Now it compiles in jar properly

.idea/gradle.xml

@@ -10,6 +10,7 @@
             <option value="$PROJECT_DIR$" />
           </set>
         </option>
+        <option name="useAutoImport" value="true" />
         <option name="useQualifiedModuleNames" value="true" />
       </GradleProjectSettings>
     </option>

build.gradle

@@ -1,47 +1,50 @@
-plugins {
-    id 'java'
-    id 'org.jetbrains.kotlin.jvm' version '1.3.21'
+buildscript {
+    ext.kotlin_version = '1.3.21'
+    
+    repositories {
+        mavenCentral()
+        jcenter()
+    }
+
+    dependencies {
+        classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:$kotlin_version"
+        classpath 'com.github.jengelman.gradle.plugins:shadow:4.0.4'
+    }
 }
+
+apply plugin: 'kotlin'
+apply plugin: 'java'
+apply plugin: 'com.github.johnrengelman.shadow'
+
 group 'io.github.chronosx88'
 version '0.1'
 
-task fatJar(type: Jar) {
-    manifest {
-        attributes(
-                'Main-Class': 'io.github.chronosx88.dhtBootstrap.MainKt'
-        )
-    }
-    baseName = project.name + '-all'
-    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
-    with jar
-}
-
-sourceCompatibility = 1.8
-
 repositories {
     mavenCentral()
-    /*maven {
-        url "http://tomp2p.net/dev/mvn/"
-    }*/
 }
 
 dependencies {
+    implementation fileTree(include: ['*.jar'], dir: 'libs')
+    implementation fileTree(include: ['*.jar'], dir: 'libs/tomp2p')
     implementation "org.jetbrains.kotlin:kotlin-stdlib-jdk8"
-    //implementation 'net.tomp2p:tomp2p-all:5.0-Beta8'
     implementation 'org.slf4j:slf4j-log4j12:+'
 }
 
 compileKotlin {
     kotlinOptions.jvmTarget = "1.8"
 }
+
 compileTestKotlin {
     kotlinOptions.jvmTarget = "1.8"
 }
+
 jar {
     manifest {
-        attributes(
-                'Main-Class': 'io.github.chronosx88.dhtBootstrap.MainKt'
-        )
+        attributes 'Main-Class': 'MainKt'
+    }
+    from {
+        configurations.compile.collect {
+            it.isDirectory() ? it : zipTree(it)
+        }
     }
-    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
 }

src/main/kotlin/io/github/chronosx88/dhtBootstrap/Main.kt

@@ -1,5 +1,4 @@
-package io.github.chronosx88.dhtBootstrap
-
+import io.github.chronosx88.dhtBootstrap.StorageBerkeleyDB
 import net.tomp2p.connection.DSASignatureFactory
 import net.tomp2p.dht.PeerBuilderDHT
 import net.tomp2p.dht.PeerDHT

src/main/resources/META-INF/MANIFEST.MF

@@ -1,12 +0,0 @@
-Manifest-Version: 1.0
-Class-Path: json-simple-1.1.jar kotlin-stdlib-common-1.3.21.jar tomp2p
- -all-5.0-Beta8.jar tomp2p-tracker-5.0-Beta8.jar netty-buffer-4.0.28.F
- inal.jar log4j-1.2.17.jar annotations-13.0.jar tomp2p-dht-5.0-Beta8.j
- ar netty-common-4.0.28.Final.jar kotlin-stdlib-1.3.21.jar gcm-server-
- 1.0.2.jar tomp2p-storage-5.0-Beta8.jar slf4j-log4j12-1.8.0-beta4.jar 
- weupnp-0.1.2.jar slf4j-api-1.8.0-beta4.jar tomp2p-replication-5.0-Bet
- a8.jar kotlin-stdlib-jdk8-1.3.21.jar tomp2p-nat-5.0-Beta8.jar netty-t
- ransport-4.0.28.Final.jar kotlin-stdlib-jdk7-1.3.21.jar tomp2p-androi
- d-5.0-Beta8.jar tomp2p-core-5.0-Beta8.jar mapdb-1.0.6.jar
-Main-Class: io.github.chronosx88.MainKt
-