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 5966616c..043e2bac 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
@@ -44,7 +44,7 @@ sealed class IFileSpec {
             val result = arrayListOf<File>()
             val includes = Glob(*spec.toTypedArray())
 
-            if (File(filePath).isDirectory) {
+            if (File(baseDir, filePath).isDirectory) {
                 val orgRootDir = (if (File(filePath).isAbsolute) Paths.get(filePath)
                     else if (baseDir != null) Paths.get(baseDir, filePath)
                     else Paths.get(filePath)).run { normalize() }
diff --git a/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/misc/JarUtils.kt b/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/misc/JarUtils.kt
index 0b39ed58..13c0ebd3 100644
--- a/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/misc/JarUtils.kt
+++ b/modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/misc/JarUtils.kt
@@ -172,7 +172,7 @@ class IncludedFile(val fromOriginal: From, val toOriginal: To, val specs: List<I
         val result = arrayListOf<File>()
         specs.forEach { spec ->
 //            val fullDir = if (directory == null) from else KFiles.joinDir(directory, from)
-            spec.toFiles(directory, from).filter { it.isFile }.forEach { source ->
+            spec.toFiles(directory, from).forEach { source ->
                 result.add(if (source.isAbsolute) source else File(source.path))
             }
         }