diff --git a/src/main/kotlin/com/beust/kobalt/plugin/packaging/JarUtils.kt b/src/main/kotlin/com/beust/kobalt/plugin/packaging/JarUtils.kt
index badb7b48..c83e2704 100644
--- a/src/main/kotlin/com/beust/kobalt/plugin/packaging/JarUtils.kt
+++ b/src/main/kotlin/com/beust/kobalt/plugin/packaging/JarUtils.kt
@@ -34,18 +34,22 @@ public class JarUtils {
                 val path = spec.toString()
                 spec.toFiles(directory + "/" + file.from).forEach { source ->
                     if (source.isDirectory) {
+                        log(2, "Writing contents of directory ${source}")
+
                         // Directory
                         var name = path
                         if (!name.isEmpty()) {
                             if (!name.endsWith("/")) name += "/"
                             val entry = JarEntry(name)
                             entry.time = source.lastModified()
-                            outputStream.putNextEntry(entry)
-                            outputStream.closeEntry()
+                            try {
+                                outputStream.putNextEntry(entry)
+                            } finally {
+                                outputStream.closeEntry()
+                            }
                         }
-                        val fileSpecs: List<IFileSpec> = source.listFiles().map { IFileSpec.FileSpec(it.name) }
-                        val subFiles = IncludedFile(From(file.from), To(file.to), fileSpecs)
-                        addSingleFile(directory, subFiles, outputStream, expandJarFiles)
+                        val includedFile = IncludedFile(From(source.path), To(""), listOf(IFileSpec.Glob("**")))
+                        addSingleFile(directory, includedFile, outputStream, expandJarFiles)
                     } else {
                         if (expandJarFiles and source.name.endsWith(".jar")) {
                             log(2, "Writing contents of jar file ${source}")
diff --git a/src/main/kotlin/com/beust/kobalt/plugin/packaging/PackagingPlugin.kt b/src/main/kotlin/com/beust/kobalt/plugin/packaging/PackagingPlugin.kt
index 671d9079..33240a2d 100644
--- a/src/main/kotlin/com/beust/kobalt/plugin/packaging/PackagingPlugin.kt
+++ b/src/main/kotlin/com/beust/kobalt/plugin/packaging/PackagingPlugin.kt
@@ -4,16 +4,14 @@ import com.beust.kobalt.IFileSpec
 import com.beust.kobalt.IFileSpec.FileSpec
 import com.beust.kobalt.IFileSpec.Glob
 import com.beust.kobalt.TaskResult
-import com.beust.kobalt.api.ConfigPlugin
-import com.beust.kobalt.api.Kobalt
-import com.beust.kobalt.api.KobaltContext
-import com.beust.kobalt.api.Project
+import com.beust.kobalt.api.*
 import com.beust.kobalt.api.annotation.Directive
 import com.beust.kobalt.api.annotation.ExportedProjectProperty
 import com.beust.kobalt.api.annotation.Task
 import com.beust.kobalt.glob
 import com.beust.kobalt.internal.JvmCompilerPlugin
 import com.beust.kobalt.maven.DependencyManager
+import com.beust.kobalt.maven.IClasspathDependency
 import com.beust.kobalt.maven.LocalRepo
 import com.beust.kobalt.misc.KFiles
 import com.beust.kobalt.misc.KobaltExecutors
@@ -161,14 +159,25 @@ class PackagingPlugin @Inject constructor(val dependencyManager : DependencyMana
         if (jar.fatJar) {
             log(2, "Creating fat jar")
 
-            listOf(dependencyManager.transitiveClosure(project.compileDependencies),
-                    dependencyManager.transitiveClosure(project.compileRuntimeDependencies)).forEach { dep ->
-                dep.map { it.jarFile.get() }.forEach {
-                    if (!isExcluded(it, jar.excludes)) {
-                        allFiles.add(IncludedFile(arrayListOf(FileSpec(it.path))))
-                    }
-                }
-            }
+            val seen = hashSetOf<String>()
+            val dependentProjects = project.projectProperties.get(JvmCompilerPlugin.DEPENDENT_PROJECTS)
+                    as List<ProjectDescription>
+            listOf(dependencyManager.calculateDependencies(project, context, dependentProjects,
+                        project.compileDependencies),
+                    dependencyManager.calculateDependencies(project, context, dependentProjects,
+                            project.compileRuntimeDependencies))
+                        .forEach { deps : List<IClasspathDependency> ->
+                                deps.map {
+                                    it.jarFile.get()
+                                }.forEach { file : File ->
+                                    if (! seen.contains(file.name)) {
+                                        seen.add(file.name)
+                                        if (!isExcluded(file, jar.excludes)) {
+                                            allFiles.add(IncludedFile(arrayListOf(FileSpec(file.path))))
+                                        }
+                                    }
+                                }
+                        }
         }
 
         //