diff --git a/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/FileSpec.kt b/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/FileSpec.kt
index af798ac6..480a8553 100644
--- a/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/FileSpec.kt
+++ b/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/FileSpec.kt
@@ -22,32 +22,37 @@ sealed class IFileSpec {
 
         constructor(spec: String) : this(arrayListOf(spec))
 
-        private fun isIncluded(excludes: List<Glob>, rel: Path) : Boolean {
+        private fun isIncluded(includeMatchers: Glob, excludes: List<Glob>, rel: Path) : Boolean {
             excludes.forEach {
                 if (it.matches(rel)) {
                     log(2, "Excluding ${rel.toFile()}")
                     return false
                 }
             }
-            log(2, "Including ${rel.toFile().absolutePath}")
-            return true
+            if (includeMatchers.matches(rel)) {
+                log(2, "Including ${rel.toFile().absolutePath}")
+                return true
+            }
+            log(2, "Excluding ${rel.toFile()} (not matching any include pattern")
+            return false
         }
 
         override fun toFiles(filePath: String, excludes: List<Glob>): List<File> {
             val result = arrayListOf<File>()
+            val includes = Glob(*spec.toTypedArray())
 
             if (File(filePath).isDirectory) {
                 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(excludes, rel)) {
+                        if (isIncluded(includes, excludes, rel)) {
                             result.add(rel.toFile())
                         }
                         return FileVisitResult.CONTINUE
                     }
                 })
             } else {
-                if (isIncluded(excludes, Paths.get(filePath))) {
+                if (isIncluded(includes, excludes, Paths.get(filePath))) {
                     result.add(File(filePath))
                 }
             }
diff --git a/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt b/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt
index 2f829311..cfb4f637 100644
--- a/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt
+++ b/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt
@@ -259,7 +259,7 @@ open class JvmCompilerPlugin @Inject constructor(
         buildDirectory.mkdirs()
 
 
-        val initialSourceDirectories = ArrayList<File>()
+        val initialSourceDirectories = ArrayList<File>(sourceDirectories)
         // Source directories from the contributors
         initialSourceDirectories.addAll(
             if (isTest) {
@@ -279,13 +279,9 @@ open class JvmCompilerPlugin @Inject constructor(
         }
 
         // Now that we have all the source directories, find all the source files in them
-        val sourceFiles = if (allSourceDirectories.size > 0) {
-                files.findRecursively(projectDirectory, allSourceDirectories,
-                        { file -> sourceSuffixes.any { file.endsWith(it) } })
-                        .map { File(projectDirectory, it).path }
-            } else {
-                emptyList()
-            }
+        val sourceFiles = files.findRecursively(projectDirectory, allSourceDirectories,
+                { file -> sourceSuffixes.any { file.endsWith(it) }})
+                .map { File(projectDirectory, it).path }
 
         // Special treatment if we are compiling Kotlin files and the project also has a java source
         // directory. In this case, also pass that java source directory to the Kotlin compiler as is
diff --git a/src/test/kotlin/com/beust/kobalt/VerifyKobaltZip.kt b/src/test/kotlin/com/beust/kobalt/VerifyKobaltZip.kt
index 6d6d1bb2..fa209399 100644
--- a/src/test/kotlin/com/beust/kobalt/VerifyKobaltZip.kt
+++ b/src/test/kotlin/com/beust/kobalt/VerifyKobaltZip.kt
@@ -4,42 +4,19 @@ import com.beust.kobalt.api.Kobalt
 import com.beust.kobalt.misc.KFiles
 import com.beust.kobalt.misc.log
 import org.testng.annotations.Test
-import java.io.File
 import java.io.FileInputStream
-import java.io.InputStream
 import java.util.jar.JarFile
 import java.util.jar.JarInputStream
 
-@Test
 class VerifyKobaltZipTest : KobaltTest() {
-    private fun assertExistsInJar(jarName: String, fileName: String) {
-        val sourceJarPath = KFiles.joinDir("kobaltBuild", "libs", jarName)
-        assertExistsInJar(JarInputStream(FileInputStream(File(sourceJarPath))), fileName)
-    }
-
-    fun assertExistsInJar(stream: JarInputStream, fileName: String) {
-        var entry = stream.nextEntry
-        var found = false
-        while (entry != null) {
-            if (entry.name == fileName) found = true
-            entry = stream.nextEntry
-        }
-        if (! found) {
-            throw AssertionError("Couldn't find Main.kt in $fileName")
-        }
-    }
-
-    fun verifySourceFile() {
-        assertExistsInJar("kobalt-" + Kobalt.version + "-sources.jar", "com/beust/kobalt/Main.kt")
-    }
-
+    @Test
     fun verifyZipFile() {
         var success = true
         var foundKobaltw = false
         var foundJar = false
         var foundWrapperJar = false
 
-        val mainJarFilePath = "kobalt-" + Kobalt.version + ".jar"
+        val jarFilePath = "kobalt-" + Kobalt.version + ".jar"
         val zipFilePath = KFiles.joinDir("kobaltBuild", "libs", "kobalt-" + Kobalt.version + ".zip")
         val zipFile = JarFile(zipFilePath)
         val stream = JarInputStream(FileInputStream(zipFilePath))
@@ -47,12 +24,11 @@ class VerifyKobaltZipTest : KobaltTest() {
         while (entry != null) {
             if (entry.name == "kobaltw") {
                 foundKobaltw = true
-            } else if (entry.name.endsWith(mainJarFilePath)) {
+            } else if (entry.name.endsWith(jarFilePath)) {
                 val ins = zipFile.getInputStream(entry)
                 if (ins.available() < 20000000) {
-                    throw AssertionError(mainJarFilePath + " is too small: " + mainJarFilePath)
+                    throw KobaltException(jarFilePath + " is too small: " + jarFilePath)
                 }
-                verifyMainJarFile(ins)
                 foundJar = true
             } else if (entry.name.endsWith("kobalt-wrapper.jar")) {
                 foundWrapperJar = true
@@ -62,21 +38,17 @@ class VerifyKobaltZipTest : KobaltTest() {
             entry = stream.nextEntry
         }
         if (! success) {
-            throw AssertionError("Found unexpected file in $zipFilePath")
+            throw KobaltException("Found unexpected file in $zipFilePath")
         }
         if (! foundKobaltw) {
-            throw AssertionError("Couldn't find kobaltw in $zipFilePath")
+            throw KobaltException("Couldn't find kobaltw in $zipFilePath")
         }
         if (! foundJar) {
-            throw AssertionError("Couldn't find jar in $zipFilePath")
+            throw KobaltException("Couldn't find jar in $zipFilePath")
         }
         if (! foundWrapperJar) {
-            throw AssertionError("Couldn't find wrapper jar in $zipFilePath")
+            throw KobaltException("Couldn't find wrapper jar in $zipFilePath")
         }
         log(1, "$zipFilePath looks correct")
     }
-
-    private fun verifyMainJarFile(ins: InputStream) {
-        assertExistsInJar(JarInputStream(ins), "com/beust/kobalt/MainKt.class")
-    }
 }