diff --git a/blueprint_impl.bash b/blueprint_impl.bash
index 514ba31..6f5abba 100644
--- a/blueprint_impl.bash
+++ b/blueprint_impl.bash
@@ -28,6 +28,8 @@ source "${BLUEPRINTDIR}/microfactory/microfactory.bash"
 
 BUILDDIR="${BUILDDIR}/.minibootstrap" build_go minibp github.com/google/blueprint/bootstrap/minibp
 
+BUILDDIR="${BUILDDIR}/.minibootstrap" build_go bpglob github.com/google/blueprint/bootstrap/bpglob
+
 # Build the bootstrap build.ninja
 "${NINJA}" -w dupbuild=err -f "${BUILDDIR}/.minibootstrap/build.ninja"
 
diff --git a/bootstrap.bash b/bootstrap.bash
index 24f16c2..c02fe81 100755
--- a/bootstrap.bash
+++ b/bootstrap.bash
@@ -107,6 +107,10 @@ echo "extraArgs = $EXTRA_ARGS" >> $BUILDDIR/.minibootstrap/build.ninja
 echo "builddir = $NINJA_BUILDDIR" >> $BUILDDIR/.minibootstrap/build.ninja
 echo "include $BLUEPRINTDIR/bootstrap/build.ninja" >> $BUILDDIR/.minibootstrap/build.ninja
 
+if [ ! -f "$BUILDDIR/.minibootstrap/build-globs.ninja" ]; then
+    touch "$BUILDDIR/.minibootstrap/build-globs.ninja"
+fi
+
 echo "BLUEPRINT_BOOTSTRAP_VERSION=2" > $BUILDDIR/.blueprint.bootstrap
 echo "SRCDIR=\"${SRCDIR}\"" >> $BUILDDIR/.blueprint.bootstrap
 echo "BLUEPRINTDIR=\"${BLUEPRINTDIR}\"" >> $BUILDDIR/.blueprint.bootstrap
diff --git a/bootstrap/bootstrap.go b/bootstrap/bootstrap.go
index e9a8f01..92b8a32 100644
--- a/bootstrap/bootstrap.go
+++ b/bootstrap/bootstrap.go
@@ -17,6 +17,8 @@ package bootstrap
 import (
 	"fmt"
 	"go/build"
+	"io/ioutil"
+	"os"
 	"path/filepath"
 	"runtime"
 	"strings"
@@ -118,14 +120,14 @@ var (
 
 	generateBuildNinja = pctx.StaticRule("build.ninja",
 		blueprint.RuleParams{
-			Command:     "$builder $extra -b $buildDir -n $ninjaBuildDir -d $out.d -o $out $in",
+			Command:     "$builder $extra -b $buildDir -n $ninjaBuildDir -d $out.d -globFile $globFile -o $out $in",
 			CommandDeps: []string{"$builder"},
 			Description: "$builder $out",
 			Deps:        blueprint.DepsGCC,
 			Depfile:     "$out.d",
 			Restat:      true,
 		},
-		"builder", "extra", "generator")
+		"builder", "extra", "generator", "globFile")
 
 	// Work around a Ninja issue.  See https://github.com/martine/ninja/pull/634
 	phony = pctx.StaticRule("phony",
@@ -668,32 +670,33 @@ func (s *singleton) GenerateBuildActions(ctx blueprint.SingletonContext) {
 	topLevelBlueprints := filepath.Join("$srcDir",
 		filepath.Base(s.config.topLevelBlueprintsFile))
 
-	mainNinjaFile := filepath.Join("$buildDir", "build.ninja")
-	primaryBuilderNinjaFile := filepath.Join(bootstrapDir, "build.ninja")
-
 	ctx.SetNinjaBuildDir(pctx, "${ninjaBuildDir}")
 
-	// Build the main build.ninja
-	ctx.Build(pctx, blueprint.BuildParams{
-		Rule:    generateBuildNinja,
-		Outputs: []string{mainNinjaFile},
-		Inputs:  []string{topLevelBlueprints},
-		Args: map[string]string{
-			"builder": primaryBuilderFile,
-			"extra":   primaryBuilderExtraFlags,
-		},
-	})
+	if s.config.stage == StagePrimary {
+		mainNinjaFile := filepath.Join("$buildDir", "build.ninja")
+		primaryBuilderNinjaGlobFile := filepath.Join(BuildDir, bootstrapSubDir, "build-globs.ninja")
 
-	// Add a way to rebuild the primary build.ninja so that globs works
-	ctx.Build(pctx, blueprint.BuildParams{
-		Rule:    generateBuildNinja,
-		Outputs: []string{primaryBuilderNinjaFile},
-		Inputs:  []string{topLevelBlueprints},
-		Args: map[string]string{
-			"builder": minibpFile,
-			"extra":   extraSharedFlagString,
-		},
-	})
+		if _, err := os.Stat(primaryBuilderNinjaGlobFile); os.IsNotExist(err) {
+			err = ioutil.WriteFile(primaryBuilderNinjaGlobFile, nil, 0666)
+			if err != nil {
+				ctx.Errorf("Failed to create empty ninja file: %s", err)
+			}
+		}
+
+		ctx.AddSubninja(primaryBuilderNinjaGlobFile)
+
+		// Build the main build.ninja
+		ctx.Build(pctx, blueprint.BuildParams{
+			Rule:    generateBuildNinja,
+			Outputs: []string{mainNinjaFile},
+			Inputs:  []string{topLevelBlueprints},
+			Args: map[string]string{
+				"builder":  primaryBuilderFile,
+				"extra":    primaryBuilderExtraFlags,
+				"globFile": primaryBuilderNinjaGlobFile,
+			},
+		})
+	}
 
 	if s.config.stage == StageMain {
 		if primaryBuilderName == "minibp" {
diff --git a/bootstrap/build.ninja b/bootstrap/build.ninja
index b338843..5787c72 100644
--- a/bootstrap/build.ninja
+++ b/bootstrap/build.ninja
@@ -7,8 +7,11 @@
 
 ninja_required_version = 1.7.0
 
+myGlobs = ${bootstrapBuildDir}/.minibootstrap/build-globs.ninja
+subninja ${myGlobs}
+
 rule build.ninja
-    command = ${builder} ${extraArgs} -b ${bootstrapBuildDir} -n ${builddir} -d ${out}.d -o ${out} ${in}
+    command = ${builder} ${extraArgs} -b ${bootstrapBuildDir} -n ${builddir} -d ${out}.d -globFile ${myGlobs} -o ${out} ${in}
     deps = gcc
     depfile = ${out}.d
     description = ${builder} ${out}
diff --git a/bootstrap/cleanup.go b/bootstrap/cleanup.go
index a4a18c7..4a8ce25 100644
--- a/bootstrap/cleanup.go
+++ b/bootstrap/cleanup.go
@@ -30,9 +30,9 @@ const logFileName = ".ninja_log"
 
 // removeAbandonedFilesUnder removes any files that appear in the Ninja log, and
 // are prefixed with one of the `under` entries, but that are not currently
-// build targets.
+// build targets, or in `exempt`
 func removeAbandonedFilesUnder(ctx *blueprint.Context, config *Config,
-	srcDir string, under []string) error {
+	srcDir string, under, exempt []string) error {
 
 	if len(under) == 0 {
 		return nil
@@ -57,6 +57,10 @@ func removeAbandonedFilesUnder(ctx *blueprint.Context, config *Config,
 		replacedTarget := replacer.Replace(target)
 		targets[filepath.Clean(replacedTarget)] = true
 	}
+	for _, target := range exempt {
+		replacedTarget := replacer.Replace(target)
+		targets[filepath.Clean(replacedTarget)] = true
+	}
 
 	filePaths, err := parseNinjaLog(ninjaBuildDir, under)
 	if err != nil {
diff --git a/bootstrap/command.go b/bootstrap/command.go
index 04eb535..ac3fd00 100644
--- a/bootstrap/command.go
+++ b/bootstrap/command.go
@@ -32,6 +32,7 @@ import (
 
 var (
 	outFile        string
+	globFile       string
 	depFile        string
 	docFile        string
 	cpuprofile     string
@@ -48,6 +49,7 @@ var (
 
 func init() {
 	flag.StringVar(&outFile, "o", "build.ninja", "the Ninja file to output")
+	flag.StringVar(&globFile, "globFile", "build-globs.ninja", "the Ninja file of globs to output")
 	flag.StringVar(&BuildDir, "b", ".", "the build output directory")
 	flag.StringVar(&NinjaBuildDir, "n", "", "the ninja builddir directory")
 	flag.StringVar(&depFile, "d", "", "the dependency file to output")
@@ -179,6 +181,18 @@ func Main(ctx *blueprint.Context, config interface{}, extraNinjaFileDeps ...stri
 		fatalf("error writing %s: %s", outFile, err)
 	}
 
+	if globFile != "" {
+		buffer, errs := generateGlobNinjaFile(ctx.Globs)
+		if len(errs) > 0 {
+			fatalErrors(errs)
+		}
+
+		err = ioutil.WriteFile(globFile, buffer, outFilePermissions)
+		if err != nil {
+			fatalf("error writing %s: %s", outFile, err)
+		}
+	}
+
 	if depFile != "" {
 		err := deptools.WriteDepFile(depFile, outFile, deps)
 		if err != nil {
@@ -187,8 +201,8 @@ func Main(ctx *blueprint.Context, config interface{}, extraNinjaFileDeps ...stri
 	}
 
 	if c, ok := config.(ConfigRemoveAbandonedFilesUnder); ok {
-		under := c.RemoveAbandonedFilesUnder()
-		err := removeAbandonedFilesUnder(ctx, bootstrapConfig, SrcDir, under)
+		under, except := c.RemoveAbandonedFilesUnder()
+		err := removeAbandonedFilesUnder(ctx, bootstrapConfig, SrcDir, under, except)
 		if err != nil {
 			fatalf("error removing abandoned files: %s", err)
 		}
diff --git a/bootstrap/config.go b/bootstrap/config.go
index 5785ea7..790ac4b 100644
--- a/bootstrap/config.go
+++ b/bootstrap/config.go
@@ -69,10 +69,11 @@ type ConfigInterface interface {
 }
 
 type ConfigRemoveAbandonedFilesUnder interface {
-	// RemoveAbandonedFilesUnder should return a slice of path prefixes that
-	// will be cleaned of files that are no longer active targets, but are
-	// listed in the .ninja_log.
-	RemoveAbandonedFilesUnder() []string
+	// RemoveAbandonedFilesUnder should return two slices:
+	// - a slice of path prefixes that will be cleaned of files that are no
+	//   longer active targets, but are listed in the .ninja_log.
+	// - a slice of paths that are exempt from cleaning
+	RemoveAbandonedFilesUnder() (under, except []string)
 }
 
 type ConfigBlueprintToolLocation interface {
diff --git a/bootstrap/doc.go b/bootstrap/doc.go
index 3c7108e..69a1784 100644
--- a/bootstrap/doc.go
+++ b/bootstrap/doc.go
@@ -120,23 +120,27 @@
 //      - Runs .bootstrap/build.ninja to build and run the primary builder
 //      - Runs build.ninja to build your code
 //
-// Microfactory takes care of building an up to date version of `minibp` under
-// the .minibootstrap/ directory.
+// Microfactory takes care of building an up to date version of `minibp` and
+// `bpglob` under the .minibootstrap/ directory.
 //
 // During <builddir>/.minibootstrap/build.ninja, the following actions are
 // taken, if necessary:
 //
 //      - Run minibp to generate .bootstrap/build.ninja (Primary stage)
+//      - Includes .minibootstrap/build-globs.ninja, which defines rules to
+//        run bpglob during incremental builds. These outputs are listed in
+//        the dependency file output by minibp.
 //
 // During the <builddir>/.bootstrap/build.ninja, the following actions are
 // taken, if necessary:
 //
-//      - Rebuild .bootstrap/build.ninja, usually due to globs changing --
-//        other dependencies will trigger it to be built during minibootstrap
 //      - Build the primary builder, anything marked `default: true`, and
 //        any dependencies.
 //      - Run the primary builder to generate build.ninja
 //      - Run the primary builder to extract documentation
+//      - Includes .bootstrap/build-globs.ninja, which defines rules to run
+//        bpglob during incremental builds. These outputs are listed in the
+//        dependency file output by the primary builder.
 //
 // Then the main stage is at <builddir>/build.ninja, and will contain all the
 // rules generated by the primary builder. In addition, the bootstrap code
diff --git a/bootstrap/glob.go b/bootstrap/glob.go
index 160ef58..9841611 100644
--- a/bootstrap/glob.go
+++ b/bootstrap/glob.go
@@ -15,6 +15,7 @@
 package bootstrap
 
 import (
+	"bytes"
 	"fmt"
 	"path/filepath"
 	"strings"
@@ -40,7 +41,7 @@ import (
 // in a build failure with a "missing and no known rule to make it" error.
 
 var (
-	globCmd = filepath.Join("$BinDir", "bpglob")
+	globCmd = filepath.Join(miniBootstrapDir, "bpglob")
 
 	// globRule rule traverses directories to produce a list of files that match $glob
 	// and writes it to $out if it has changed, and writes the directories to $out.d
@@ -111,6 +112,7 @@ func joinWithPrefixAndQuote(strs []string, prefix string) string {
 // primary builder if the results change.
 type globSingleton struct {
 	globLister func() []blueprint.GlobPath
+	writeRule  bool
 }
 
 func globSingletonFactory(ctx *blueprint.Context) func() blueprint.Singleton {
@@ -124,15 +126,52 @@ func globSingletonFactory(ctx *blueprint.Context) func() blueprint.Singleton {
 func (s *globSingleton) GenerateBuildActions(ctx blueprint.SingletonContext) {
 	for _, g := range s.globLister() {
 		fileListFile := filepath.Join(BuildDir, ".glob", g.Name)
-		depFile := fileListFile + ".d"
 
-		fileList := strings.Join(g.Files, "\n") + "\n"
-		pathtools.WriteFileIfChanged(fileListFile, []byte(fileList), 0666)
-		deptools.WriteDepFile(depFile, fileListFile, g.Deps)
+		if s.writeRule {
+			depFile := fileListFile + ".d"
 
-		GlobFile(ctx, g.Pattern, g.Excludes, fileListFile, depFile)
+			fileList := strings.Join(g.Files, "\n") + "\n"
+			pathtools.WriteFileIfChanged(fileListFile, []byte(fileList), 0666)
+			deptools.WriteDepFile(depFile, fileListFile, g.Deps)
 
-		// Make build.ninja depend on the fileListFile
-		ctx.AddNinjaFileDeps(fileListFile)
+			GlobFile(ctx, g.Pattern, g.Excludes, fileListFile, depFile)
+		} else {
+			// Make build.ninja depend on the fileListFile
+			ctx.AddNinjaFileDeps(fileListFile)
+		}
 	}
 }
+
+func generateGlobNinjaFile(globLister func() []blueprint.GlobPath) ([]byte, []error) {
+	ctx := blueprint.NewContext()
+	ctx.RegisterSingletonType("glob", func() blueprint.Singleton {
+		return &globSingleton{
+			globLister: globLister,
+			writeRule:  true,
+		}
+	})
+
+	extraDeps, errs := ctx.ResolveDependencies(nil)
+	if len(extraDeps) > 0 {
+		return nil, []error{fmt.Errorf("shouldn't have extra deps")}
+	}
+	if len(errs) > 0 {
+		return nil, errs
+	}
+
+	extraDeps, errs = ctx.PrepareBuildActions(nil)
+	if len(extraDeps) > 0 {
+		return nil, []error{fmt.Errorf("shouldn't have extra deps")}
+	}
+	if len(errs) > 0 {
+		return nil, errs
+	}
+
+	buf := bytes.NewBuffer(nil)
+	err := ctx.WriteBuildFile(buf)
+	if err != nil {
+		return nil, []error{err}
+	}
+
+	return buf.Bytes(), nil
+}
diff --git a/bootstrap/minibp/main.go b/bootstrap/minibp/main.go
index 72ed9f6..1714739 100644
--- a/bootstrap/minibp/main.go
+++ b/bootstrap/minibp/main.go
@@ -37,8 +37,12 @@ func (c Config) GeneratingPrimaryBuilder() bool {
 	return c.generatingPrimaryBuilder
 }
 
-func (c Config) RemoveAbandonedFilesUnder() []string {
-	return []string{filepath.Join(bootstrap.BuildDir, ".bootstrap")}
+func (c Config) RemoveAbandonedFilesUnder() (under, exempt []string) {
+	if c.generatingPrimaryBuilder {
+		under = []string{filepath.Join(bootstrap.BuildDir, ".bootstrap")}
+		exempt = []string{filepath.Join(bootstrap.BuildDir, ".bootstrap", "build.ninja")}
+	}
+	return
 }
 
 func main() {
diff --git a/context.go b/context.go
index 919377c..69f26f6 100644
--- a/context.go
+++ b/context.go
@@ -102,6 +102,8 @@ type Context struct {
 	requiredNinjaMinor int          // For the ninja_required_version variable
 	requiredNinjaMicro int          // For the ninja_required_version variable
 
+	subninjas []string
+
 	// set lazily by sortedModuleGroups
 	cachedSortedModuleGroups []*moduleGroup
 
@@ -2939,6 +2941,11 @@ func (c *Context) WriteBuildFile(w io.Writer) error {
 		return err
 	}
 
+	err = c.writeSubninjas(nw)
+	if err != nil {
+		return err
+	}
+
 	// TODO: Group the globals by package.
 
 	err = c.writeGlobalVariables(nw)
@@ -3048,6 +3055,13 @@ func (c *Context) writeNinjaRequiredVersion(nw *ninjaWriter) error {
 	return nw.BlankLine()
 }
 
+func (c *Context) writeSubninjas(nw *ninjaWriter) error {
+	for _, subninja := range c.subninjas {
+		nw.Subninja(subninja)
+	}
+	return nw.BlankLine()
+}
+
 func (c *Context) writeBuildDir(nw *ninjaWriter) error {
 	if c.ninjaBuildDir != nil {
 		err := nw.Assign("builddir", c.ninjaBuildDir.Value(c.pkgNames))
diff --git a/ninja_writer.go b/ninja_writer.go
index a61667d..5902986 100644
--- a/ninja_writer.go
+++ b/ninja_writer.go
@@ -193,6 +193,12 @@ func (n *ninjaWriter) Default(targets ...string) error {
 	return wrapper.Flush()
 }
 
+func (n *ninjaWriter) Subninja(file string) error {
+	n.justDidBlankLine = false
+	_, err := fmt.Fprintf(n.writer, "subninja %s\n", file)
+	return err
+}
+
 func (n *ninjaWriter) BlankLine() (err error) {
 	// We don't output multiple blank lines in a row.
 	if !n.justDidBlankLine {
diff --git a/ninja_writer_test.go b/ninja_writer_test.go
index 44e4ff8..cc880e5 100644
--- a/ninja_writer_test.go
+++ b/ninja_writer_test.go
@@ -72,6 +72,12 @@ var ninjaWriterTestCases = []struct {
 		},
 		output: "    foo = bar\n",
 	},
+	{
+		input: func(w *ninjaWriter) {
+			ck(w.Subninja("build.ninja"))
+		},
+		output: "subninja build.ninja\n",
+	},
 	{
 		input: func(w *ninjaWriter) {
 			ck(w.BlankLine())
diff --git a/singleton_ctx.go b/singleton_ctx.go
index bbfce00..333811d 100644
--- a/singleton_ctx.go
+++ b/singleton_ctx.go
@@ -47,6 +47,10 @@ type SingletonContext interface {
 	// set at most one time for a single build, later calls are ignored.
 	SetNinjaBuildDir(pctx PackageContext, value string)
 
+	// AddSubninja adds a ninja file to include with subninja. This should likely
+	// only ever be used inside bootstrap to handle glob rules.
+	AddSubninja(file string)
+
 	// Eval takes a string with embedded ninja variables, and returns a string
 	// with all of the variables recursively expanded. Any variables references
 	// are expanded in the scope of the PackageContext.
@@ -203,6 +207,10 @@ func (s *singletonContext) SetNinjaBuildDir(pctx PackageContext, value string) {
 	s.context.setNinjaBuildDir(ninjaValue)
 }
 
+func (s *singletonContext) AddSubninja(file string) {
+	s.context.subninjas = append(s.context.subninjas, file)
+}
+
 func (s *singletonContext) VisitAllModules(visit func(Module)) {
 	s.context.VisitAllModules(visit)
 }