diff --git a/main/Build.scala b/main/Build.scala
index db31db908..d0448136c 100644
--- a/main/Build.scala
+++ b/main/Build.scala
@@ -287,11 +287,16 @@ object BuildPaths
 
 	def projectStandard(base: File) = base / "project"
 	def projectHidden(base: File) = base / ConfigDirectoryName
-	def selectProjectDir(base: File) =
+	def selectProjectDir(base: File, log: Logger) =
 	{
 		val a = projectHidden(base)
 		val b = projectStandard(base)
-		if(a.exists) a else b
+		if(a.exists)
+		{
+			log.warn("Alternative project directory " + ConfigDirectoryName + " (" + a + ") has been deprecated since sbt 0.12.0.\n  Please use the standard location: " + b)
+			a
+		}
+		else b
 	}
 
 	final val PluginsDirectoryName = "plugins"
diff --git a/main/Load.scala b/main/Load.scala
index ca2a52e7e..33277aa49 100644
--- a/main/Load.scala
+++ b/main/Load.scala
@@ -373,7 +373,7 @@ object Load
 	def loadUnit(uri: URI, localBase: File, s: State, config: LoadBuildConfiguration): BuildUnit =
 	{
 		val normBase = localBase.getCanonicalFile
-		val defDir = selectProjectDir(normBase)
+		val defDir = selectProjectDir(normBase, config.log)
 		val pluginDir = pluginDirectory(defDir)
 		val (plugs, defs) = if(pluginDir.exists) loadUnitOld(defDir, pluginDir, s, config) else loadUnitNew(defDir, s, config)
 		new BuildUnit(uri, normBase, defs, plugs)