diff --git a/bootstrap/bootstrap.go b/bootstrap/bootstrap.go
index a7818ab..035e884 100644
--- a/bootstrap/bootstrap.go
+++ b/bootstrap/bootstrap.go
@@ -735,45 +735,41 @@ func (s *singleton) GenerateBuildActions(ctx blueprint.SingletonContext) {
 		ctx.AddSubninja(subninja)
 	}
 
-	if s.config.stage == StagePrimary {
-		for _, i := range s.config.primaryBuilderInvocations {
-			flags := make([]string, 0)
-			flags = append(flags, primaryBuilderCmdlinePrefix...)
-			flags = append(flags, i.Args...)
+	for _, i := range s.config.primaryBuilderInvocations {
+		flags := make([]string, 0)
+		flags = append(flags, primaryBuilderCmdlinePrefix...)
+		flags = append(flags, i.Args...)
 
-			// Build the main build.ninja
-			ctx.Build(pctx, blueprint.BuildParams{
-				Rule:    generateBuildNinja,
-				Outputs: i.Outputs,
-				Inputs:  i.Inputs,
-				Args: map[string]string{
-					"builder": primaryBuilderFile,
-					"extra":   strings.Join(flags, " "),
-				},
-				// soong_ui explicitly requests what it wants to be build. This is
-				// because the same Ninja file contains instructions to run
-				// soong_build, run bp2build and to generate the JSON module graph.
-				Optional: true,
-			})
-		}
-	}
-
-	if s.config.stage == StageMain {
-		// Add a phony target for building various tools that are part of blueprint
+		// Build the main build.ninja
 		ctx.Build(pctx, blueprint.BuildParams{
-			Rule:    blueprint.Phony,
-			Outputs: []string{"blueprint_tools"},
-			Inputs:  blueprintTools,
-		})
-
-		// Add a phony target for running go tests
-		ctx.Build(pctx, blueprint.BuildParams{
-			Rule:     blueprint.Phony,
-			Outputs:  []string{"blueprint_go_packages"},
-			Inputs:   blueprintGoPackages,
+			Rule:    generateBuildNinja,
+			Outputs: i.Outputs,
+			Inputs:  i.Inputs,
+			Args: map[string]string{
+				"builder": primaryBuilderFile,
+				"extra":   strings.Join(flags, " "),
+			},
+			// soong_ui explicitly requests what it wants to be build. This is
+			// because the same Ninja file contains instructions to run
+			// soong_build, run bp2build and to generate the JSON module graph.
 			Optional: true,
 		})
 	}
+
+	// Add a phony target for building various tools that are part of blueprint
+	ctx.Build(pctx, blueprint.BuildParams{
+		Rule:    blueprint.Phony,
+		Outputs: []string{"blueprint_tools"},
+		Inputs:  blueprintTools,
+	})
+
+	// Add a phony target for running go tests
+	ctx.Build(pctx, blueprint.BuildParams{
+		Rule:     blueprint.Phony,
+		Outputs:  []string{"blueprint_go_packages"},
+		Inputs:   blueprintGoPackages,
+		Optional: true,
+	})
 }
 
 // packageRoot returns the module-specific package root directory path.  This
diff --git a/bootstrap/command.go b/bootstrap/command.go
index dd8367d..228a0cc 100644
--- a/bootstrap/command.go
+++ b/bootstrap/command.go
@@ -30,24 +30,24 @@ import (
 )
 
 type Args struct {
-	OutFile                  string
-	Subninjas                []string
-	Cpuprofile               string
-	Memprofile               string
-	DelveListen              string
-	DelvePath                string
-	TraceFile                string
-	RunGoTests               bool
-	UseValidations           bool
-	NoGC                     bool
-	EmptyNinjaFile           bool
-	BuildDir                 string
-	ModuleListFile           string
-	NinjaBuildDir            string
-	TopFile                  string
-	GeneratingPrimaryBuilder bool
+	ModuleListFile string
+	OutDir         string
+	SoongOutDir    string
 
+	OutFile                   string
+	Subninjas                 []string
 	PrimaryBuilderInvocations []PrimaryBuilderInvocation
+
+	RunGoTests     bool
+	UseValidations bool
+	EmptyNinjaFile bool
+
+	NoGC        bool
+	Cpuprofile  string
+	Memprofile  string
+	DelveListen string
+	DelvePath   string
+	TraceFile   string
 }
 
 func PrimaryBuilderExtraFlags(args Args, mainNinjaFile string) []string {
@@ -105,7 +105,7 @@ func RunBlueprint(args Args, ctx *blueprint.Context, config interface{}) []strin
 		defer trace.Stop()
 	}
 
-	srcDir := filepath.Dir(args.TopFile)
+	srcDir := "."
 
 	ninjaDeps := make([]string, 0)
 
@@ -122,11 +122,6 @@ func RunBlueprint(args Args, ctx *blueprint.Context, config interface{}) []strin
 
 	soongOutDir := config.(BootstrapConfig).SoongOutDir()
 
-	stage := StageMain
-	if args.GeneratingPrimaryBuilder {
-		stage = StagePrimary
-	}
-
 	mainNinjaFile := filepath.Join("$soongOutDir", "build.ninja")
 
 	var invocations []PrimaryBuilderInvocation
@@ -135,19 +130,15 @@ func RunBlueprint(args Args, ctx *blueprint.Context, config interface{}) []strin
 		invocations = args.PrimaryBuilderInvocations
 	} else {
 		primaryBuilderArgs := PrimaryBuilderExtraFlags(args, mainNinjaFile)
-		primaryBuilderArgs = append(primaryBuilderArgs, args.TopFile)
 
 		invocations = []PrimaryBuilderInvocation{{
-			Inputs:  []string{args.TopFile},
+			Inputs:  []string{},
 			Outputs: []string{mainNinjaFile},
 			Args:    primaryBuilderArgs,
 		}}
 	}
 
 	bootstrapConfig := &Config{
-		stage: stage,
-
-		topLevelBlueprintsFile:    args.TopFile,
 		subninjas:                 args.Subninjas,
 		runGoTests:                args.RunGoTests,
 		useValidations:            args.UseValidations,
@@ -160,7 +151,7 @@ func RunBlueprint(args Args, ctx *blueprint.Context, config interface{}) []strin
 	ctx.RegisterModuleType("blueprint_go_binary", newGoBinaryModuleFactory(bootstrapConfig, true))
 	ctx.RegisterSingletonType("bootstrap", newSingletonFactory(bootstrapConfig))
 
-	blueprintFiles, errs := ctx.ParseFileList(filepath.Dir(args.TopFile), filesToParse, config)
+	blueprintFiles, errs := ctx.ParseFileList(".", filesToParse, config)
 	if len(errs) > 0 {
 		fatalErrors(errs)
 	}
@@ -203,7 +194,7 @@ func RunBlueprint(args Args, ctx *blueprint.Context, config interface{}) []strin
 		}
 	}
 
-	if stage != StageMain || !args.EmptyNinjaFile {
+	if !args.EmptyNinjaFile {
 		f, err = os.OpenFile(joinPath(ctx.SrcDir(), args.OutFile), os.O_WRONLY|os.O_CREATE|os.O_TRUNC, outFilePermissions)
 		if err != nil {
 			fatalf("error opening Ninja file: %s", err)
diff --git a/bootstrap/config.go b/bootstrap/config.go
index 8f5fb11..3706fbe 100644
--- a/bootstrap/config.go
+++ b/bootstrap/config.go
@@ -113,13 +113,6 @@ type ConfigStopBefore interface {
 	StopBefore() StopBefore
 }
 
-type Stage int
-
-const (
-	StagePrimary Stage = iota
-	StageMain
-)
-
 type PrimaryBuilderInvocation struct {
 	Inputs  []string
 	Outputs []string
@@ -127,10 +120,7 @@ type PrimaryBuilderInvocation struct {
 }
 
 type Config struct {
-	stage Stage
-
-	topLevelBlueprintsFile string
-	subninjas              []string
+	subninjas []string
 
 	runGoTests     bool
 	useValidations bool