First commit.

.gitattributes

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+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+# batch files are specific to windows and always crlf
+*.bat eol=crlf

.gitignore

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+**/.idea/dictionaries
+**/.idea/gradle.xml
+**/.idea/libraries
+**/.idea/tasks.xml
+**/.idea/workspace.xml
+*.iws
+.classpath
+.DS_Store
+.gradle
+.kobalt
+.nb-gradle
+.project
+.settings
+/bin
+/build
+/deploy
+/dist
+/gen
+/gradle.properties
+/local.properties
+/out
+/proguard-project.txt
+/project.properties
+/target
+/test-output
+ehthumbs.db
+kobaltBuild
+Thumbs.db

kobalt/Build.kt.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module external.linked.project.id="Build.kt" external.linked.project.path="$MODULE_DIR$/.." external.root.project.path="$MODULE_DIR$/.." external.system.id="KOBALT" type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <output url="file://$MODULE_DIR$/out/classes" />
+    <output-test url="file://$MODULE_DIR$/out/test-classes" />
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module-library">
+      <library name="Kobalt: com.beust.kobalt:kobalt:jar:1.0.59">
+        <CLASSES>
+          <root url="jar://$USER_HOME$/.kobalt/wrapper/dist/kobalt-1.0.59/kobalt/wrapper/kobalt-1.0.59.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
+  </component>
+</module>

kobalt/src/Build.kt

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+
+import com.beust.kobalt.buildScript
+import com.beust.kobalt.plugin.application.application
+import com.beust.kobalt.plugin.packaging.assemble
+import com.beust.kobalt.project
+
+val bs = buildScript {
+    repos()
+}
+
+
+val p = project {
+
+    name = "fatjar"
+    group = "com.example"
+    artifactId = name
+    version = "0.1"
+
+    sourceDirectories {
+        path("src/main/kotlin")
+    }
+
+    sourceDirectoriesTest {
+        path("src/test/kotlin")
+    }
+
+    dependencies {
+        compile("org.apache.commons:commons-compress:1.13")
+        compile("commons-io:commons-io:2.5")
+    }
+
+    dependenciesTest {
+        compile("org.testng:testng:6.11")
+
+    }
+
+    assemble {
+        jar {
+        }
+    }
+
+    application {
+        mainClass = "com.example.MainKt"
+    }
+
+
+}

kobalt/wrapper/kobalt-wrapper.properties

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+kobalt.version=1.0.59

kobaltw

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+#!/usr/bin/env sh
+java -jar "`dirname "$0"`/kobalt/wrapper/kobalt-wrapper.jar" $*

kobaltw.bat

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+@echo off
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+java -jar "%DIRNAME%/kobalt/wrapper/kobalt-wrapper.jar" %*

src/main/kotlin/com/example/Main.kt

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+package com.example
+
+import org.apache.commons.compress.archivers.zip.*
+import java.io.File
+import java.util.*
+
+internal var allFilesPredicate: ZipArchiveEntryPredicate = ZipArchiveEntryPredicate { true }
+
+fun main(args: Array<String>) {
+    val kobalt = File("kobalt-1.0.58.jar")
+    val zip = File("kobalt-1.0.58.zip")
+    val src = File("kobalt-1.0.58-sources.jar")
+
+    //rezip2(kobalt, zip)
+    rezip3(kobalt, src, zip)
+}
+
+fun rezip(jarIn: File, zipOut: File) {
+    val s = System.currentTimeMillis()
+    val zos = ZipArchiveOutputStream(zipOut)
+    zos.encoding = "UTF-8"
+    val zip = ZipFile(jarIn)
+    zip.copyRawEntries(zos, allFilesPredicate)
+    zos.close()
+    zip.close()
+
+    println("Rezip Time: " + (System.currentTimeMillis() - s) + "ms")
+}
+
+fun rezip2(jarIn: File, zipOut: File) {
+    val s = System.currentTimeMillis()
+    val zos = ZipArchiveOutputStream(zipOut)
+    zos.encoding = "UTF-8"
+    val zip = ZipFile(jarIn)
+
+    for (entry in zip.entries) {
+        zos.addRawArchiveEntry(entry, zip.getRawInputStream(entry))
+    }
+
+    zos.close()
+
+    zip.close()
+
+    println("Rezip2 Time: " + (System.currentTimeMillis() - s) + "ms")
+}
+
+fun rezip3(jarIn: File, srcJar: File, zipOut: File) {
+    val s = System.currentTimeMillis()
+    val zos = ZipArchiveOutputStream(zipOut)
+    zos.encoding = "UTF-8"
+    val jar = ZipFile(jarIn)
+    
+    val jarEntries = jar.entries
+
+    for (entry in jar.entries) {
+        zos.addRawArchiveEntry(entry, jar.getRawInputStream(entry))
+    }
+
+    jar.close()
+
+    val src = ZipFile(srcJar)
+
+    for (entry in src.entries) {
+        if (!entryExists(jarEntries, entry)) {
+            zos.addRawArchiveEntry(entry, src.getRawInputStream(entry))
+        }
+    }
+
+    src.close()
+
+    zos.close()
+
+    println("Rezip3 Time: " + (System.currentTimeMillis() - s) + "ms")
+}
+
+fun entryExists(jarEntries: Enumeration<ZipArchiveEntry>, entry: ZipArchiveEntry): Boolean {
+    for (e in jarEntries) {
+        if (e.name == entry.name) {
+            return true
+        }
+    }
+    return false
+}
+

src/test/kotlin/com/example/MainTest.kt

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+package com.example
+
+import org.testng.annotations.Test
+
+class ExampleTest {
+    @Test
+    fun f() = println("Running test")
+}