Make "run" use the transitive closure of dependencies.

Necessary if fatJar=false.

src/main/kotlin/com/beust/kobalt/internal/JvmCompiler.kt

@@ -2,7 +2,6 @@ package com.beust.kobalt.internal
 
 import com.beust.kobalt.KobaltException
 import com.beust.kobalt.TaskResult
-import com.beust.kobalt.api.IClasspathContributor
 import com.beust.kobalt.api.KobaltContext
 import com.beust.kobalt.api.Project
 import com.beust.kobalt.maven.DependencyManager
@@ -25,7 +24,8 @@ class JvmCompiler @Inject constructor(val dependencyManager: DependencyManager)
             : TaskResult {
 
         // Dependencies
-        val allDependencies = info.dependencies + calculateDependencies(project, context!!, info.dependencies)
+        val allDependencies = info.dependencies +
+                dependencyManager.calculateDependencies(project, context!!, info.dependencies)
 
         // Plugins that add flags to the compiler
         val addedFlags = ArrayList(info.compilerArgs) +
@@ -48,30 +48,6 @@ class JvmCompiler @Inject constructor(val dependencyManager: DependencyManager)
             }
         }
     }
-
-    /**
-     * @return the classpath for this project, including the IClasspathContributors.
-     */
-    fun calculateDependencies(project: Project?, context: KobaltContext,
-            vararg allDependencies: List<IClasspathDependency>): List<IClasspathDependency> {
-        var result = arrayListOf<IClasspathDependency>()
-        allDependencies.forEach { dependencies ->
-            result.addAll(dependencyManager.transitiveClosure(dependencies))
-        }
-        result.addAll(runClasspathContributors(project, context))
-
-        return result
-    }
-
-    private fun runClasspathContributors(project: Project?, context: KobaltContext) :
-            Collection<IClasspathDependency> {
-        val result = hashSetOf<IClasspathDependency>()
-        context.pluginInfo.classpathContributors.forEach { it: IClasspathContributor ->
-            result.addAll(it.entriesFor(project))
-        }
-        return result
-    }
-
 }
 
 data class CompilerActionInfo(val directory: String?, val dependencies: List<IClasspathDependency>,

src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt

@@ -59,7 +59,7 @@ abstract class JvmCompilerPlugin @Inject constructor(
         with(project) {
             arrayListOf(compileDependencies, compileProvidedDependencies, testDependencies,
                     testProvidedDependencies).forEach {
-                result.addAll(jvmCompiler.calculateDependencies(project, context, it))
+                result.addAll(dependencyManager.calculateDependencies(project, context, it))
             }
         }
         return dependencyManager.reorderDependencies(result)

src/main/kotlin/com/beust/kobalt/kotlin/BuildFileCompiler.kt

@@ -5,8 +5,8 @@ import com.beust.kobalt.KobaltException
 import com.beust.kobalt.Plugins
 import com.beust.kobalt.api.*
 import com.beust.kobalt.api.annotation.Task
-import com.beust.kobalt.internal.JvmCompiler
 import com.beust.kobalt.internal.PluginInfo
+import com.beust.kobalt.maven.DependencyManager
 import com.beust.kobalt.maven.IClasspathDependency
 import com.beust.kobalt.misc.KFiles
 import com.beust.kobalt.misc.Topological
@@ -34,7 +34,7 @@ import javax.inject.Inject
  */
 public class BuildFileCompiler @Inject constructor(@Assisted("buildFiles") val buildFiles: List<BuildFile>,
         @Assisted val pluginInfo: PluginInfo, val files: KFiles, val plugins: Plugins,
-        val jvmCompiler: JvmCompiler, val pluginProperties: PluginProperties) {
+        val dependencyManager: DependencyManager, val pluginProperties: PluginProperties) {
 
     interface IFactory {
         fun create(@Assisted("buildFiles") buildFiles: List<BuildFile>, pluginInfo: PluginInfo) : BuildFileCompiler
@@ -183,7 +183,7 @@ public class BuildFileCompiler @Inject constructor(@Assisted("buildFiles") val b
         }
 
     private fun generateJarFile(context: KobaltContext, buildFile: BuildFile, buildScriptJarFile: File) {
-        val kotlintDeps = jvmCompiler.calculateDependencies(null, context, listOf<IClasspathDependency>())
+        val kotlintDeps = dependencyManager.calculateDependencies(null, context, listOf<IClasspathDependency>())
         val deps: List<String> = kotlintDeps.map { it.jarFile.get().absolutePath }
         kotlinCompilePrivate {
             classpath(files.kobaltJar)

src/main/kotlin/com/beust/kobalt/maven/DependencyManager.kt

@@ -1,5 +1,8 @@
 package com.beust.kobalt.maven
 
+import com.beust.kobalt.api.IClasspathContributor
+import com.beust.kobalt.api.KobaltContext
+import com.beust.kobalt.api.Project
 import com.beust.kobalt.misc.KobaltExecutors
 import com.google.common.collect.ArrayListMultimap
 import java.util.*
@@ -9,6 +12,30 @@ import javax.inject.Singleton
 @Singleton
 public class DependencyManager @Inject constructor(val executors: KobaltExecutors,
         val depFactory: DepFactory){
+
+    /**
+     * @return the classpath for this project, including the IClasspathContributors.
+     */
+    fun calculateDependencies(project: Project?, context: KobaltContext,
+            vararg allDependencies: List<IClasspathDependency>): List<IClasspathDependency> {
+        var result = arrayListOf<IClasspathDependency>()
+        allDependencies.forEach { dependencies ->
+            result.addAll(transitiveClosure(dependencies))
+        }
+        result.addAll(runClasspathContributors(project, context))
+
+        return result
+    }
+
+    private fun runClasspathContributors(project: Project?, context: KobaltContext) :
+            Collection<IClasspathDependency> {
+        val result = hashSetOf<IClasspathDependency>()
+        context.pluginInfo.classpathContributors.forEach { it: IClasspathContributor ->
+            result.addAll(it.entriesFor(project))
+        }
+        return result
+    }
+
     fun transitiveClosure(dependencies : List<IClasspathDependency>): List<IClasspathDependency> {
         var executor = executors.newExecutor("JvmCompiler}", 10)
 

src/main/kotlin/com/beust/kobalt/plugin/application/ApplicationPlugin.kt

@@ -5,8 +5,10 @@ import com.beust.kobalt.api.BasePlugin
 import com.beust.kobalt.api.Project
 import com.beust.kobalt.api.annotation.Directive
 import com.beust.kobalt.api.annotation.Task
+import com.beust.kobalt.maven.DependencyManager
 import com.beust.kobalt.misc.KobaltExecutors
 import com.beust.kobalt.misc.RunCommand
+import com.beust.kobalt.plugin.packaging.PackageConfig
 import com.beust.kobalt.plugin.packaging.PackagingPlugin
 import com.google.inject.Inject
 import com.google.inject.Singleton
@@ -29,7 +31,8 @@ fun Project.application(init: ApplicationConfig.() -> Unit) {
 }
 
 @Singleton
-class ApplicationPlugin @Inject constructor(val executors: KobaltExecutors) : BasePlugin() {
+class ApplicationPlugin @Inject constructor(val executors: KobaltExecutors,
+        val dependencyManager: DependencyManager) : BasePlugin() {
 
     companion object {
         const val NAME = "application"
@@ -49,7 +52,18 @@ class ApplicationPlugin @Inject constructor(val executors: KobaltExecutors) : Ba
             val java = JavaInfo.create(File(SystemProperties.javaBase)).javaExecutable!!
             if (config.mainClass != null) {
                 val jarName = context.pluginProperties.get("packaging", PackagingPlugin.JAR_NAME) as String
-                val args = listOf("-classpath", jarName) + config.jvmArgs + config.mainClass!!
+                val packages = context.pluginProperties.get("packaging", PackagingPlugin.PACKAGES)
+                        as List<PackageConfig>
+                val allDeps = arrayListOf(jarName)
+                if (! isFatJar(packages, jarName)) {
+                    // If the jar file is not fat, we need to add the transitive closure of all dependencies
+                    // on the classpath
+                    allDeps.addAll(
+                            dependencyManager.calculateDependencies(project, context, project.compileDependencies)
+                                .map { it.jarFile.get().path })
+                }
+                val allDepsJoined = allDeps.joinToString(File.pathSeparator)
+                val args = listOf("-classpath", allDepsJoined) + config.jvmArgs + config.mainClass!!
                 RunCommand(java.absolutePath).run(args, successCallback = { output: List<String> ->
                     println(output.joinToString("\n"))
                 })
@@ -59,5 +73,16 @@ class ApplicationPlugin @Inject constructor(val executors: KobaltExecutors) : Ba
         }
         return TaskResult()
     }
+
+    private fun isFatJar(packages: List<PackageConfig>, jarName: String): Boolean {
+        packages.forEach { pc ->
+            pc.jars.forEach { jar ->
+                if ((jar.name == null || jar.name == jarName) && jar.fatJar) {
+                    return true
+                }
+            }
+        }
+        return false
+    }
 }
 

src/main/kotlin/com/beust/kobalt/plugin/kotlin/KotlinPlugin.kt

@@ -1,11 +1,11 @@
 package com.beust.kobalt.plugin.kotlin
 
+import com.beust.kobalt.TaskResult
 import com.beust.kobalt.api.*
 import com.beust.kobalt.api.annotation.Directive
 import com.beust.kobalt.api.annotation.Task
 import com.beust.kobalt.internal.JvmCompiler
 import com.beust.kobalt.internal.JvmCompilerPlugin
-import com.beust.kobalt.TaskResult
 import com.beust.kobalt.maven.*
 import com.beust.kobalt.misc.KFiles
 import com.beust.kobalt.misc.KobaltExecutors
@@ -36,7 +36,7 @@ class KotlinPlugin @Inject constructor(
     @Task(name = TASK_COMPILE, description = "Compile the project")
     fun taskCompile(project: Project): TaskResult {
         copyResources(project, JvmCompilerPlugin.SOURCE_SET_MAIN)
-        val classpath = jvmCompiler.calculateDependencies(project, context, project.compileDependencies,
+        val classpath = dependencyManager.calculateDependencies(project, context, project.compileDependencies,
                 project.compileProvidedDependencies)
 
         val projectDirectory = java.io.File(project.directory)

src/main/kotlin/com/beust/kobalt/plugin/packaging/PackagingPlugin.kt

@@ -45,6 +45,9 @@ class PackagingPlugin @Inject constructor(val dependencyManager : DependencyMana
         @ExportedProperty
         const val JAR_NAME = "jarName"
 
+        @ExportedProperty
+        const val PACKAGES = "packages"
+
         const val TASK_ASSEMBLE: String = "assemble"
         const val TASK_INSTALL: String = "install"
     }
@@ -62,6 +65,7 @@ class PackagingPlugin @Inject constructor(val dependencyManager : DependencyMana
 
     @Task(name = TASK_ASSEMBLE, description = "Package the artifacts", runAfter = arrayOf(JavaPlugin.TASK_COMPILE))
     fun taskAssemble(project: Project) : TaskResult {
+    context.pluginProperties.put(PLUGIN_NAME, PACKAGES, packages)
         packages.filter { it.project.name == project.name }.forEach { pkg ->
             pkg.jars.forEach { generateJar(pkg.project, it) }
             pkg.wars.forEach { generateWar(pkg.project, it) }
@@ -277,11 +281,8 @@ fun Project.install(init: InstallConfig.() -> Unit) {
 
 class InstallConfig(var libDir : String = "libs")
 
-@Directive
+fun Project.assemble(init: PackageConfig.(p: Project) -> Unit) = let {
-fun Project.assemble(init: PackageConfig.(p: Project) -> Unit): PackageConfig {
+    PackageConfig(this).apply { init(it) }
-    val pd = PackageConfig(this)
-    pd.init(this)
-    return pd
 }
 
 class PackageConfig(val project: Project) : AttributeHolder {