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 8d4ea7bd..dc34f0f2 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
@@ -341,8 +341,9 @@ open class JvmCompilerPlugin @Inject constructor(
             }
         }
 
-        extraSourceFiles.addAll(contributedSourceDirs.filter { it.exists() }.map { it.path })
-        val allSources= (sourceFiles + extraSourceFiles).distinct()
+        val allSources = (sourceFiles + extraSourceFiles).distinct().filter { File(it).exists() }.map {
+            File(projectDirectory, it).path
+        }
         // Finally, alter the info with the compiler interceptors before returning it
         val initialActionInfo = CompilerActionInfo(projectDirectory.path, classpath, allSources,
                 sourceSuffixes, buildDirectory, emptyList() /* the flags will be provided by flag contributors */)
diff --git a/src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt b/src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt
index 688651ab..860a6ea0 100644
--- a/src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt
+++ b/src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt
@@ -73,7 +73,7 @@ class JavaCompiler @Inject constructor(val jvmCompiler: JvmCompiler) {
                     }
 
                     allArgs.addAll(info.compilerArgs)
-                    allArgs.addAll(info.sourceFiles)
+                    allArgs.addAll(info.sourceFiles.filter { File(it).isFile })
 
                     val pb = ProcessBuilder(allArgs)
                     pb.inheritIO()