diff --git a/src/main/kotlin/com/beust/kobalt/Main.kt b/src/main/kotlin/com/beust/kobalt/Main.kt
index 02130286..be86def3 100644
--- a/src/main/kotlin/com/beust/kobalt/Main.kt
+++ b/src/main/kotlin/com/beust/kobalt/Main.kt
@@ -11,7 +11,6 @@ import com.beust.kobalt.kotlin.BuildFile
 import com.beust.kobalt.kotlin.BuildFileCompiler
 import com.beust.kobalt.maven.DepFactory
 import com.beust.kobalt.maven.Http
-import com.beust.kobalt.maven.KobaltException
 import com.beust.kobalt.maven.LocalRepo
 import com.beust.kobalt.misc.*
 import com.beust.kobalt.wrapper.Wrapper
@@ -145,25 +144,8 @@ private class Main @Inject constructor(
             if (! buildFile.exists()) {
                 error(buildFile.path.toFile().path + " does not exist")
             } else {
-                var allProjects = arrayListOf<Project>()
-                try {
-                    allProjects.addAll(buildFileCompilerFactory.create(listOf(buildFile), pluginInfo)
-                            .compileBuildFiles(args))
-                } catch(ex: KobaltException) {
-                    throw ex
-                } catch(ex: Throwable) {
-                    ex.printStackTrace()
-                    // This can happen if the ABI for the build script file changed. Try to wipe .kobalt.
-                    log(2, "Couldn't parse preBuildScript.jar: ${ex.message}")
-                    if (! File(".kobalt").deleteRecursively()) {
-                        warn("Couldn't delete the .kobalt directory, please delete it manually and try again")
-                        return 1
-                    } else {
-                        log(1, "Deleted .kobalt")
-                        allProjects.addAll(buildFileCompilerFactory.create(listOf(buildFile), pluginInfo)
-                                .compileBuildFiles(args))
-                    }
-                }
+                val allProjects = buildFileCompilerFactory.create(listOf(buildFile), pluginInfo)
+                        .compileBuildFiles(args)
 
                 //
                 // Now that we have projects, add all the repos from repo contributors that need a Project
@@ -171,6 +153,7 @@ private class Main @Inject constructor(
                 allProjects.forEach { addReposFromContributors(it) }
 
                 log(2, "Final list of repos:\n  " + Kobalt.repos.joinToString("\n  "))
+
                 if (args.tasks) {
                     //
                     // List of tasks
diff --git a/src/main/kotlin/com/beust/kobalt/kotlin/BuildFileCompiler.kt b/src/main/kotlin/com/beust/kobalt/kotlin/BuildFileCompiler.kt
index 975952a7..2faed971 100644
--- a/src/main/kotlin/com/beust/kobalt/kotlin/BuildFileCompiler.kt
+++ b/src/main/kotlin/com/beust/kobalt/kotlin/BuildFileCompiler.kt
@@ -26,6 +26,11 @@ import java.util.*
 import java.util.jar.JarInputStream
 import javax.inject.Inject
 
+/**
+ * Manage the compilation of Build.kt. There are two passes for this processing:
+ * 1) Extract the repos() and plugins() statements in a separate .kt and compile it into preBuildScript.jar.
+ * 2) Actually build the whole Build.kt file after adding to the classpath whatever phase 1 found (plugins, repos)
+ */
 public class BuildFileCompiler @Inject constructor(@Assisted("buildFiles") val buildFiles: List<BuildFile>,
         @Assisted val pluginInfo: PluginInfo, val files: KFiles, val plugins: Plugins,
         val jvmCompiler: JvmCompiler, val pluginProperties: PluginProperties) {
@@ -39,14 +44,20 @@ public class BuildFileCompiler @Inject constructor(@Assisted("buildFiles") val b
     private val SCRIPT_JAR = "buildScript.jar"
 
     fun compileBuildFiles(args: Args): List<Project> {
+        //
+        // Create the KobaltContext
+        //
         val context = KobaltContext(args)
         context.pluginInfo = pluginInfo
         context.pluginProperties = pluginProperties
         Kobalt.context = context
 
+        //
+        // Find all the projects in the build file, possibly compiling them
+        //
         val allProjects = findProjects(context)
-
         plugins.applyPlugins(context, allProjects)
+
         return allProjects
     }
 
@@ -56,6 +67,15 @@ public class BuildFileCompiler @Inject constructor(@Assisted("buildFiles") val b
             val pluginUrls = findPlugInUrls(context, buildFile)
             val buildScriptJarFile = File(KFiles.findBuildScriptLocation(buildFile, SCRIPT_JAR))
 
+            // If the script jar files were generated by a different version, wipe them in case the API
+            // changed in-between
+            buildScriptJarFile.parentFile.let { dir ->
+                if (! isSameVersionFile(dir)) {
+                    log(1, "Detected new installation, wiping $dir")
+                    dir.listFiles().map { it.delete() }
+                }
+            }
+
             maybeCompileBuildFile(context, buildFile, buildScriptJarFile, pluginUrls)
             val buildScriptInfo = parseBuildScriptJarFile(buildScriptJarFile, pluginUrls)
             result.addAll(buildScriptInfo.projects)
@@ -127,6 +147,7 @@ public class BuildFileCompiler @Inject constructor(@Assisted("buildFiles") val b
         if (! isUpToDate(buildFile, File(buildScriptJar))) {
             buildScriptJarFile.parentFile.mkdirs()
             generateJarFile(context, BuildFile(Paths.get(pluginSourceFile.path), "Plugins"), buildScriptJarFile)
+            generateVersionFile(buildScriptJarFile.parentFile)
         }
 
         //
@@ -144,6 +165,15 @@ public class BuildFileCompiler @Inject constructor(@Assisted("buildFiles") val b
         return result
     }
 
+    private val VERSION_FILE = "version.txt"
+
+    private fun generateVersionFile(directory: File) {
+        KFiles.saveFile(File(directory, VERSION_FILE), Kobalt.version)
+    }
+
+    private fun isSameVersionFile(directory: File) =
+        File(directory, VERSION_FILE).readText() == Kobalt.version
+
     private fun generateJarFile(context: KobaltContext, buildFile: BuildFile, buildScriptJarFile: File) {
         val kotlintDeps = jvmCompiler.calculateDependencies(null, context, listOf<IClasspathDependency>())
         val deps: List<String> = kotlintDeps.map { it.jarFile.get().absolutePath }