Fix source jar file.

modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/FileSpec.kt

@@ -10,10 +10,10 @@ import java.nio.file.attribute.BasicFileAttributes
  * and GlobSpec (a spec defined by a glob, e.g. ** slash *Test.class)
  */
 sealed class IFileSpec {
-    abstract fun toFiles(filePath: String, excludes: List<Glob> = emptyList<Glob>()): List<File>
+    abstract fun toFiles(baseDir: String?, filePath: String, excludes: List<Glob> = emptyList<Glob>()): List<File>
 
     class FileSpec(val spec: String) : IFileSpec() {
-        override public fun toFiles(filePath: String, excludes: List<Glob>) = listOf(File(spec))
+        override public fun toFiles(baseDir: String?, filePath: String, excludes: List<Glob>) = listOf(File(spec))
 
         override public fun toString() = spec
     }
@@ -30,14 +30,14 @@ sealed class IFileSpec {
                 }
             }
             if (includeMatchers.matches(rel)) {
-                log(2, "Including ${rel.toFile().absolutePath}")
+                log(2, "Including ${rel.toFile().path}")
                 return true
             }
             log(2, "Excluding ${rel.toFile()} (not matching any include pattern")
             return false
         }
 
-        override fun toFiles(filePath: String, excludes: List<Glob>): List<File> {
+        override fun toFiles(baseDir: String?, filePath: String, excludes: List<Glob>): List<File> {
             val result = arrayListOf<File>()
             val includes = Glob(*spec.toTypedArray())
 
@@ -45,7 +45,7 @@ sealed class IFileSpec {
                 Files.walkFileTree(Paths.get(filePath), object : SimpleFileVisitor<Path>() {
                     override public fun visitFile(path: Path, attrs: BasicFileAttributes): FileVisitResult {
                         val rel = Paths.get(filePath).relativize(path)
-                        if (isIncluded(includes, excludes, rel)) {
+                        if (isIncluded(includes, excludes, path)) {
                             result.add(rel.toFile())
                         }
                         return FileVisitResult.CONTINUE

modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/internal/GenericRunner.kt

@@ -24,10 +24,10 @@ abstract class GenericTestRunner : ITestRunnerContributor {
             else 0
 
     protected fun findTestClasses(project: Project, testConfig: TestConfig): List<String> {
-        val path = KFiles.joinDir(project.directory, project.buildDirectory, KFiles.TEST_CLASSES_DIR)
+        val path = KFiles.joinDir(project.buildDirectory, KFiles.TEST_CLASSES_DIR)
 
         val result = IFileSpec.GlobSpec(toClassPaths(testConfig.testIncludes))
-            .toFiles(path, testConfig.testExcludes.map {
+            .toFiles(project.directory, path, testConfig.testExcludes.map {
                     Glob(it)
                 }).map {
                     it.toString().replace("/", ".").replace("\\", ".").replace(".class", "")

modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/misc/JarUtils.kt

@@ -36,9 +36,16 @@ public class JarUtils {
                 expandJarFiles: Boolean, onError: (Exception) -> Unit = DEFAULT_HANDLER) {
             val allFiles = file.allFromFiles(directory)
             allFiles.forEach { relSource ->
-                val source =
+                val source = relSource
-                        if (relSource.isAbsolute) relSource
+
-                        else File(KFiles.joinDir(directory, file.from, relSource.path))
+                val entryFile = if (File(source.path).isAbsolute) File(source.path)
+                    else if (! file.fromOriginal.isCurrentDir()) File(KFiles.joinDir(file.from, source.path))
+                    else File(source.path)
+
+                if (!entryFile.exists()) {
+                    throw AssertionError("File should exist: $entryFile")
+                }
+
                 if (source.isDirectory) {
                     log(2, "Writing contents of directory $source")
 
@@ -61,22 +68,21 @@ public class JarUtils {
                 } else {
                     if (expandJarFiles && source.name.endsWith(".jar") && ! source.path.contains("resources")) {
                         log(2, "Writing contents of jar file $source")
-                        val stream = JarInputStream(FileInputStream(source))
+                        val stream = JarInputStream(FileInputStream(entryFile))
                         var entry = stream.nextEntry
                         while (entry != null) {
                             if (!entry.isDirectory && !KFiles.isExcluded(entry.name, DEFAULT_JAR_EXCLUDES)) {
-                                val ins = JarFile(source).getInputStream(entry)
+                                val ins = JarFile(entryFile).getInputStream(entry)
                                 addEntry(ins, JarEntry(entry), outputStream, onError)
                             }
                             entry = stream.nextEntry
                         }
                     } else {
-                        val entry = JarEntry(file.to + relSource.path.replace("\\", "/"))
+                        val fixedSource = relSource.path.replace("\\", "/")
+                        val entryFileName = if (file.toOriginal.isCurrentDir()) fixedSource
+                            else file.to + fixedSource
+                        val entry = JarEntry(entryFileName)
                         entry.time = source.lastModified()
-                        val entryFile = source
-                        if (!entryFile.exists()) {
-                            throw AssertionError("File should exist: $entryFile")
-                        }
                         addEntry(FileInputStream(entryFile), entry, outputStream, onError)
                     }
                 }
@@ -143,8 +149,12 @@ public class JarUtils {
 }
 
 open class Direction(open val p: String) {
-    override public fun toString() = path
+    override fun toString() = path
-    public val path: String get() = if (p.isEmpty() or p.endsWith("/")) p else p + "/"
+    fun isCurrentDir() = path == "./"
+    val path: String get() =
+        if (p.isEmpty()) "./"
+        else if (p.startsWith("/") || p.endsWith("/")) p
+        else p + "/"
 }
 
 class IncludedFile(val fromOriginal: From, val toOriginal: To, val specs: List<IFileSpec>) {
@@ -159,8 +169,8 @@ class IncludedFile(val fromOriginal: From, val toOriginal: To, val specs: List<I
     fun allFromFiles(directory: String? = null): List<File> {
         val result = arrayListOf<File>()
         specs.forEach { spec ->
-            val fullDir = if (directory == null) from else KFiles.joinDir(directory, from)
+//            val fullDir = if (directory == null) from else KFiles.joinDir(directory, from)
-            spec.toFiles(fullDir).forEach { source ->
+            spec.toFiles(directory, from).forEach { source ->
                 result.add(if (source.isAbsolute) source else File(source.path))
             }
         }

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

@@ -38,7 +38,7 @@ class JarGenerator @Inject constructor(val dependencyManager: DependencyManager)
             filesNotExcluded.forEach {
                 fileSpecs.add(IFileSpec.FileSpec(it.path.toString().substring(prefixPath.toString().length + 1)))
             }
-            result.add(IncludedFile(From(prefixPath.toString() + "/"), To(""), fileSpecs))
+            result.add(IncludedFile(From(project.directory + "/" + prefixPath.toString() + "/"), To(""), fileSpecs))
 
             // Resources, if applicable
             context.variant.resourceDirectories(project).forEach {

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

@@ -48,9 +48,9 @@ class PackagingPlugin @Inject constructor(val dependencyManager : DependencyMana
             files.forEach { includedFile ->
                 val includedSpecs = arrayListOf<IFileSpec>()
                 includedFile.specs.forEach { spec ->
-                    val fromPath = directory + "/" + includedFile.from
+                    val fromPath = includedFile.from
                     if (File(fromPath).exists()) {
-                        spec.toFiles(fromPath).forEach { file ->
+                        spec.toFiles(directory, fromPath).forEach { file ->
                             val fullFile = File(fromPath, file.path)
                             if (! fullFile.exists()) {
                                 throw AssertionError("File should exist: $fullFile")
@@ -245,7 +245,7 @@ class PackageConfig(val project: Project) : AttributeHolder {
         jar {
             name = "${project.name}-${project.version}-sources.jar"
             project.sourceDirectories.forEach {
-                include(from(it), to(""), glob("src/**"))
+                include(from(project.directory + "/" + it), to(""), glob("**"))
             }
         }
         jar {

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

@@ -6,11 +6,8 @@ import com.beust.kobalt.maven.DependencyManager
 import com.google.inject.Inject
 
 class ZipGenerator @Inject constructor(val dependencyManager: DependencyManager){
-    fun findIncludedFiles(project: Project, context: KobaltContext, zip: Zip)
-        = PackagingPlugin.findIncludedFiles(project.directory, zip.includedFiles, zip.excludes)
-
     fun generateZip(project: Project, context: KobaltContext, zip: Zip) {
-        val allFiles = findIncludedFiles(project, context, zip)
+        val allFiles = PackagingPlugin.findIncludedFiles(project.directory, zip.includedFiles, zip.excludes)
         PackagingPlugin.generateArchive(project, context, zip.name, ".zip", allFiles)
     }
 }

src/test/kotlin/com/beust/kobalt/IncludeExcludeTest.kt

@@ -1,5 +1,8 @@
 package com.beust.kobalt
 
+import com.beust.kobalt.misc.From
+import com.beust.kobalt.misc.IncludedFile
+import com.beust.kobalt.misc.To
 import org.testng.Assert
 import org.testng.annotations.BeforeClass
 import org.testng.annotations.DataProvider
@@ -45,7 +48,16 @@ class IncludeExcludeTest : KobaltTest() {
     @Test(dataProvider = "dp")
     fun shouldInclude(root: File, includedSpec: List<String>, excludedSpec: List<String>, expectedFiles: List<String>) {
         val g = IFileSpec.GlobSpec(includedSpec)
-        val files = g.toFiles(root.path, excludedSpec.map { Glob(it) })
+        val files = g.toFiles("", root.path, excludedSpec.map { Glob(it) })
         Assert.assertEquals(files.map { it.name }, expectedFiles)
     }
+
+    @Test
+    private fun f() {
+        val spec = IFileSpec.GlobSpec("src/**")
+        val files = spec.toFiles(homeDir("kotlin/kobalt"), "src/main/kotlin")
+        val inc = IncludedFile(From("src/main/kotlin"), To(""), listOf(IFileSpec.GlobSpec("**")))
+//        val files = inc.allFromFiles(homeDir("kotlin/kobalt"))
+        println("FILES: " + files)
+    }
 }