diff --git a/src/main/kotlin/com/beust/kobalt/app/BuildFileCompiler.kt b/src/main/kotlin/com/beust/kobalt/app/BuildFileCompiler.kt
index 7037dcdc..89250464 100644
--- a/src/main/kotlin/com/beust/kobalt/app/BuildFileCompiler.kt
+++ b/src/main/kotlin/com/beust/kobalt/app/BuildFileCompiler.kt
@@ -83,6 +83,15 @@ class BuildFileCompiler @Inject constructor(@Assisted("buildSources") val buildS
         var errorTaskResult: TaskResult? = null
         val projects = arrayListOf<Project>()
 
+        // If buildScript.jar was generated by a different version, wipe our temporary build directory
+        val buildScriptJarDir = KFiles.findBuildScriptDir(root.absolutePath)
+        buildScriptJarDir.let { dir ->
+            if (! VersionFile.isSameVersionFile(dir)) {
+                kobaltLog(1, "Detected new installation, wiping $dir")
+                dir.listFiles().map(File::delete)
+            }
+        }
+
         // Parse the build files in kobalt/src/*.kt, which will analyze all the buildScriptInfo{} sections
         // and possibly add new source build directories. The output of this process is a new Build.kt
         // file that contains the aggregation of all the build files with the profiles applied and with
@@ -94,16 +103,6 @@ class BuildFileCompiler @Inject constructor(@Assisted("buildSources") val buildS
         //
         context.internalContext.absoluteDir = buildSources.root
 
-        // If buildScript.jar was generated by a different version, wipe them it case the API
-        // changed in-between
-        val buildScriptJarDir = KFiles.findBuildScriptDir(root.absolutePath)
-        buildScriptJarDir.let { dir ->
-            if (! VersionFile.isSameVersionFile(dir)) {
-                kobaltLog(1, "Detected new installation, wiping $dir")
-                dir.listFiles().map(File::delete)
-            }
-        }
-
         val buildScriptJarFile = File(KFiles.findBuildScriptDir(root.absolutePath), SCRIPT_JAR)
 
         //