example code
        System.out.println("DIRT BLOCK >> "+Blocks.dirt.getUnlocalizedName());
        

            Connection c = null;
            try {
              Class.forName("org.sqlite.JDBC");
              c = DriverManager.getConnection("jdbc:sqlite:test.db");
            } catch ( Exception e ) {
              System.err.println( e.getClass().getName() + ": " + e.getMessage() );
              System.exit(0);
            }
            System.out.println("Opened database successfully");

        
    }
}