diff --git a/checker/repacker.go b/checker/repacker.go
index be885c16f..513a48352 100644
--- a/checker/repacker.go
+++ b/checker/repacker.go
@@ -12,16 +12,15 @@ import (
 // new packs.
 type Repacker struct {
 	unusedBlobs backend.IDSet
-	src, dst    *repository.Repository
+	repo        *repository.Repository
 }
 
 // NewRepacker returns a new repacker that (when Repack() in run) cleans up the
 // repository and creates new packs and indexs so that all blobs in unusedBlobs
 // aren't used any more.
-func NewRepacker(src, dst *repository.Repository, unusedBlobs backend.IDSet) *Repacker {
+func NewRepacker(repo *repository.Repository, unusedBlobs backend.IDSet) *Repacker {
 	return &Repacker{
-		src:         src,
-		dst:         dst,
+		repo:        repo,
 		unusedBlobs: unusedBlobs,
 	}
 }
@@ -31,14 +30,14 @@ func NewRepacker(src, dst *repository.Repository, unusedBlobs backend.IDSet) *Re
 func (r *Repacker) Repack() error {
 	debug.Log("Repacker.Repack", "searching packs for %v", r.unusedBlobs)
 
-	packs, err := FindPacksForBlobs(r.src, r.unusedBlobs)
+	unneededPacks, err := FindPacksForBlobs(r.repo, r.unusedBlobs)
 	if err != nil {
 		return err
 	}
 
-	debug.Log("Repacker.Repack", "found packs: %v", packs)
+	debug.Log("Repacker.Repack", "found packs: %v", unneededPacks)
 
-	blobs, err := FindBlobsForPacks(r.src, packs)
+	blobs, err := FindBlobsForPacks(r.repo, unneededPacks)
 	if err != nil {
 		return err
 	}
@@ -52,19 +51,39 @@ func (r *Repacker) Repack() error {
 
 	debug.Log("Repacker.Repack", "need to repack blobs: %v", blobs)
 
-	err = RepackBlobs(r.src, r.dst, blobs)
+	err = RepackBlobs(r.repo, r.repo, blobs)
 	if err != nil {
 		return err
 	}
 
-	debug.Log("Repacker.Repack", "remove unneeded packs: %v", packs)
-	for packID := range packs {
-		err = r.src.Backend().Remove(backend.Data, packID.String())
+	debug.Log("Repacker.Repack", "remove unneeded packs: %v", unneededPacks)
+	for packID := range unneededPacks {
+		err = r.repo.Backend().Remove(backend.Data, packID.String())
 		if err != nil {
 			return err
 		}
 	}
 
+	debug.Log("Repacker.Repack", "rebuild index")
+	idx, err := r.repo.Index().RebuildIndex(unneededPacks)
+
+	newIndexID, err := repository.SaveIndex(r.repo, idx)
+	debug.Log("Repacker.Repack", "saved new index at %v, err %v", newIndexID, err)
+	if err != nil {
+		return err
+	}
+
+	debug.Log("Repacker.Repack", "remove old indexes: %v", idx.Supersedes())
+	for _, id := range idx.Supersedes() {
+		err = r.repo.Backend().Remove(backend.Index, id.String())
+		if err != nil {
+			debug.Log("Repacker.Repack", "error removing index %v: %v", id.Str(), err)
+			return err
+		}
+
+		debug.Log("Repacker.Repack", "removed index %v", id.Str())
+	}
+
 	return nil
 }
 
@@ -140,10 +159,5 @@ func RepackBlobs(src, dst *repository.Repository, blobIDs backend.IDSet) (err er
 		return err
 	}
 
-	err = dst.SaveIndex()
-	if err != nil {
-		return err
-	}
-
 	return nil
 }
diff --git a/checker/repacker_test.go b/checker/repacker_test.go
index f3e5bead8..dcf7b2040 100644
--- a/checker/repacker_test.go
+++ b/checker/repacker_test.go
@@ -111,7 +111,7 @@ func TestRepacker(t *testing.T) {
 			t.Fatalf("expected unused blobs:\n  %v\ngot:\n  %v", unusedBlobs, list)
 		}
 
-		repacker := checker.NewRepacker(repo, repo, unusedBlobs)
+		repacker := checker.NewRepacker(repo, unusedBlobs)
 		OK(t, repacker.Repack())
 
 		chkr = checker.New(repo)
diff --git a/repository/index.go b/repository/index.go
index bb62f2ae9..f305a7bcb 100644
--- a/repository/index.go
+++ b/repository/index.go
@@ -439,7 +439,12 @@ func (idx *Index) Dump(w io.Writer) error {
 		return err
 	}
 
-	buf, err := json.MarshalIndent(list, "", "  ")
+	outer := jsonIndex{
+		Supersedes: idx.Supersedes(),
+		Packs:      list,
+	}
+
+	buf, err := json.MarshalIndent(outer, "", "  ")
 	if err != nil {
 		return err
 	}
diff --git a/repository/master_index.go b/repository/master_index.go
index bc3dea768..0de8e9c31 100644
--- a/repository/master_index.go
+++ b/repository/master_index.go
@@ -240,3 +240,47 @@ func (mi *MasterIndex) All() []*Index {
 
 	return mi.idx
 }
+
+// RebuildIndex combines all known indexes to a new index, leaving out any
+// packs whose ID is contained in packBlacklist. The new index contains the IDs
+// of all known indexes in the "supersedes" field.
+func (mi *MasterIndex) RebuildIndex(packBlacklist backend.IDSet) (*Index, error) {
+	mi.idxMutex.Lock()
+	defer mi.idxMutex.Unlock()
+
+	debug.Log("MasterIndex.RebuildIndex", "start rebuilding index, blob blacklist: %v", packBlacklist)
+
+	newIndex := NewIndex()
+	done := make(chan struct{})
+	defer close(done)
+
+	for i, idx := range mi.idx {
+		debug.Log("MasterIndex.RebuildIndex", "adding %d index ", i)
+
+		for pb := range idx.Each(done) {
+			if packBlacklist.Has(pb.PackID) {
+				continue
+			}
+
+			newIndex.Store(pb)
+		}
+
+		if !idx.Final() {
+			continue
+		}
+
+		id, err := idx.ID()
+		if err != nil {
+			return nil, err
+		}
+
+		debug.Log("MasterIndex.RebuildIndex", "adding index id %v to supersedes field", id)
+
+		err = newIndex.AddToSupersedes(id)
+		if err != nil {
+			return nil, err
+		}
+	}
+
+	return newIndex, nil
+}