diff --git a/compile/integration/src/main/scala/sbt/compiler/AggressiveCompile.scala b/compile/integration/src/main/scala/sbt/compiler/AggressiveCompile.scala
index 2ff410e4d..b9f62b912 100644
--- a/compile/integration/src/main/scala/sbt/compiler/AggressiveCompile.scala
+++ b/compile/integration/src/main/scala/sbt/compiler/AggressiveCompile.scala
@@ -180,7 +180,8 @@ class AggressiveCompile(cacheFile: File)
 	private[this] def explicitBootClasspath(options: Seq[String]): Seq[File] =
 		options.dropWhile(_ != CompilerArguments.BootClasspathOption).drop(1).take(1).headOption.toList.flatMap(IO.parseClasspath)
 
-	import AnalysisFormats._
+	val formats = new sbt.inc.InternedAnalysisFormats()
+	import formats._
 	val store = AggressiveCompile.staticCache(cacheFile, AnalysisStore.sync(AnalysisStore.cached(FileBasedStore(cacheFile))))
 }
 object AggressiveCompile
diff --git a/compile/integration/src/main/scala/sbt/compiler/IncrementalCompiler.scala b/compile/integration/src/main/scala/sbt/compiler/IncrementalCompiler.scala
index daad493f1..fddb04f09 100644
--- a/compile/integration/src/main/scala/sbt/compiler/IncrementalCompiler.scala
+++ b/compile/integration/src/main/scala/sbt/compiler/IncrementalCompiler.scala
@@ -42,7 +42,8 @@ object IC extends IncrementalCompiler[Analysis, AnalyzingCompiler]
 	def readCacheUncaught(file: File): (Analysis, CompileSetup) =
 	{
 		import sbinary.DefaultProtocol.{immutableMapFormat, immutableSetFormat, StringFormat, tuple2Format}
-		import sbt.inc.AnalysisFormats._
+		val formats = new sbt.inc.InternedAnalysisFormats()
+		import formats._
 		sbt.IO.gzipFileIn(file)( in => sbinary.Operations.read[(Analysis, CompileSetup)](in) )
 	}
 }
diff --git a/compile/persist/src/main/scala/sbt/inc/AnalysisFormats.scala b/compile/persist/src/main/scala/sbt/inc/AnalysisFormats.scala
index cf6e05bd9..dc452565a 100644
--- a/compile/persist/src/main/scala/sbt/inc/AnalysisFormats.scala
+++ b/compile/persist/src/main/scala/sbt/inc/AnalysisFormats.scala
@@ -15,6 +15,7 @@ package inc
 	import Logger.{m2o, position, problem}
 	import Relations.{Source => RSource}
 
+@deprecated("Replaced by InternedAnalysisFormats. OK to remove in 0.14.", since="0.13.1")
 object AnalysisFormats
 {
 	type RFF = Relation[File, File]
diff --git a/compile/persist/src/main/scala/sbt/inc/InternedAnalysisFormats.scala b/compile/persist/src/main/scala/sbt/inc/InternedAnalysisFormats.scala
new file mode 100644
index 000000000..c9c299722
--- /dev/null
+++ b/compile/persist/src/main/scala/sbt/inc/InternedAnalysisFormats.scala
@@ -0,0 +1,98 @@
+/* sbt -- Simple Build Tool
+ * Copyright 2010 Mark Harrah
+ */
+package sbt
+package inc
+
+import java.io.File
+import sbinary._
+import DefaultProtocol.{FileFormat => _, _}
+import xsbti.api._
+import xsbti.compile.{Output => APIOutput, SingleOutput, MultipleOutput}
+import MultipleOutput.OutputGroup
+
+
+/**
+ * sbinary serialization format for Analysis objects.
+ *
+ * Uses an intern pool for entities that are repeated many times in relations: File and Compilation instances.
+ *
+ * Has state, so cannot be an object. To use, wild-card import the implicits from an instance of this class.
+ */
+private[sbt] final class InternedAnalysisFormats
+{
+	// Formats that reads/write internable objects directly (i.e., not via the intern pool).
+	// Note: Not implicit. We only want to use the full format explicitly, in specific places (such as when
+	// serializing the pool itself).
+	val fullFileFormat: Format[File] =  AnalysisFormats.fileFormat
+
+	// Format that reads/writes files via the intern pool.
+	val filePool = new InternPoolFormats[File](fullFileFormat)
+	implicit val fileFormat = filePool.itemFormat
+
+	// A convenient wrapper class for pool serialization. We can add more pools here in the future if needed.
+	final class Pools(var fileP: InternPool[File])
+
+	def initPools(analysis: Analysis) = new Pools(
+		filePool.initPool(allFiles(analysis))
+	)
+
+	val poolsFormat: Format[Pools] = wrap[Pools, InternPool[File]](_.fileP, new Pools(_))(filePool.poolFormat)
+
+	// Get all files mentioned in an Analysis.
+	// We take the union of all possible file sets, even though in theory some of these should be contained in others.
+	// This is safer in cases where the Analysis has discrepancies, for whatever reason.
+	def allFiles(analysis: Analysis): Array[File] = {
+		def all(rel: Relation[File, File]) = rel._1s ++ rel._2s
+		(analysis.stamps.allInternalSources ++ analysis.stamps.allBinaries ++ analysis.stamps.allProducts ++
+		 analysis.stamps.classNames.keySet ++ analysis.apis.allInternalSources ++
+		 all(analysis.relations.srcProd) ++ all(analysis.relations.binaryDep) ++ all(analysis.relations.internalSrcDep) ++
+		 analysis.relations.externalDep._1s ++ analysis.relations.classes._1s ++
+		 analysis.infos.allInfos.keySet).toArray
+	}
+
+	// Format that tacks a serialized version of the File and Compilation intern pools in front of the serialized Analysis.
+	def tupleToAnalysis(pools: Pools, stamps: Stamps, apis: APIs, relations: Relations, infos: SourceInfos, compilations: Compilations) = {
+		Analysis.Empty.copy(stamps, apis, relations, infos, compilations) // Ignore the pools. Their work is done.
+	}
+	def analysisToTuple(a: Analysis) = (initPools(a), a.stamps, a.apis, a.relations, a.infos, a.compilations)
+	implicit def analysisFormat(implicit stampsF: Format[Stamps], apisF: Format[APIs], relationsF: Format[Relations],
+															infosF: Format[SourceInfos], compilationsF: Format[Compilations]): Format[Analysis] =
+		asProduct6(tupleToAnalysis)(analysisToTuple)(poolsFormat, stampsF, apisF, relationsF, infosF, compilationsF)
+
+	// Formats in which we use the fullFileFormat. We don't want to use the pool when serializing CompileSetup.
+	implicit val outputGroupFormat: Format[OutputGroup] =
+		asProduct2((a: File,b: File) => new OutputGroup{ def sourceDirectory = a; def outputDirectory = b })({ out => (out.sourceDirectory, out.outputDirectory) })(fullFileFormat, fullFileFormat)
+
+	val multipleOutputFormat: Format[MultipleOutput] =
+		wrap[MultipleOutput, Array[OutputGroup]](_.outputGroups, { groups => new MultipleOutput { def outputGroups = groups }	})
+
+	val singleOutputFormat: Format[SingleOutput] =
+		wrap[SingleOutput, File](_.outputDirectory,{ out => new SingleOutput{def outputDirectory = out } })(fullFileFormat)
+
+	implicit val outputFormat: Format[APIOutput] = asUnion(singleOutputFormat, multipleOutputFormat)
+
+	// We use these implementations unchanged.
+	// TODO: Refactor out so we can import them with a wildcard?
+	implicit def relationFormat[A,B](implicit af: Format[Map[A, Set[B]]], bf: Format[Map[B, Set[A]]]) = AnalysisFormats.relationFormat(af, bf)
+	implicit def seqFormat[T](implicit optionFormat: Format[T]): Format[Seq[T]] = AnalysisFormats.seqFormat(optionFormat)
+	implicit val integerFormat = AnalysisFormats.integerFormat
+	implicit val severityFormat = AnalysisFormats.severityFormat
+	implicit val orderFormat = AnalysisFormats.orderFormat
+	implicit val existsFormat = AnalysisFormats.existsFormat
+	implicit val infoFormat = AnalysisFormats.infoFormat
+	implicit val infosFormat = AnalysisFormats.infosFormat
+	implicit val problemFormat = AnalysisFormats.problemFormat
+	implicit val positionFormat = AnalysisFormats.positionFormat
+	implicit val sourceFormat = AnalysisFormats.sourceFormat
+	implicit val apisFormat = AnalysisFormats.apisFormat
+	implicit val relationsSourceFormat = AnalysisFormats.relationsSourceFormat
+	implicit val relationsFormat = AnalysisFormats.relationsFormat
+	implicit val optsFormat = AnalysisFormats.optsFormat
+	implicit val hashStampFormat = AnalysisFormats.hashStampFormat
+	implicit val lastModFormat = AnalysisFormats.lastModFormat
+	implicit val stampFormat = AnalysisFormats.stampFormat
+	implicit val stampsFormat = AnalysisFormats.stampsFormat
+	implicit val setupFormat = AnalysisFormats.setupFormat
+	implicit val compilationsFormat = AnalysisFormats.compilationsFormat
+}
diff --git a/main/actions/src/main/scala/sbt/Sync.scala b/main/actions/src/main/scala/sbt/Sync.scala
index 6c64d9b66..2851e2414 100644
--- a/main/actions/src/main/scala/sbt/Sync.scala
+++ b/main/actions/src/main/scala/sbt/Sync.scala
@@ -71,7 +71,8 @@ object Sync
 		import sbinary._
 		import Operations.{read, write}
 		import DefaultProtocol.{FileFormat => _, _}
-		import inc.AnalysisFormats._
+		val formats = new sbt.inc.InternedAnalysisFormats()
+		import formats._
 
 	def writeInfo[F <: FileInfo](file: File, relation: Relation[File, File], info: Map[File, F])(implicit infoFormat: Format[F]): Unit =
 		IO.gzipFileOut(file) { out =>