diff --git a/java/app.go b/java/app.go
index 490a03d..42ae236 100644
--- a/java/app.go
+++ b/java/app.go
@@ -89,7 +89,7 @@
 		publicResourcesFile, proguardOptionsFile, aaptJavaFileList :=
 			CreateResourceJavaFiles(ctx, aaptRJavaFlags, aaptDeps)
 		a.aaptJavaFileList = aaptJavaFileList
-		a.ExtraSrcLists = append(a.ExtraSrcLists, aaptJavaFileList)
+		// TODO(ccross):  export aapt generated java files as a src jar
 
 		if a.appProperties.Export_package_resources {
 			aaptPackageFlags := append([]string(nil), aaptFlags...)
diff --git a/java/builder.go b/java/builder.go
index 8992f68..efe6256 100644
--- a/java/builder.go
+++ b/java/builder.go
@@ -40,7 +40,7 @@
 		blueprint.RuleParams{
 			Command: `rm -rf "$outDir" "$annoDir" && mkdir -p "$outDir" "$annoDir" && ` +
 				`${config.JavacWrapper}${config.JavacCmd} ${config.JavacHeapFlags} ${config.CommonJdkFlags} ` +
-				`$javacFlags $bootClasspath $classpath ` +
+				`$javacFlags $sourcepath $bootClasspath $classpath ` +
 				`-source $javaVersion -target $javaVersion ` +
 				`-d $outDir -s $annoDir @$out.rsp && ` +
 				`${config.SoongZipCmd} -jar -o $out -C $outDir -D $outDir`,
@@ -48,13 +48,13 @@
 			Rspfile:        "$out.rsp",
 			RspfileContent: "$in",
 		},
-		"javacFlags", "bootClasspath", "classpath", "outDir", "annoDir", "javaVersion")
+		"javacFlags", "sourcepath", "bootClasspath", "classpath", "outDir", "annoDir", "javaVersion")
 
 	errorprone = pctx.AndroidStaticRule("errorprone",
 		blueprint.RuleParams{
 			Command: `rm -rf "$outDir" "$annoDir" && mkdir -p "$outDir" "$annoDir" && ` +
 				`${config.ErrorProneCmd} ` +
-				`$javacFlags $bootClasspath $classpath ` +
+				`$javacFlags $sourcepath $bootClasspath $classpath ` +
 				`-source $javaVersion -target $javaVersion ` +
 				`-d $outDir -s $annoDir @$out.rsp && ` +
 				`${config.SoongZipCmd} -jar -o $out -C $outDir -D $outDir`,
@@ -67,7 +67,7 @@
 			Rspfile:        "$out.rsp",
 			RspfileContent: "$in",
 		},
-		"javacFlags", "bootClasspath", "classpath", "outDir", "annoDir", "javaVersion")
+		"javacFlags", "sourcepath", "bootClasspath", "classpath", "outDir", "annoDir", "javaVersion")
 
 	jar = pctx.AndroidStaticRule("jar",
 		blueprint.RuleParams{
@@ -135,49 +135,41 @@
 	protoOutFlag string
 }
 
-func TransformJavaToClasses(ctx android.ModuleContext, srcFiles, srcFileLists android.Paths,
-	flags javaBuilderFlags, deps android.Paths) android.ModuleOutPath {
+func TransformJavaToClasses(ctx android.ModuleContext, outputFile android.WritablePath,
+	srcFiles android.Paths, srcJars classpath,
+	flags javaBuilderFlags, deps android.Paths) {
 
-	return transformJavaToClasses(ctx, srcFiles, srcFileLists, flags, deps,
-		"classes-compiled.jar", "", "javac", javac)
+	transformJavaToClasses(ctx, outputFile, srcFiles, srcJars, flags, deps,
+		"", "javac", javac)
 }
 
-func RunErrorProne(ctx android.ModuleContext, srcFiles, srcFileLists android.Paths,
-	flags javaBuilderFlags) android.Path {
+func RunErrorProne(ctx android.ModuleContext, outputFile android.WritablePath,
+	srcFiles android.Paths, srcJars classpath,
+	flags javaBuilderFlags) {
 
 	if config.ErrorProneJar == "" {
 		ctx.ModuleErrorf("cannot build with Error Prone, missing external/error_prone?")
-		return nil
 	}
 
-	return transformJavaToClasses(ctx, srcFiles, srcFileLists, flags, nil,
-		"classes-errorprone.list", "-errorprone", "errorprone", errorprone)
+	transformJavaToClasses(ctx, outputFile, srcFiles, srcJars, flags, nil,
+		"-errorprone", "errorprone", errorprone)
 }
 
 // transformJavaToClasses takes source files and converts them to a jar containing .class files.
-// srcFiles is a list of paths to sources, srcFileLists is a list of paths to files that contain
-// paths to sources.  There is no dependency on the sources passed through srcFileLists, those
-// must be added through the deps argument, which contains a list of paths that should be added
-// as implicit dependencies.  flags contains various command line flags to be passed to the
-// compiler.
+// srcFiles is a list of paths to sources, srcJars is a list of paths to jar files that contain
+// sources.  flags contains various command line flags to be passed to the compiler.
 //
 // This method may be used for different compilers, including javac and Error Prone.  The rule
 // argument specifies which command line to use and desc sets the description of the rule that will
 // be printed at build time.  The stem argument provides the file name of the output jar, and
 // suffix will be appended to various intermediate files and directories to avoid collisions when
 // this function is called twice in the same module directory.
-func transformJavaToClasses(ctx android.ModuleContext, srcFiles, srcFileLists android.Paths,
-	flags javaBuilderFlags, deps android.Paths, stem, suffix, desc string,
-	rule blueprint.Rule) android.ModuleOutPath {
+func transformJavaToClasses(ctx android.ModuleContext, outputFile android.WritablePath,
+	srcFiles android.Paths, srcJars classpath,
+	flags javaBuilderFlags, deps android.Paths,
+	intermediatesSuffix, desc string, rule blueprint.Rule) {
 
-	outputFile := android.PathForModuleOut(ctx, stem)
-
-	javacFlags := flags.javacFlags
-	if len(srcFileLists) > 0 {
-		javacFlags += " " + android.JoinWithPrefix(srcFileLists.Strings(), "@")
-	}
-
-	deps = append(deps, srcFileLists...)
+	deps = append(deps, srcJars...)
 
 	var bootClasspath string
 	if flags.javaVersion == "1.9" {
@@ -197,22 +189,19 @@
 		Inputs:      srcFiles,
 		Implicits:   deps,
 		Args: map[string]string{
-			"javacFlags":    javacFlags,
+			"javacFlags":    flags.javacFlags,
 			"bootClasspath": bootClasspath,
+			"sourcepath":    srcJars.JavaSourcepath(),
 			"classpath":     flags.classpath.JavaClasspath(),
-			"outDir":        android.PathForModuleOut(ctx, "classes"+suffix).String(),
-			"annoDir":       android.PathForModuleOut(ctx, "anno"+suffix).String(),
+			"outDir":        android.PathForModuleOut(ctx, "classes"+intermediatesSuffix).String(),
+			"annoDir":       android.PathForModuleOut(ctx, "anno"+intermediatesSuffix).String(),
 			"javaVersion":   flags.javaVersion,
 		},
 	})
-
-	return outputFile
 }
 
-func TransformResourcesToJar(ctx android.ModuleContext, jarArgs []string,
-	deps android.Paths) android.Path {
-
-	outputFile := android.PathForModuleOut(ctx, "res.jar")
+func TransformResourcesToJar(ctx android.ModuleContext, outputFile android.WritablePath,
+	jarArgs []string, deps android.Paths) {
 
 	ctx.ModuleBuild(pctx, android.ModuleBuildParams{
 		Rule:        jar,
@@ -223,18 +212,10 @@
 			"jarArgs": strings.Join(jarArgs, " "),
 		},
 	})
-
-	return outputFile
 }
 
-func TransformJarsToJar(ctx android.ModuleContext, stem string, jars android.Paths,
-	manifest android.OptionalPath, stripDirs bool) android.Path {
-
-	outputFile := android.PathForModuleOut(ctx, stem)
-
-	if len(jars) == 1 && !manifest.Valid() {
-		return jars[0]
-	}
+func TransformJarsToJar(ctx android.ModuleContext, outputFile android.WritablePath,
+	jars android.Paths, manifest android.OptionalPath, stripDirs bool) {
 
 	var deps android.Paths
 
@@ -258,14 +239,11 @@
 			"jarArgs": strings.Join(jarArgs, " "),
 		},
 	})
-
-	return outputFile
 }
 
-func TransformDesugar(ctx android.ModuleContext, classesJar android.Path,
-	flags javaBuilderFlags) android.Path {
+func TransformDesugar(ctx android.ModuleContext, outputFile android.WritablePath,
+	classesJar android.Path, flags javaBuilderFlags) {
 
-	outputFile := android.PathForModuleOut(ctx, "classes-desugar.jar")
 	dumpDir := android.PathForModuleOut(ctx, "desugar_dumped_classes")
 
 	javaFlags := ""
@@ -294,17 +272,14 @@
 			"desugarFlags":   flags.desugarFlags,
 		},
 	})
-
-	return outputFile
 }
 
 // Converts a classes.jar file to classes*.dex, then combines the dex files with any resources
 // in the classes.jar file into a dex jar.
-func TransformClassesJarToDexJar(ctx android.ModuleContext, stem string, classesJar android.Path,
-	flags javaBuilderFlags) android.Path {
+func TransformClassesJarToDexJar(ctx android.ModuleContext, outputFile android.WritablePath,
+	classesJar android.Path, flags javaBuilderFlags) {
 
 	outDir := android.PathForModuleOut(ctx, "dex")
-	outputFile := android.PathForModuleOut(ctx, stem)
 
 	ctx.ModuleBuild(pctx, android.ModuleBuildParams{
 		Rule:        dx,
@@ -316,12 +291,10 @@
 			"outDir":  outDir.String(),
 		},
 	})
-
-	return outputFile
 }
 
-func TransformJarJar(ctx android.ModuleContext, classesJar android.Path, rulesFile android.Path) android.ModuleOutPath {
-	outputFile := android.PathForModuleOut(ctx, "classes-jarjar.jar")
+func TransformJarJar(ctx android.ModuleContext, outputFile android.WritablePath,
+	classesJar android.Path, rulesFile android.Path) {
 	ctx.ModuleBuild(pctx, android.ModuleBuildParams{
 		Rule:        jarjar,
 		Description: "jarjar",
@@ -332,12 +305,20 @@
 			"rulesFile": rulesFile.String(),
 		},
 	})
-
-	return outputFile
 }
 
 type classpath []android.Path
 
+// Returns a -sourcepath argument in the form javac expects.  If the list is empty returns
+// -sourcepath "" to ensure javac does not fall back to searching the classpath for sources.
+func (x *classpath) JavaSourcepath() string {
+	if len(*x) > 0 {
+		return "-sourcepath " + strings.Join(x.Strings(), ":")
+	} else {
+		return `-sourcepath ""`
+	}
+}
+
 // Returns a -classpath argument in the form java or javac expects
 func (x *classpath) JavaClasspath() string {
 	if len(*x) > 0 {
diff --git a/java/gen.go b/java/gen.go
index e55be91..e12a71c 100644
--- a/java/gen.go
+++ b/java/gen.go
@@ -85,7 +85,7 @@
 }
 
 func (j *Module) genSources(ctx android.ModuleContext, srcFiles android.Paths,
-	flags javaBuilderFlags) (android.Paths, android.Paths) {
+	flags javaBuilderFlags) (android.Paths, classpath) {
 
 	var protoFiles android.Paths
 	outSrcFiles := make(android.Paths, 0, len(srcFiles))
@@ -106,16 +106,17 @@
 		}
 	}
 
-	var outSrcFileLists android.Paths
+	var outSrcJars classpath
 
 	if len(protoFiles) > 0 {
-		protoFileList := genProto(ctx, protoFiles,
+		protoSrcJar := android.PathForModuleGen(ctx, "proto.src.jar")
+		genProto(ctx, protoSrcJar, protoFiles,
 			flags.protoFlags, flags.protoOutFlag, "")
 
-		outSrcFileLists = append(outSrcFileLists, protoFileList)
+		outSrcJars = append(outSrcJars, protoSrcJar)
 	}
 
-	return outSrcFiles, outSrcFileLists
+	return outSrcFiles, outSrcJars
 }
 
 func LogtagsSingleton() blueprint.Singleton {
diff --git a/java/java.go b/java/java.go
index c3b7557..770c9c1 100644
--- a/java/java.go
+++ b/java/java.go
@@ -169,9 +169,9 @@
 
 	logtagsSrcs android.Paths
 
-	// filelists of extra source files that should be included in the javac command line,
+	// jars containing source files that should be included in the javac command line,
 	// for example R.java generated by aapt for android apps
-	ExtraSrcLists android.Paths
+	ExtraSrcJars android.Paths
 
 	// installed file for binary dependency
 	installFile android.Path
@@ -370,7 +370,7 @@
 	staticJars         android.Paths
 	staticJarResources android.Paths
 	aidlIncludeDirs    android.Paths
-	srcFileLists       android.Paths
+	srcJars            android.Paths
 	systemModules      android.Path
 	aidlPreprocess     android.OptionalPath
 }
@@ -422,7 +422,7 @@
 			if ctx.ModuleName() == "framework" {
 				// framework.jar has a one-off dependency on the R.java and Manifest.java files
 				// generated by framework-res.apk
-				deps.srcFileLists = append(deps.srcFileLists, module.(*AndroidApp).aaptJavaFileList)
+				// TODO(ccross): aapt java files should go in a src jar
 			}
 		default:
 			panic(fmt.Errorf("unknown dependency %q for %q", otherName, ctx.ModuleName()))
@@ -483,13 +483,12 @@
 		flags = protoFlags(ctx, &j.protoProperties, flags)
 	}
 
-	var srcFileLists android.Paths
+	var srcJars classpath
+	srcFiles, srcJars = j.genSources(ctx, srcFiles, flags)
 
-	srcFiles, srcFileLists = j.genSources(ctx, srcFiles, flags)
+	srcJars = append(srcJars, deps.srcJars...)
 
-	srcFileLists = append(srcFileLists, deps.srcFileLists...)
-
-	srcFileLists = append(srcFileLists, j.ExtraSrcLists...)
+	srcJars = append(srcJars, j.ExtraSrcJars...)
 
 	var jars android.Paths
 
@@ -501,12 +500,14 @@
 			// a rebuild when error-prone is turned off).
 			// TODO(ccross): Once we always compile with javac9 we may be able to conditionally
 			//    enable error-prone without affecting the output class files.
-			errorprone := RunErrorProne(ctx, srcFiles, srcFileLists, flags)
+			errorprone := android.PathForModuleOut(ctx, "classes-errorprone.list")
+			RunErrorProne(ctx, errorprone, srcFiles, srcJars, flags)
 			extraJarDeps = append(extraJarDeps, errorprone)
 		}
 
 		// Compile java sources into .class files
-		classes := TransformJavaToClasses(ctx, srcFiles, srcFileLists, flags, extraJarDeps)
+		classes := android.PathForModuleOut(ctx, "classes-compiled.jar")
+		TransformJavaToClasses(ctx, classes, srcFiles, srcJars, flags, extraJarDeps)
 		if ctx.Failed() {
 			return
 		}
@@ -533,7 +534,8 @@
 	}
 
 	if len(resArgs) > 0 {
-		resourceJar := TransformResourcesToJar(ctx, resArgs, resDeps)
+		resourceJar := android.PathForModuleOut(ctx, "res.jar")
+		TransformResourcesToJar(ctx, resourceJar, resArgs, resDeps)
 		if ctx.Failed() {
 			return
 		}
@@ -548,12 +550,23 @@
 
 	// Combine the classes built from sources, any manifests, and any static libraries into
 	// classes.jar.  If there is only one input jar this step will be skipped.
-	outputFile := TransformJarsToJar(ctx, "classes.jar", jars, manifest, false)
+	var outputFile android.Path
+
+	if len(jars) == 1 && !manifest.Valid() {
+		// Optimization: skip the combine step if there is nothing to do
+		outputFile = jars[0]
+	} else {
+		combinedJar := android.PathForModuleOut(ctx, "classes.jar")
+		TransformJarsToJar(ctx, combinedJar, jars, manifest, false)
+		outputFile = combinedJar
+	}
 
 	if j.properties.Jarjar_rules != nil {
 		jarjar_rules := android.PathForModuleSrc(ctx, *j.properties.Jarjar_rules)
 		// Transform classes.jar into classes-jarjar.jar
-		outputFile = TransformJarJar(ctx, outputFile, jarjar_rules)
+		jarjarFile := android.PathForModuleOut(ctx, "classes-jarjar.jar")
+		TransformJarJar(ctx, jarjarFile, outputFile, jarjar_rules)
+		outputFile = jarjarFile
 		if ctx.Failed() {
 			return
 		}
@@ -609,13 +622,17 @@
 
 		flags.desugarFlags = strings.Join(desugarFlags, " ")
 
-		desugarJar := TransformDesugar(ctx, outputFile, flags)
+		desugarJar := android.PathForModuleOut(ctx, "classes-desugar.jar")
+		TransformDesugar(ctx, desugarJar, outputFile, flags)
+		outputFile = desugarJar
 		if ctx.Failed() {
 			return
 		}
 
 		// Compile classes.jar into classes.dex and then javalib.jar
-		outputFile = TransformClassesJarToDexJar(ctx, "javalib.jar", desugarJar, flags)
+		javalibJar := android.PathForModuleOut(ctx, "javalib.jar")
+		TransformClassesJarToDexJar(ctx, javalibJar, desugarJar, flags)
+		outputFile = javalibJar
 		if ctx.Failed() {
 			return
 		}
@@ -790,7 +807,9 @@
 func (j *Import) GenerateAndroidBuildActions(ctx android.ModuleContext) {
 	j.classpathFiles = android.PathsForModuleSrc(ctx, j.properties.Jars)
 
-	j.combinedClasspathFile = TransformJarsToJar(ctx, "classes.jar", j.classpathFiles, android.OptionalPath{}, false)
+	outputFile := android.PathForModuleOut(ctx, "classes.jar")
+	TransformJarsToJar(ctx, outputFile, j.classpathFiles, android.OptionalPath{}, false)
+	j.combinedClasspathFile = outputFile
 }
 
 var _ Dependency = (*Import)(nil)
diff --git a/java/proto.go b/java/proto.go
index dd8cabd..fc259a5 100644
--- a/java/proto.go
+++ b/java/proto.go
@@ -30,20 +30,21 @@
 		blueprint.RuleParams{
 			Command: `rm -rf $outDir && mkdir -p $outDir && ` +
 				`$protocCmd $protoOut=$protoOutFlags:$outDir $protoFlags $in && ` +
-				`find $outDir -name "*.java" > $out`,
-			CommandDeps: []string{"$protocCmd"},
+				`${config.SoongZipCmd} -jar -o $out -C $outDir -D $outDir`,
+			CommandDeps: []string{
+				"$protocCmd",
+				"${config.SoongZipCmd}",
+			},
 		}, "protoFlags", "protoOut", "protoOutFlags", "outDir")
 )
 
-func genProto(ctx android.ModuleContext, protoFiles android.Paths,
-	protoFlags string, protoOut, protoOutFlags string) android.WritablePath {
-
-	protoFileList := android.PathForModuleGen(ctx, "proto.filelist")
+func genProto(ctx android.ModuleContext, outputSrcJar android.WritablePath,
+	protoFiles android.Paths, protoFlags string, protoOut, protoOutFlags string) {
 
 	ctx.ModuleBuild(pctx, android.ModuleBuildParams{
 		Rule:        proto,
 		Description: "protoc " + protoFiles[0].Rel(),
-		Output:      protoFileList,
+		Output:      outputSrcJar,
 		Inputs:      protoFiles,
 		Args: map[string]string{
 			"outDir":        android.ProtoDir(ctx).String(),
@@ -52,8 +53,6 @@
 			"protoFlags":    protoFlags,
 		},
 	})
-
-	return protoFileList
 }
 
 func protoDeps(ctx android.BottomUpMutatorContext, p *android.ProtoProperties) {