diff --git a/cmd/syncthing/main.go b/cmd/syncthing/main.go
index 8a2f9bbc6..952d25edd 100644
--- a/cmd/syncthing/main.go
+++ b/cmd/syncthing/main.go
@@ -290,6 +290,7 @@ func main() {
 		rateBucket = ratelimit.NewBucketWithRate(float64(1000*cfg.Options.MaxSendKbps), int64(5*1000*cfg.Options.MaxSendKbps))
 	}
 
+	removeLegacyIndexes()
 	db, err := leveldb.OpenFile(filepath.Join(confDir, "index"), nil)
 	if err != nil {
 		l.Fatalln("leveldb.OpenFile():", err)
@@ -519,7 +520,12 @@ func resetRepositories() {
 		}
 	}
 
-	pat := filepath.Join(confDir, "*.idx.gz")
+	idx := filepath.Join(confDir, "index")
+	os.RemoveAll(idx)
+}
+
+func removeLegacyIndexes() {
+	pat := filepath.Join(confDir, "*.idx.gz*")
 	idxs, err := filepath.Glob(pat)
 	if err == nil {
 		for _, idx := range idxs {
diff --git a/model/model.go b/model/model.go
index 3f075d3ee..28502c46e 100644
--- a/model/model.go
+++ b/model/model.go
@@ -701,8 +701,11 @@ func (m *Model) CleanRepos() {
 
 func (m *Model) ScanRepo(repo string) error {
 	m.rmut.RLock()
+	fs := m.repoFiles[repo]
+	dir := m.repoCfgs[repo].Directory
+
 	w := &scanner.Walker{
-		Dir:          m.repoCfgs[repo].Directory,
+		Dir:          dir,
 		IgnoreFile:   ".stignore",
 		BlockSize:    scanner.StandardBlockSize,
 		TempNamer:    defTempNamer,
@@ -711,12 +714,47 @@ func (m *Model) ScanRepo(repo string) error {
 		IgnorePerms:  m.repoCfgs[repo].IgnorePerms,
 	}
 	m.rmut.RUnlock()
+
 	m.setState(repo, RepoScanning)
-	fs, _, err := w.Walk()
+	fchan, _, err := w.Walk()
+
 	if err != nil {
 		return err
 	}
-	m.ReplaceLocal(repo, fs)
+	batch := make([]protocol.FileInfo, 0, indexBatchSize)
+	for f := range fchan {
+		if len(batch) == indexBatchSize {
+			fs.Update(protocol.LocalNodeID, batch)
+			batch = batch[:0]
+		}
+		batch = append(batch, f)
+	}
+	if len(batch) > 0 {
+		fs.Update(protocol.LocalNodeID, batch)
+	}
+
+	batch = batch[:0]
+	fs.WithHave(protocol.LocalNodeID, func(f protocol.FileInfo) bool {
+		if !protocol.IsDeleted(f.Flags) {
+			if len(batch) == indexBatchSize {
+				fs.Update(protocol.LocalNodeID, batch)
+				batch = batch[:0]
+			}
+			if _, err := os.Stat(filepath.Join(dir, f.Name)); err != nil && os.IsNotExist(err) {
+				// File has been deleted
+				f.Blocks = nil
+				f.Flags |= protocol.FlagDeleted
+				f.Version = lamport.Default.Tick(f.Version)
+				f.LocalVersion = 0
+				batch = append(batch, f)
+			}
+		}
+		return true
+	})
+	if len(batch) > 0 {
+		fs.Update(protocol.LocalNodeID, batch)
+	}
+
 	m.setState(repo, RepoIdle)
 	return nil
 }
@@ -790,6 +828,7 @@ func (m *Model) Override(repo string) {
 			*f = h
 		}
 		f.Version = lamport.Default.Tick(f.Version)
+		f.LocalVersion = 0
 	}
 
 	r.Update(protocol.LocalNodeID, fs)
diff --git a/scanner/walk.go b/scanner/walk.go
index cc4725395..2d114439d 100644
--- a/scanner/walk.go
+++ b/scanner/walk.go
@@ -6,7 +6,6 @@ package scanner
 
 import (
 	"bytes"
-	"code.google.com/p/go.text/unicode/norm"
 	"errors"
 	"fmt"
 	"io/ioutil"
@@ -15,6 +14,7 @@ import (
 	"runtime"
 	"strings"
 	"time"
+	"code.google.com/p/go.text/unicode/norm"
 
 	"github.com/calmh/syncthing/lamport"
 	"github.com/calmh/syncthing/protocol"
@@ -60,7 +60,7 @@ type CurrentFiler interface {
 
 // Walk returns the list of files found in the local repository by scanning the
 // file system. Files are blockwise hashed.
-func (w *Walker) Walk() (files []protocol.FileInfo, ignore map[string][]string, err error) {
+func (w *Walker) Walk() (files chan protocol.FileInfo, ignore map[string][]string, err error) {
 	if debug {
 		l.Debugln("Walk", w.Dir, w.BlockSize, w.IgnoreFile)
 	}
@@ -70,21 +70,16 @@ func (w *Walker) Walk() (files []protocol.FileInfo, ignore map[string][]string,
 		return
 	}
 
-	t0 := time.Now()
-
 	ignore = make(map[string][]string)
-	hashFiles := w.walkAndHashFiles(&files, ignore)
+	files = make(chan protocol.FileInfo)
+	hashFiles := w.walkAndHashFiles(files, ignore)
 
-	filepath.Walk(w.Dir, w.loadIgnoreFiles(w.Dir, ignore))
-	filepath.Walk(w.Dir, hashFiles)
+	go func() {
+		filepath.Walk(w.Dir, w.loadIgnoreFiles(w.Dir, ignore))
+		filepath.Walk(w.Dir, hashFiles)
+		close(files)
+	}()
 
-	if debug {
-		t1 := time.Now()
-		d := t1.Sub(t0).Seconds()
-		l.Debugf("Walk in %.02f ms, %.0f files/s", d*1000, float64(len(files))/d)
-	}
-
-	err = checkDir(w.Dir)
 	return
 }
 
@@ -122,7 +117,7 @@ func (w *Walker) loadIgnoreFiles(dir string, ign map[string][]string) filepath.W
 	}
 }
 
-func (w *Walker) walkAndHashFiles(res *[]protocol.FileInfo, ign map[string][]string) filepath.WalkFunc {
+func (w *Walker) walkAndHashFiles(fchan chan protocol.FileInfo, ign map[string][]string) filepath.WalkFunc {
 	return func(p string, info os.FileInfo, err error) error {
 		if err != nil {
 			if debug {
@@ -175,7 +170,6 @@ func (w *Walker) walkAndHashFiles(res *[]protocol.FileInfo, ign map[string][]str
 					if debug {
 						l.Debugln("unchanged:", cf)
 					}
-					*res = append(*res, cf)
 					return nil
 				}
 			}
@@ -195,7 +189,7 @@ func (w *Walker) walkAndHashFiles(res *[]protocol.FileInfo, ign map[string][]str
 			if debug {
 				l.Debugln("dir:", f)
 			}
-			*res = append(*res, f)
+			fchan <- f
 			return nil
 		}
 
@@ -207,7 +201,6 @@ func (w *Walker) walkAndHashFiles(res *[]protocol.FileInfo, ign map[string][]str
 					if debug {
 						l.Debugln("unchanged:", cf)
 					}
-					*res = append(*res, cf)
 					return nil
 				}
 
@@ -220,7 +213,7 @@ func (w *Walker) walkAndHashFiles(res *[]protocol.FileInfo, ign map[string][]str
 						if debug {
 							l.Debugln("suppressed:", cf)
 						}
-						*res = append(*res, cf)
+						fchan <- cf
 						return nil
 					} else if prev && !cur {
 						l.Infof("Changes to %q are no longer suppressed.", p)
@@ -265,7 +258,7 @@ func (w *Walker) walkAndHashFiles(res *[]protocol.FileInfo, ign map[string][]str
 				Modified: info.ModTime().Unix(),
 				Blocks:   blocks,
 			}
-			*res = append(*res, f)
+			fchan <- f
 		}
 
 		return nil