prune/repair index: reset in-memory index after command

The current in-memory index becomes stale after prune or repair index
have run. Thus, just drop the in-memory index altogether once these
commands have finished.

internal/repository/repository.go

@@ -142,9 +142,6 @@ func (r *Repository) DisableAutoIndexUpdate() {
 // setConfig assigns the given config and updates the repository parameters accordingly
 func (r *Repository) setConfig(cfg restic.Config) {
 	r.cfg = cfg
-	if r.cfg.Version >= 2 {
-		r.idx.MarkCompressed()
-	}
 }
 
 // Config returns the repository configuration.
@@ -637,9 +634,21 @@ func (r *Repository) Index() restic.MasterIndex {
 // SetIndex instructs the repository to use the given index.
 func (r *Repository) SetIndex(i restic.MasterIndex) error {
 	r.idx = i.(*index.MasterIndex)
+	r.configureIndex()
 	return r.prepareCache()
 }
 
+func (r *Repository) ClearIndex() {
+	r.idx = index.NewMasterIndex()
+	r.configureIndex()
+}
+
+func (r *Repository) configureIndex() {
+	if r.cfg.Version >= 2 {
+		r.idx.MarkCompressed()
+	}
+}
+
 // LoadIndex loads all index files from the backend in parallel and stores them
 func (r *Repository) LoadIndex(ctx context.Context, p *progress.Counter) error {
 	debug.Log("Loading index")
@@ -662,6 +671,9 @@ func (r *Repository) LoadIndex(ctx context.Context, p *progress.Counter) error {
 		defer p.Done()
 	}
 
+	// reset in-memory index before loading it from the repository
+	r.ClearIndex()
+
 	err = index.ForAllIndexes(ctx, indexList, r, func(_ restic.ID, idx *index.Index, _ bool, err error) error {
 		if err != nil {
 			return err