diff --git a/src/main/scala/sbt/BasicProjectTypes.scala b/src/main/scala/sbt/BasicProjectTypes.scala
index 299e21631..b512e70d1 100644
--- a/src/main/scala/sbt/BasicProjectTypes.scala
+++ b/src/main/scala/sbt/BasicProjectTypes.scala
@@ -254,7 +254,7 @@ trait BasicManagedProject extends ManagedProject with ReflectiveManagedProject w
 				Configurations.removeDuplicates(Configurations.defaultMavenConfigurations ++ reflective ++ extra)
 		}
 		else
-			reflective ++ extraDefaultConfigurations
+			reflective ++ extra
 	}
 	def extraDefaultConfigurations: List[Configuration] = Nil
 	def useIntegrationTestConfiguration = false
diff --git a/src/main/scala/sbt/FileUtilities.scala b/src/main/scala/sbt/FileUtilities.scala
index 6bb4ff04c..4174d9ab6 100644
--- a/src/main/scala/sbt/FileUtilities.scala
+++ b/src/main/scala/sbt/FileUtilities.scala
@@ -148,12 +148,12 @@ object FileUtilities
 				nextEntry.setTime(sourceFile.lastModified)
 				output.putNextEntry(nextEntry)
 				transferAndClose(new FileInputStream(sourceFile), output, log)
+				output.closeEntry()
 			}
 			else
 				log.warn("\tSource " + source + " does not exist.")
 		}
 		sources.foreach(add)
-		output.closeEntry()
 		None
 	}
 	
diff --git a/src/main/scala/sbt/ManageDependencies.scala b/src/main/scala/sbt/ManageDependencies.scala
index d7bfb4f4f..e136e64b7 100644
--- a/src/main/scala/sbt/ManageDependencies.scala
+++ b/src/main/scala/sbt/ManageDependencies.scala
@@ -235,7 +235,10 @@ object ManageDependencies
 					val (module, conf) = moduleAndConf
 					val explicitCheck =
 						if(check.checkExplicit)
+						{
+							log.debug("Checking explicit Scala dependencies")
 							checkDependencies(module, check.scalaVersion, check.configurations)
+						}
 						else
 							None
 					explicitCheck match
@@ -243,15 +246,18 @@ object ManageDependencies
 						case None =>
 							if(check.filterImplicit)
 							{
+								log.debug("Filtering transitive Scala dependencies")
 								val asDefault = toDefaultModuleDescriptor(module)
-								excludeScalaJars(asDefault, check.configurations)
+								excludeScalaJars(asDefault, check.configurations, config.log)
 								Right( (asDefault, conf) )
 							}
 							else
 								Right(moduleAndConf)
 						case Some(err) => Left(err)
 					}
-				case None => Right(moduleAndConf)
+				case None =>
+					log.debug("Not checking Scala dependencies")
+					Right(moduleAndConf)
 			}
 		
 		this.synchronized // Ivy is not thread-safe.  In particular, it uses a static DocumentBuilder, which is not thread-safe
@@ -294,7 +300,7 @@ object ManageDependencies
 	/** Adds exclusions for the scala library and compiler jars so that they are not downloaded.  This is
 	* done because normally these jars are already on the classpath and cannot/should not be overridden.  The version
 	* of Scala to use is done by setting scala.version in the project definition. */
-	private def excludeScalaJars(module: DefaultModuleDescriptor, configurations: Iterable[Configuration])
+	private def excludeScalaJars(module: DefaultModuleDescriptor, configurations: Iterable[Configuration], log: Logger)
 	{
 		val configurationNames =
 		{
@@ -310,7 +316,7 @@ object ManageDependencies
 			}
 		}
 		def excludeScalaJar(name: String): Unit =
-			module.addExcludeRule(excludeRule(ScalaArtifacts.Organization, name, configurationNames))
+			module.addExcludeRule(excludeRule(ScalaArtifacts.Organization, name, configurationNames, log))
 		excludeScalaJar(ScalaArtifacts.LibraryID)
 		excludeScalaJar(ScalaArtifacts.CompilerID)
 	}
@@ -325,9 +331,10 @@ object ManageDependencies
 	}
 	/** Creates an ExcludeRule that excludes artifacts with the given module organization and name for
 	* the given configurations. */
-	private def excludeRule(organization: String, name: String, configurationNames: Iterable[String]): ExcludeRule =
+	private def excludeRule(organization: String, name: String, configurationNames: Iterable[String], log: Logger): ExcludeRule =
 	{
 		val artifact = new ArtifactId(ModuleId.newInstance(organization, name), "*", "*", "*")
+		log.debug("Excluding " + artifact + " in " + configurationNames.mkString(", "))
 		val rule = new DefaultExcludeRule(artifact, ExactPatternMatcher.INSTANCE, Collections.emptyMap[AnyRef,AnyRef])
 		configurationNames.foreach(rule.addConfiguration)
 		rule
diff --git a/src/main/scala/sbt/Project.scala b/src/main/scala/sbt/Project.scala
index d1b6dcaad..19e88d85a 100644
--- a/src/main/scala/sbt/Project.scala
+++ b/src/main/scala/sbt/Project.scala
@@ -214,10 +214,10 @@ trait Project extends TaskManager with Dag[Project] with BasicEnvironment
 	* version of Scala being used to build the project.  ScalaVersion.current and ScalaVersion.cross should be used
 	* to read the version of Scala building the project.  This should only be used to change the version of Scala used
 	* for normal development (not cross-building)*/
-	final val scalaVersion = propertyOptional[String]("")
-	final val sbtVersion = propertyOptional[String]("")
+	final val scalaVersion = propertyOptional[String]("", true)
+	final val sbtVersion = propertyOptional[String]("", true)
 	final val projectInitialize = propertyOptional[Boolean](false)
-	final val projectScratch = propertyOptional[Boolean](false)
+	final val projectScratch = propertyOptional[Boolean](false, true)
 
 	/** If this project is cross-building, returns `base` with an additional path component containing the scala version.
 	* Otherwise, this returns `base`.
diff --git a/src/main/scala/sbt/ScalaProject.scala b/src/main/scala/sbt/ScalaProject.scala
index a6e42e9b2..c894637c1 100644
--- a/src/main/scala/sbt/ScalaProject.scala
+++ b/src/main/scala/sbt/ScalaProject.scala
@@ -120,8 +120,8 @@ trait ScalaProject extends SimpleScalaProject with FileTasks with MultiTaskProje
 	} completeWith(classNames(conditional, compilePath))
 	private def classNames(conditional: CompileConditional, compilePath: Path) =
 	{
-		val classes = conditional.analysis.allProducts.flatMap(Path.relativize(compilePath, _))
-		classes.map(_.relativePath.replace(java.io.File.separatorChar, '.').toList.dropRight(".class".length).mkString).toSeq
+		val classes = conditional.analysis.allProducts.flatMap(path => Path.relativize(compilePath.asFile, path.asFile))
+		classes.map(_.replace(java.io.File.separatorChar, '.').toList.dropRight(".class".length).mkString).toSeq
 	}
 	
 	def consoleTask(classpath : PathFinder): Task =