Delete metadata directories a backup left without a manifest (closes #390)

A backup that stopped between uploading db.zst.age and its manifest
left that directory under metadata/ on the destination for good:
prune deleted nothing there.

The blob step of prune, which snapshot create --prune also runs, now
deletes each directory under metadata/ that has no manifest.json.zst,
that no local snapshot record claims, and all of whose objects are
older than prune_grace_period; an object listed with no time keeps its
directory, and only names that are remote keys are deleted. The prompt
and the --force output name each such directory, the --json result
counts them (metadata_dirs_deleted, metadata_dirs_failed), and a failed
delete fails the run. Every description of the grace period now
covers these directories.

Model: opus-5-5

README.md

@@ -96,6 +96,15 @@ vaultik snapshot restore <snapshot-id> ~/vaultik-restore
 # 0 3 * * * vaultik snapshot create --cron --prune --keep-newer-than 4w
 ```
 
+On a destination shared between hosts or users, the prune in that cron line
+relies on `prune_grace_period` (default `24h`) to leave the blobs of a backup
+another one is still running, and its directory under `metadata/` that has no
+manifest yet, so it must be longer than the longest backup run. It does not
+protect a blob that backup reuses from an earlier run that stopped before its
+manifest: the prune can delete such a blob, and the new snapshot then cannot
+be restored. To not depend on the grace period, give each host its own prefix
+or directory. See [locking](#locking).
+
 ## restoring on another machine
 
 Restoring on a host that never ran the backup — a replacement machine
@@ -192,7 +201,23 @@ process-wide lock at `$XDG_DATA_HOME/vaultik/vaultik.pid`
 (`~/.local/share/vaultik/vaultik.pid` on Linux) for the whole run. Only
 one of them runs at a time: a second one exits immediately with an
 "already running" error rather than waiting, so two writers can never
-corrupt the local index or the destination store.
+corrupt the local index.
+
+The lock covers one user on one machine. It does not stop another user,
+or another host, from writing to the same destination store at the same
+time. A backup uploads its blobs, and then its `db.zst.age`, before the
+manifest that lists them, so a prune from elsewhere at that moment finds
+blobs no snapshot lists and a directory under `metadata/` with no manifest. It
+deletes such a blob only once it is older than `prune_grace_period` (default
+`24h`), and such a directory only once every object in it is, so the grace
+period must be longer than the longest backup run of any host or user sharing
+the destination. The grace period does not protect a blob a backup reuses
+from an earlier run that stopped before its manifest: a backup skips the
+upload of a blob already on the destination, so that blob keeps the time of
+its first upload, and a prune from elsewhere during the backup can delete it;
+the new snapshot then cannot be restored. `remote nuke` deletes everything
+regardless. To not depend on the grace period, give each host or user its own
+prefix (or directory) on the destination.
 
 Read-only commands — `info`, `snapshot list`, `snapshot verify`, and
 `remote info` — do not take the lock and are never blocked, so they run
@@ -295,8 +320,12 @@ value where a list belongs or a word where a number belongs), is refused.
   error that explains how to fix it
 * `--cron`: Silent on total success; warnings and errors are still printed
   (for crontab)
-* `--prune`: After backup, drop older snapshots of each backed-up name and
-  remove orphaned blobs from remote storage. By default keeps only the latest
+* `--prune`: After backup, drop older snapshots of each backed-up name,
+  remove orphaned blobs older than `prune_grace_period` from remote storage,
+  and delete each directory under `metadata/` that has no
+  `manifest.json.zst` once every object in it is older than
+  `prune_grace_period` and its snapshot is not in the local index, as `prune`
+  does. By default keeps only the latest
   snapshot per name; use `--keep-newer-than` for a rolling window. When
   `--skip-errors` skipped a file or directory it could not read or list, the
   prune does not run and every older snapshot is kept, since one of them may
@@ -423,19 +452,35 @@ local snapshot whose remote metadata is missing is dropped from the
 local index; (2) delete orphaned local rows (files, chunks, blobs no
 longer referenced by any completed snapshot); (3) list every remote
 manifest on the destination store to compute the still-referenced blob
-set and delete any blob not in that set. Step (3) reads all remote
-manifests — network cost scales with the number of snapshots. `snapshot
-create --prune` runs the same cleanup automatically; this is the
+set and delete any blob not in that set that is older than
+`prune_grace_period` (default `24h`). A newer one is kept and counted: it
+may belong to a backup still running, on this host or another sharing the
+destination store, that has not yet uploaded its manifest. The grace period
+does not protect a blob such a backup reuses from an earlier run that stopped
+before its manifest: that blob keeps the time of its first upload, so it can
+be deleted. Step (3) also deletes each directory under `metadata/` that has
+no `manifest.json.zst`, as a backup leaves when it stops after uploading
+`db.zst.age` but before its manifest, once every object in it is older than
+`prune_grace_period` and its snapshot is not in the local index. An object the
+listing gives no time for keeps its directory, and a directory whose name is
+not a remote key is left alone. Step (3) reads all remote manifests — network
+cost scales with the number of snapshots.
+`snapshot create --prune` runs the same cleanup automatically; this is the
 manual entry point for the same work. If the destination store cannot
 be listed, or the local index holds snapshots and the destination has
 no `vaultik-destination.txt` (an unplugged volume's empty mount point),
 prune fails and deletes nothing. `snapshot purge` does the same. If a
-blob cannot be deleted, the command (and `snapshot create --prune`)
-exits non-zero.
+blob or such a directory cannot be deleted, the command (and
+`snapshot create --prune`) exits non-zero.
 * `--force`: Skip confirmation prompt
 * `--json`: Output stats as JSON. Also skips the confirmation prompt, as
   `--force` does. A blob that cannot be deleted is counted in
   `blobs_failed`, and the document is printed before the non-zero exit.
+  A blob kept for being newer than `prune_grace_period`, or because the
+  listing of the destination gives no time for it, is counted in
+  `blobs_too_new` and not in `blobs_found`. A directory under `metadata/`
+  with no manifest is counted in `metadata_dirs_deleted` once deleted, or
+  in `metadata_dirs_failed` if it cannot be.
 
 **`info`**: Display system configuration, storage settings, encryption
 recipients, and local database statistics.
@@ -510,6 +555,15 @@ being written, a killed upload can leave a truncated object under its name,
 which a later backup takes for complete. A leftover `.partial` file is ignored
 and can be deleted.
 
+A destination shared between hosts or users, each with its own local index,
+relies on `prune_grace_period` to keep one's prune from deleting the blobs of
+another's backup still running, or its directory under `metadata/` that has
+no manifest yet, so it must be longer than the longest backup run. It does not
+protect a blob that backup reuses from an earlier run that
+stopped before its manifest, which the prune can delete. To not depend on the
+grace period, give each host its own prefix (or directory). See
+[locking](#locking).
+
 Legacy S3 configuration via `s3.*` fields (endpoint, bucket, prefix, etc.) is
 still supported for backward compatibility. `storage_url` takes precedence if
 both are set.
@@ -596,7 +650,11 @@ format does and does not protect.
 1. List all snapshot manifests
 2. Build set of all referenced blob hashes
 3. List all blobs in storage
-4. Delete any blob not in the referenced set
+4. Delete any blob not in the referenced set that is older than
+   `prune_grace_period`
+5. Delete each directory under `metadata/` with no manifest whose objects
+   are all older than `prune_grace_period`, unless its snapshot is in the
+   local index
 
 ### chunking and deduplication
 
@@ -641,6 +699,7 @@ complete annotated example also lives in
 | `chunk_size` | `10MB` | Average chunk size for content-defined chunking |
 | `blob_size_limit` | `10GB` | Maximum blob size before splitting. Must be at least four times `chunk_size` (the largest chunk the chunker can emit), otherwise a single-chunk blob could exceed the limit. A backup needs free temporary space, because each blob is written whole to a temporary file before it is uploaded (up to about `blob_size_limit`; an rclone destination that cannot stream uploads needs about twice that) and the metadata export writes copies of the local index. Temporary files go to `$TMPDIR` (default `/tmp`); with `TMPDIR` unset, SQLite writes one of those copies to `/var/tmp` |
 | `compression_level` | `3` | zstd compression level (1-19) |
+| `prune_grace_period` | `24h` | How old a blob that no snapshot lists must be before `prune` deletes it, and how old every object in a directory under `metadata/` with no manifest must be before `prune` deletes that directory. A backup uploads its blobs and its `db.zst.age` before the manifest that lists them, so on a destination shared between hosts or users this must be longer than the longest backup run (see [locking](#locking)). It does not protect a blob a backup reuses from an earlier run that stopped before its manifest: that blob keeps the time of its first upload, so a prune can delete it. A duration such as `36h` or `90m`; `0s` deletes such blobs and directories at once |
 | `hostname` | system hostname | Hostname used in snapshot IDs |
 | `index_path` | platform data dir | Local SQLite index path |
 

config.example.yml

@@ -328,6 +328,20 @@ storage_url: "rclone://myremote/path/to/backups"
 # Higher = better compression but slower
 # Default: 3
 compression_level: 5
+
+# How old a blob that no snapshot lists must be before prune deletes it, and
+# how old every object in a directory under metadata/ with no manifest must
+# be before prune deletes that directory
+# A backup uploads its blobs and its db.zst.age before the manifest that
+# lists them, so on a destination shared between hosts or users this must be
+# longer than the longest backup run
+# It does not protect a blob a backup reuses from an earlier run that stopped
+# before its manifest: that blob keeps the time of its first upload, so a
+# prune can delete it
+# Supports: 36h, 90m, etc.; 0s deletes them at once
+# Default: 24h
+#prune_grace_period: 24h
+
 # Hostname to use in backup metadata
 # Default: system hostname
 #hostname: myserver

docs/DATAMODEL.md

@@ -228,7 +228,12 @@ The restore process doesn't use the local database. Instead:
 
 1. **Identify Unreferenced Blobs**
    - Query blobs not referenced by any remaining snapshot
-   - Delete from S3 and local database
+   - Delete from S3, once older than `prune_grace_period`, and from the local
+     database
+2. **Delete Metadata Directories With No Manifest**
+   - Delete each directory under `metadata/` that has no `manifest.json.zst`
+     and no local snapshot record, once every object in it is older than
+     `prune_grace_period`
 
 ### 6. Incomplete Snapshot Cleanup
 

docs/REPOSTRUCTURE.md

@@ -163,10 +163,10 @@ These are known, deliberate properties of the format and the tooling, recorded s
 ## Pruning Safety
 
 The prune operation is safe because:
-1. It keeps every blob listed in any snapshot's manifest and deletes only blobs that no manifest references
+1. It keeps every blob listed in any snapshot's manifest and deletes only blobs that no manifest references. Under `metadata/` it deletes only a directory that has no `manifest.json.zst`, whose name is a remote key, and that no local snapshot record claims
 2. Manifests are unencrypted and can be read without keys
 3. If any manifest cannot be downloaded or decoded, prune deletes nothing and exits with an error, rather than treating that snapshot's blobs as unreferenced
-4. Prune requires exclusive access to the destination: running it during a concurrent backup can race a snapshot whose manifest is not yet written, so do not prune while a backup is in progress
+4. It deletes an unreferenced blob only once the blob is older than `prune_grace_period` (default `24h`), and a directory under `metadata/` with no manifest only once every object in it is. A backup uploads its blobs and its `db.zst.age` before the manifest that lists them, so a prune running meanwhile, on this host or another sharing the destination, leaves them as long as no backup run takes longer than the grace period. The grace period does not protect a blob a backup reuses from an earlier run that stopped before its manifest: the backup skips the upload of a blob already on the destination, so that blob keeps the time of its first upload, and a prune before the backup's manifest is written can delete it; the new snapshot then cannot be restored. `remote nuke` has no such check
 
 ## Restoration Requirements
 

internal/cli/config.go

@@ -239,6 +239,18 @@ storage_url: ""
 # Default: 3
 # compression_level: 3
 
+# How old a blob that no snapshot lists must be before prune deletes it,
+# and how old every object in a directory under metadata/ with no manifest
+# must be before prune deletes that directory. A backup uploads its blobs
+# and its db.zst.age before the manifest that lists them, so on a
+# destination shared between hosts or users this must be longer than the
+# longest backup run. It does not protect a blob a backup reuses from an
+# earlier run that stopped before its manifest: that blob keeps the time of
+# its first upload, so a prune can delete it.
+# Accepts: 36h, 90m, etc. 0s deletes them at once.
+# Default: 24h
+# prune_grace_period: 24h
+
 # Hostname used in snapshot IDs. Default: system hostname.
 # hostname: myserver
 

internal/cli/entry_prune_quiet_test.go

@@ -5,6 +5,7 @@ import (
 	"path/filepath"
 	"strings"
 	"testing"
+	"time"
 
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
@@ -14,8 +15,8 @@ import (
 const flagCron = "--cron"
 
 // plantUnreferencedBlob writes a blob that no snapshot references to the
-// destination store at storeDir, so that a prune deletes it. Returns its
-// path.
+// destination store at storeDir, dated long before any prune grace period,
+// so that a prune deletes it. Returns its path.
 func plantUnreferencedBlob(t *testing.T, storeDir string) string {
 	t.Helper()
 
@@ -25,6 +26,9 @@ func plantUnreferencedBlob(t *testing.T, storeDir string) string {
 	require.NoError(t, os.MkdirAll(filepath.Dir(path), 0o750))
 	require.NoError(t, os.WriteFile(path, []byte("unreferenced"), 0o600))
 
+	longAgo := time.Unix(0, 0)
+	require.NoError(t, os.Chtimes(path, longAgo, longAgo))
+
 	return path
 }
 

internal/cli/prune.go

@@ -20,7 +20,16 @@ Local cleanup drops incomplete snapshots and any files, chunks, or
 blobs no longer referenced by a completed snapshot. Remote cleanup
 scans every snapshot manifest in the destination store, builds the
 set of still-referenced blob hashes, and deletes any blob not in that
-set.
+set that is older than prune_grace_period (default 24h). A newer one
+is kept: it may belong to a backup still running, on this host or
+another sharing the destination store, that has not yet uploaded its
+manifest. The grace period does not protect a blob such a backup
+reuses from an earlier run that stopped before its manifest: that
+blob keeps the time of its first upload, so it can be deleted.
+Remote cleanup also deletes each directory under metadata/ with no
+manifest, as a backup that stopped before its manifest leaves, once
+all its objects are older than prune_grace_period and its snapshot is
+not in the local index.
 
 Snapshot create --prune runs the same cleanup automatically; this
 command is the manual entry point for the same work (e.g. after a

internal/cli/snapshot.go

@@ -131,9 +131,12 @@ on Linux), then /etc/vaultik/config.yml.`,
 	cmd.Flags().BoolVar(&opts.Cron, "cron", false,
 		"Run in cron mode (silent unless warning or error)")
 	cmd.Flags().BoolVar(&opts.Prune, "prune", false,
-		"After backup, drop older snapshots of the same name and remove "+
-			"orphaned blobs (not after a backup that skipped unreadable "+
-			"files)")
+		"After backup, drop older snapshots of the same name, remove "+
+			"orphaned blobs older than prune_grace_period, and delete each "+
+			"directory under metadata/ with no manifest once all its "+
+			"objects are older than prune_grace_period and its snapshot is "+
+			"not in the local index (not after a backup that skipped "+
+			"unreadable files)")
 	cmd.Flags().StringVar(&opts.KeepNewerThan, "keep-newer-than", "",
 		"With --prune: keep snapshots newer than this duration "+
 			"(e.g. 30d, 4w, 6mo, 1y; m is minutes, mo is months) "+

internal/config/config.go

@@ -11,6 +11,7 @@ import (
 	"path/filepath"
 	"sort"
 	"strings"
+	"time"
 
 	"filippo.io/age"
 	"git.eeqj.de/sneak/smartconfig"
@@ -38,6 +39,7 @@ const (
 	defaultChunkSize        = Size(10 * 1000 * 1000)        // 10MB
 	defaultS3PartSize       = Size(5 * 1024 * 1024)         // 5MiB
 	defaultCompressionLevel = 3
+	defaultPruneGracePeriod = 24 * time.Hour
 	minChunkSize            = 1000 * 1000 // 1MB
 	minCompressionLevel     = 1
 	maxCompressionLevel     = 19
@@ -67,6 +69,8 @@ var (
 	errFileURLNotAbsolute = errors.New(
 		"a file:// storage_url needs an absolute path, " +
 			"as in file:///path/to/backup")
+	errNegativePruneGracePeriod = errors.New(
+		"prune_grace_period must not be negative")
 	errStorageNotConfigured = errors.New(
 		"storage not configured; set storage_url or provide s3.endpoint + " +
 			"s3.bucket + credentials")
@@ -187,6 +191,15 @@ type Config struct {
 	Snapshots        map[string]SnapshotConfig `yaml:"snapshots"`
 	CompressionLevel int                       `yaml:"compression_level"`
 
+	// PruneGracePeriod is how old a blob no manifest lists must be before
+	// a prune deletes it, and how old every object in a directory under
+	// metadata/ with no manifest must be before a prune deletes that
+	// directory. A backup writes its manifest only once it has uploaded
+	// all its blobs and its db.zst.age, so a younger blob or directory may
+	// belong to a backup still running, on this host or another sharing
+	// the destination store.
+	PruneGracePeriod time.Duration `yaml:"prune_grace_period"`
+
 	// StorageURL specifies the storage backend using a URL format.
 	// Takes precedence over S3Config if set.
 	// Supported formats:
@@ -288,6 +301,7 @@ func Parse(data []byte) (*Config, error) {
 		ChunkSize:        defaultChunkSize,
 		IndexPath:        filepath.Join(xdg.DataHome, appName, "index.sqlite"),
 		CompressionLevel: defaultCompressionLevel,
+		PruneGracePeriod: defaultPruneGracePeriod,
 		S3:               S3Config{PartSize: defaultS3PartSize},
 	}
 
@@ -356,6 +370,7 @@ func Parse(data []byte) (*Config, error) {
 //     exceeds the configured limit
 //   - Compression level must be between 1 and 19
 //   - S3 part size must be between 5MiB and 5GiB, the part sizes S3 accepts
+//   - Prune grace period must not be negative
 //
 // Returns an error describing the first validation failure encountered.
 func (c *Config) Validate() error {
@@ -405,6 +420,10 @@ func (c *Config) Validate() error {
 		return errBadS3PartSize
 	}
 
+	if c.PruneGracePeriod < 0 {
+		return errNegativePruneGracePeriod
+	}
+
 	return nil
 }
 

internal/config/config_test.go

@@ -6,6 +6,7 @@ import (
 	"path/filepath"
 	"strings"
 	"testing"
+	"time"
 
 	"sneak.berlin/go/vaultik/internal/chunker"
 	"sneak.berlin/go/vaultik/internal/log"
@@ -412,6 +413,73 @@ func TestDocumentedSizeExamples(t *testing.T) {
 	}
 }
 
+// TestValidatePruneGracePeriod checks that a negative prune_grace_period
+// is refused rather than acting like 0s, which deletes unreferenced blobs
+// at once, and that 0s and the documented examples are accepted.
+func TestValidatePruneGracePeriod(t *testing.T) {
+	t.Parallel()
+
+	const withoutGracePeriod = "snapshots:\n" +
+		"  test:\n" +
+		"    paths: [/tmp/vaultik-test-source]\n" +
+		"storage_url: file:///tmp/vaultik-test-storage\n"
+
+	tests := []struct {
+		setting string
+		wantErr error
+	}{
+		{"prune_grace_period: 0s", nil},
+		{"prune_grace_period: 90m", nil},
+		{"prune_grace_period: 36h", nil},
+		{"prune_grace_period: -1h", errNegativePruneGracePeriod},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.setting, func(t *testing.T) {
+			t.Parallel()
+
+			cfg, err := Parse([]byte(withoutGracePeriod + tt.setting + "\n"))
+			if err != nil {
+				t.Fatalf("Parse() unexpected error: %v", err)
+			}
+
+			err = cfg.Validate()
+			if !errors.Is(err, tt.wantErr) {
+				t.Fatalf("Validate() error = %v, want %v", err, tt.wantErr)
+			}
+		})
+	}
+}
+
+// TestLoadPruneGracePeriod checks that a config file without
+// prune_grace_period loads with the documented 24h. The value is written out
+// here rather than taken from defaultPruneGracePeriod, so that a change of the
+// default fails this test.
+func TestLoadPruneGracePeriod(t *testing.T) {
+	t.Parallel()
+
+	const withoutGracePeriod = "snapshots:\n" +
+		"  test:\n" +
+		"    paths: [/tmp/vaultik-test-source]\n" +
+		"storage_url: file:///tmp/vaultik-test-storage\n"
+
+	path := filepath.Join(t.TempDir(), "config.yml")
+
+	err := os.WriteFile(path, []byte(withoutGracePeriod), 0o600)
+	if err != nil {
+		t.Fatalf("write config: %v", err)
+	}
+
+	cfg, err := Load(path)
+	if err != nil {
+		t.Fatalf("Load() unexpected error: %v", err)
+	}
+
+	if cfg.PruneGracePeriod != 24*time.Hour {
+		t.Errorf("prune_grace_period = %s, want 24h", cfg.PruneGracePeriod)
+	}
+}
+
 // TestLoadRejectsRelativeFileURL checks that a file:// storage_url with a
 // relative path fails at load. Accepted, it would resolve against the
 // working directory, so a backup run from another directory would write

internal/s3/client.go

@@ -8,6 +8,7 @@ import (
 	"io"
 	"strings"
 	"sync/atomic"
+	"time"
 
 	"github.com/aws/aws-sdk-go-v2/aws"
 	"github.com/aws/aws-sdk-go-v2/config"
@@ -302,7 +303,10 @@ func IsNotFound(err error) bool {
 type ObjectInfo struct {
 	Key  string
 	Size int64
-	Err  error
+	// ModTime is the object's LastModified time. Only ListObjectsStream
+	// sets it.
+	ModTime time.Time
+	Err     error
 }
 
 // ListObjectsStream lists objects with the given prefix and returns a channel.
@@ -343,8 +347,9 @@ func (c *Client) ListObjectsStream(
 					}
 
 					ch <- ObjectInfo{
-						Key:  key,
-						Size: *obj.Size,
+						Key:     key,
+						Size:    *obj.Size,
+						ModTime: aws.ToTime(obj.LastModified),
 					}
 				}
 			}

internal/storage/conformance_test.go

@@ -8,6 +8,7 @@ import (
 	"reflect"
 	"sort"
 	"testing"
+	"time"
 
 	"sneak.berlin/go/vaultik/internal/storage"
 )
@@ -19,15 +20,17 @@ import (
 // constructor, so the contract is defined once.
 //
 // It exercises the public Storer interface: round-trip, stat, list with
-// prefix filtering, overwrite, delete, delete-of-missing, and not-found on
-// Get and Stat. Each section takes its own fresh backend instance, so the
-// order of sections never matters and no section sees another's objects.
+// prefix filtering, the modification time ListStream reports, overwrite,
+// delete, delete-of-missing, and not-found on Get and Stat. Each section
+// takes its own fresh backend instance, so the order of sections never
+// matters and no section sees another's objects.
 func runStorerConformance(t *testing.T, newStorer func(*testing.T) storage.Storer) {
 	t.Helper()
 
 	conformanceRoundTrip(t, newStorer(t))
 	conformanceOverwrite(t, newStorer(t))
 	conformanceList(t, newStorer(t))
+	conformanceListStreamModTime(t, newStorer(t))
 	conformanceDelete(t, newStorer(t))
 	conformanceNotFound(t, newStorer(t))
 }
@@ -118,6 +121,35 @@ func conformanceList(t *testing.T, s storage.Storer) {
 	}
 }
 
+// conformanceListStreamModTime checks that ListStream gives an object
+// just written a modification time of about now, which prune compares
+// with its grace period.
+func conformanceListStreamModTime(t *testing.T, s storage.Storer) {
+	t.Helper()
+
+	ctx := context.Background()
+
+	err := s.Put(ctx, "blobs/dd/written-now", bytes.NewReader([]byte("data")))
+	if err != nil {
+		t.Fatalf("Put: %v", err)
+	}
+
+	var listed []storage.ObjectInfo
+
+	for info := range s.ListStream(ctx, "blobs/") {
+		listed = append(listed, info)
+	}
+
+	if len(listed) != 1 || listed[0].Err != nil {
+		t.Fatalf("ListStream(\"blobs/\") = %v, want the one object", listed)
+	}
+
+	if time.Since(listed[0].ModTime).Abs() > time.Minute {
+		t.Errorf("ListStream ModTime = %v, want within a minute of now",
+			listed[0].ModTime)
+	}
+}
+
 // conformanceDelete checks that Delete removes an object and that deleting
 // a missing key is not an error.
 func conformanceDelete(t *testing.T, s storage.Storer) {

internal/storage/file.go

@@ -235,8 +235,9 @@ func (f *FileStorer) ListStream(ctx context.Context, prefix string) <-chan Objec
 				// Normalize path separators
 				relPath = strings.ReplaceAll(relPath, string(filepath.Separator), "/")
 				ch <- ObjectInfo{
-					Key:  relPath,
-					Size: info.Size(),
+					Key:     relPath,
+					Size:    info.Size(),
+					ModTime: info.ModTime(),
 				}
 			}
 

internal/storage/rclone.go

@@ -53,6 +53,14 @@ func NewRcloneStorer(ctx context.Context, remote, path string) (*RcloneStorer, e
 		rclonePath += path
 	}
 
+	// On S3, Swift and some other remotes rclone keeps a time of its own in
+	// each object's metadata, which costs one request per object to read.
+	// rclone's use_server_modtime setting makes ModTime the time the
+	// listing gives instead: when the object was stored, which is what
+	// prune compares with prune_grace_period.
+	ctx, ci := fs.AddConfig(ctx)
+	ci.UseServerModTime = true
+
 	// Create the rclone filesystem
 	fsys, err := fs.NewFs(ctx, rclonePath)
 	if err != nil {
@@ -211,8 +219,9 @@ func (r *RcloneStorer) ListStream(
 
 			if prefix == "" || strings.HasPrefix(key, prefix) {
 				ch <- ObjectInfo{
-					Key:  key,
-					Size: obj.Size(),
+					Key:     key,
+					Size:    obj.Size(),
+					ModTime: obj.ModTime(ctx),
 				}
 			}
 		})

internal/storage/rclone_test.go

@@ -5,11 +5,17 @@ import (
 	"context"
 	"errors"
 	"io"
+	"net/http"
+	"net/http/httptest"
 	"os"
 	"path/filepath"
 	"strings"
+	"sync/atomic"
 	"testing"
+	"time"
 
+	"github.com/johannesboyne/gofakes3"
+	"github.com/johannesboyne/gofakes3/backend/s3mem"
 	"github.com/rclone/rclone/fs"
 	"github.com/rclone/rclone/fs/config"
 	"github.com/rclone/rclone/fs/config/configmap"
@@ -429,3 +435,72 @@ func TestNewRcloneStorerReadsRcloneConfigEnv(t *testing.T) {
 		t.Errorf("object is not in the remote's directory: %v", err)
 	}
 }
+
+// TestRcloneListStreamOnS3MakesNoRequestPerObject checks that listing an
+// rclone S3 remote takes each object's time from the listing itself. By
+// default rclone reads the time it keeps in each object's metadata, one
+// request per object, and every command that lists the destination store
+// would slow down as it grows.
+//
+//nolint:paralleltest // NewRcloneStorer installs the process-global rclone config
+func TestRcloneListStreamOnS3MakesNoRequestPerObject(t *testing.T) {
+	backend := s3mem.New()
+
+	err := backend.CreateBucket(s3TestBucket)
+	if err != nil {
+		t.Fatalf("create bucket: %v", err)
+	}
+
+	const body = "blob-bytes"
+
+	_, err = backend.PutObject(s3TestBucket, testBlobKey, nil,
+		strings.NewReader(body), int64(len(body)))
+	if err != nil {
+		t.Fatalf("seed object: %v", err)
+	}
+
+	var headRequests atomic.Int64
+
+	fakeS3 := gofakes3.New(backend).Server()
+	srv := httptest.NewServer(http.HandlerFunc(
+		func(w http.ResponseWriter, r *http.Request) {
+			if r.Method == http.MethodHead {
+				headRequests.Add(1)
+			}
+
+			fakeS3.ServeHTTP(w, r)
+		}))
+	t.Cleanup(srv.Close)
+
+	remote := ":s3,provider=Other" +
+		",access_key_id=" + s3TestAccessKeyID +
+		",secret_access_key=" + s3TestSecretAccessKey +
+		",endpoint='" + srv.URL + "'"
+	ctx := context.Background()
+
+	s, err := storage.NewRcloneStorer(ctx, remote, s3TestBucket)
+	if err != nil {
+		t.Fatalf("NewRcloneStorer: %v", err)
+	}
+
+	headRequests.Store(0)
+
+	var listed []storage.ObjectInfo
+
+	for info := range s.ListStream(ctx, "blobs/") {
+		listed = append(listed, info)
+	}
+
+	if len(listed) != 1 || listed[0].Err != nil {
+		t.Fatalf("ListStream(\"blobs/\") = %v, want the one object", listed)
+	}
+
+	if time.Since(listed[0].ModTime).Abs() > time.Minute {
+		t.Errorf("ListStream ModTime = %v, want within a minute of now",
+			listed[0].ModTime)
+	}
+
+	if n := headRequests.Load(); n != 0 {
+		t.Errorf("ListStream made %d HEAD request(s), want none", n)
+	}
+}

internal/storage/s3.go

@@ -89,9 +89,10 @@ func (s *S3Storer) ListStream(ctx context.Context, prefix string) <-chan ObjectI
 
 		for info := range s.client.ListObjectsStream(ctx, prefix, false) {
 			ch <- ObjectInfo{
-				Key:  info.Key,
-				Size: info.Size,
-				Err:  info.Err,
+				Key:     info.Key,
+				Size:    info.Size,
+				ModTime: info.ModTime,
+				Err:     info.Err,
 			}
 		}
 	}()

internal/storage/storer.go

@@ -14,6 +14,7 @@ import (
 	"context"
 	"errors"
 	"io"
+	"time"
 )
 
 // ErrNotFound is returned when an object does not exist.
@@ -27,7 +28,10 @@ type ProgressCallback func(bytesTransferred int64) error
 type ObjectInfo struct {
 	Key  string // Object key/path
 	Size int64  // Size in bytes
-	Err  error  // Error for streaming results (nil on success)
+	// ModTime is when the object was written, as the store reports it.
+	// Only ListStream sets it; Stat leaves it zero.
+	ModTime time.Time
+	Err     error // Error for streaming results (nil on success)
 }
 
 // Info provides human-readable storage configuration.
@@ -67,7 +71,8 @@ type Storer interface {
 	// For large result sets, prefer ListStream.
 	List(ctx context.Context, prefix string) ([]string, error)
 
-	// ListStream returns a channel of ObjectInfo for large result sets.
+	// ListStream returns a channel of ObjectInfo, with each object's key,
+	// size and modification time, for large result sets.
 	// The channel is closed when listing completes.
 	// If an error occurs during listing, the final item will have Err set.
 	ListStream(ctx context.Context, prefix string) <-chan ObjectInfo

internal/vaultik/info.go

@@ -457,9 +457,9 @@ func (v *Vaultik) scanRemoteBlobStorage(
 		return err
 	}
 
-	for _, size := range allBlobs {
+	for _, blob := range allBlobs {
 		result.TotalBlobCount++
-		result.TotalBlobSize += size
+		result.TotalBlobSize += blob.Size
 	}
 
 	// A blob named only by a manifest that could not be read, or by one
@@ -474,10 +474,10 @@ func (v *Vaultik) scanRemoteBlobStorage(
 		orphanedSize  int64
 	)
 
-	for hash, size := range allBlobs {
+	for hash, blob := range allBlobs {
 		if _, referenced := referencedBlobs[hash]; !referenced {
 			orphanedCount++
-			orphanedSize += size
+			orphanedSize += blob.Size
 		}
 	}
 

internal/vaultik/prune.go

@@ -4,9 +4,13 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
+	"sort"
 	"strings"
+	"time"
 
 	"sneak.berlin/go/vaultik/internal/log"
+	"sneak.berlin/go/vaultik/internal/snapshot"
+	"sneak.berlin/go/vaultik/internal/storage"
 )
 
 // PruneOptions contains options for the prune command
@@ -22,6 +26,11 @@ var errNukeRequiresForce = errors.New(
 // errBlobDeleteFailed reports unreferenced blobs prune could not delete.
 var errBlobDeleteFailed = errors.New("blob(s) could not be deleted")
 
+// errMetadataDirDeleteFailed reports directories under metadata/ with no
+// manifest that prune could not delete.
+var errMetadataDirDeleteFailed = errors.New(
+	"metadata director(ies) with no manifest could not be deleted")
+
 // errObjectsLeft reports objects remote nuke still finds on the backup
 // destination store after deleting.
 var errObjectsLeft = errors.New(
@@ -29,7 +38,8 @@ var errObjectsLeft = errors.New(
 
 // nukeCommandHint is the command suggested when a remote nuke could not
 // delete everything: running it again deletes what is left, which
-// `vaultik prune` does not do for snapshot metadata.
+// `vaultik prune` does not do for snapshot metadata that has its
+// manifest.
 const nukeCommandHint = "vaultik remote nuke --force"
 
 // metadataDirName is the top-level remote directory holding snapshot
@@ -163,6 +173,15 @@ type PruneBlobsResult struct {
 	BlobsDeleted int   `json:"blobs_deleted"`
 	BlobsFailed  int   `json:"blobs_failed,omitempty"`
 	BytesFreed   int64 `json:"bytes_freed"`
+	// BlobsTooNew counts the unreferenced blobs kept because they are
+	// newer than the prune grace period, or of unknown age. BlobsFound
+	// does not include them.
+	BlobsTooNew int `json:"blobs_too_new"`
+	// MetadataDirsDeleted counts the directories under metadata/ with no
+	// manifest that prune deleted, and MetadataDirsFailed those it could
+	// not delete.
+	MetadataDirsDeleted int `json:"metadata_dirs_deleted"`
+	MetadataDirsFailed  int `json:"metadata_dirs_failed,omitempty"`
 }
 
 // Prune removes orphaned data from the local index database AND
@@ -194,11 +213,17 @@ func (v *Vaultik) Prune(opts *PruneOptions) error {
 	return v.PruneBlobs(opts)
 }
 
-// PruneBlobs removes unreferenced blobs from storage
+// PruneBlobs removes unreferenced blobs from storage, and each directory
+// under metadata/ that a backup left with no manifest.
 func (v *Vaultik) PruneBlobs(opts *PruneOptions) error {
 	log.Info("Starting prune operation")
 
-	allBlobsReferenced, err := v.collectReferencedBlobs()
+	metadataObjects, err := v.listMetadataObjects()
+	if err != nil {
+		return err
+	}
+
+	allBlobsReferenced, err := v.collectReferencedBlobs(metadataObjects)
 	if err != nil {
 		return err
 	}
@@ -208,11 +233,22 @@ func (v *Vaultik) PruneBlobs(opts *PruneOptions) error {
 		return err
 	}
 
-	unreferencedBlobs, totalSize := v.findUnreferencedBlobs(allBlobs, allBlobsReferenced)
+	unreferencedBlobs, totalSize, tooNew := v.findUnreferencedBlobs(
+		allBlobs, allBlobsReferenced)
 
-	result := &PruneBlobsResult{BlobsFound: len(unreferencedBlobs)}
+	dirsWithoutManifest, err := v.findMetadataDirsWithoutManifest(metadataObjects)
+	if err != nil {
+		return err
+	}
 
-	if len(unreferencedBlobs) == 0 {
+	result := &PruneBlobsResult{
+		BlobsFound:  len(unreferencedBlobs),
+		BlobsTooNew: tooNew,
+	}
+
+	v.reportBlobsTooNew(tooNew, opts)
+
+	if len(unreferencedBlobs) == 0 && len(dirsWithoutManifest) == 0 {
 		log.Info("No unreferenced blobs found")
 
 		if opts.JSON {
@@ -225,38 +261,16 @@ func (v *Vaultik) PruneBlobs(opts *PruneOptions) error {
 	}
 
 	log.Info("Found unreferenced blobs",
-		"count", len(unreferencedBlobs), "total_size", ubytes(totalSize))
+		"count", len(unreferencedBlobs), "total_size", ubytes(totalSize),
+		"metadata_dirs_without_manifest", len(dirsWithoutManifest))
 
-	if opts.Force && !opts.JSON {
-		v.UI.Infof("Found %d unreferenced blob(s) totaling %s.",
-			len(unreferencedBlobs), ubytes(totalSize))
-	}
-
-	if !opts.Force && !opts.JSON {
-		// The count, the prompt and its answer bypass the UI: they are an
-		// interactive exchange the operator must see, so --quiet does not
-		// silence them.
-		v.stdoutf("Found %d unreferenced blob(s) totaling %s.\n",
-			len(unreferencedBlobs), ubytes(totalSize))
-		v.stdoutf("\nDelete %d unreferenced blob(s)? [y/N] ", len(unreferencedBlobs))
-
-		var confirm string
-
-		_, err = v.scanStdin(&confirm)
-		if err != nil {
-			v.printlnStdout("Cancelled")
-
-			return nil //nolint:nilerr // read failure means no confirmation
-		}
-
-		if strings.ToLower(confirm) != "y" {
-			v.printlnStdout("Cancelled")
-
-			return nil
-		}
+	if !v.confirmPrune(opts, len(unreferencedBlobs), totalSize,
+		dirsWithoutManifest) {
+		return nil
 	}
 
 	v.deleteUnreferencedBlobs(unreferencedBlobs, allBlobs, result)
+	v.deleteMetadataDirs(dirsWithoutManifest, result)
 
 	if opts.JSON {
 		err = v.outputPruneBlobsJSON(result)
@@ -264,33 +278,140 @@ func (v *Vaultik) PruneBlobs(opts *PruneOptions) error {
 			return err
 		}
 	} else {
+		v.reportPruneDeletions(result, len(dirsWithoutManifest))
+	}
+
+	var failures []error
+
+	if result.BlobsFailed > 0 {
+		failures = append(failures,
+			fmt.Errorf("%d %w", result.BlobsFailed, errBlobDeleteFailed))
+	}
+
+	if result.MetadataDirsFailed > 0 {
+		failures = append(failures, fmt.Errorf("%d %w",
+			result.MetadataDirsFailed, errMetadataDirDeleteFailed))
+	}
+
+	return errors.Join(failures...)
+}
+
+// confirmPrune states what prune found to delete, naming each directory
+// under metadata/ by its remote key, and, unless --force or --json is
+// given, asks the operator to confirm. It reports whether to go ahead.
+func (v *Vaultik) confirmPrune(
+	opts *PruneOptions, blobCount int, blobsSize int64, dirs []string,
+) bool {
+	if opts.JSON {
+		return true
+	}
+
+	dirCount := len(dirs)
+	blobsFound := fmt.Sprintf("Found %d unreferenced blob(s) totaling %s.",
+		blobCount, ubytes(blobsSize))
+	dirsFound := fmt.Sprintf("Found %d metadata director(ies) left by "+
+		"backups that stopped before their manifest:", dirCount)
+
+	if opts.Force {
+		if blobCount > 0 {
+			v.UI.Infof("%s", blobsFound)
+		}
+
+		if dirCount > 0 {
+			v.UI.Infof("%s", dirsFound)
+
+			for _, remoteKey := range dirs {
+				v.UI.Detailf("metadata/%s/", remoteKey)
+			}
+		}
+
+		return true
+	}
+
+	// The counts, the names, the prompt and its answer bypass the UI:
+	// they are an interactive exchange the operator must see, so --quiet
+	// does not silence them.
+	if blobCount > 0 {
+		v.stdoutf("%s\n", blobsFound)
+	}
+
+	if dirCount > 0 {
+		v.stdoutf("%s\n", dirsFound)
+
+		for _, remoteKey := range dirs {
+			v.stdoutf("  metadata/%s/\n", remoteKey)
+		}
+	}
+
+	switch {
+	case dirCount == 0:
+		v.stdoutf("\nDelete %d unreferenced blob(s)? [y/N] ", blobCount)
+	case blobCount == 0:
+		v.stdoutf("\nDelete %d metadata director(ies)? [y/N] ", dirCount)
+	default:
+		v.stdoutf("\nDelete %d unreferenced blob(s) and %d metadata "+
+			"director(ies)? [y/N] ", blobCount, dirCount)
+	}
+
+	var confirm string
+
+	// A failure to read the answer means no confirmation.
+	_, err := v.scanStdin(&confirm)
+	if err != nil || strings.ToLower(confirm) != "y" {
+		v.printlnStdout("Cancelled")
+
+		return false
+	}
+
+	return true
+}
+
+// reportPruneDeletions says how many blobs and metadata directories
+// prune deleted, naming each kind only when it found some to delete.
+func (v *Vaultik) reportPruneDeletions(result *PruneBlobsResult, dirCount int) {
+	if result.BlobsFound > 0 {
 		v.UI.Infof("Deleted %d blob(s) totaling %s.",
 			result.BlobsDeleted, ubytes(result.BytesFreed))
 	}
 
-	if result.BlobsFailed > 0 {
-		return fmt.Errorf("%d %w", result.BlobsFailed, errBlobDeleteFailed)
+	if dirCount > 0 {
+		v.UI.Infof("Deleted %d metadata director(ies) with no manifest.",
+			result.MetadataDirsDeleted)
 	}
-
-	return nil
 }
 
-// collectReferencedBlobs downloads all manifests and returns the set of
-// referenced blob hashes.
+// listMetadataObjects lists every object under metadata/ on the
+// destination store.
+func (v *Vaultik) listMetadataObjects() ([]storage.ObjectInfo, error) {
+	log.Info("Listing remote snapshots")
+
+	var objects []storage.ObjectInfo
+
+	for object := range v.Storage.ListStream(v.ctx, "metadata/") {
+		if object.Err != nil {
+			return nil, fmt.Errorf("listing metadata objects: %w", object.Err)
+		}
+
+		objects = append(objects, object)
+	}
+
+	return objects, nil
+}
+
+// collectReferencedBlobs downloads every manifest among the listed
+// metadata objects and returns the set of referenced blob hashes.
 //
 // Every manifest must be read successfully. A manifest that cannot be
 // downloaded or decoded means its snapshot's blobs are unknown, so
 // treating them as unreferenced would let prune delete data a snapshot
 // still needs. Rather than risk that silent loss, any failure returns an
 // error naming the remote key and prune deletes nothing.
-func (v *Vaultik) collectReferencedBlobs() (map[string]bool, error) {
-	log.Info("Listing remote snapshots")
-	// IDs returned by listUniqueSnapshotIDs are remote keys (hashed
+func (v *Vaultik) collectReferencedBlobs(
+	metadataObjects []storage.ObjectInfo,
+) (map[string]bool, error) {
+	// IDs returned by uniqueSnapshotIDs are remote keys (hashed
 	// subdirectories under metadata/), not human snapshot IDs.
-	remoteKeys, err := v.listUniqueSnapshotIDs()
-	if err != nil {
-		return nil, fmt.Errorf("listing snapshot keys: %w", err)
-	}
+	remoteKeys := uniqueSnapshotIDs(metadataObjects)
 
 	log.Info("Found manifests in remote storage", "count", len(remoteKeys))
 
@@ -315,18 +436,14 @@ func (v *Vaultik) collectReferencedBlobs() (map[string]bool, error) {
 	return allBlobsReferenced, nil
 }
 
-// listUniqueSnapshotIDs returns deduplicated snapshot IDs from remote metadata
-func (v *Vaultik) listUniqueSnapshotIDs() ([]string, error) {
-	objectCh := v.Storage.ListStream(v.ctx, "metadata/")
+// uniqueSnapshotIDs returns deduplicated snapshot IDs from the listed
+// metadata objects.
+func uniqueSnapshotIDs(metadataObjects []storage.ObjectInfo) []string {
 	seen := make(map[string]bool)
 
 	var snapshotIDs []string
 
-	for object := range objectCh {
-		if object.Err != nil {
-			return nil, fmt.Errorf("listing metadata objects: %w", object.Err)
-		}
-
+	for _, object := range metadataObjects {
 		parts := strings.Split(object.Key, "/")
 		if len(parts) >= minSnapshotIDParts &&
 			parts[0] == metadataDirName && parts[1] != "" {
@@ -341,14 +458,15 @@ func (v *Vaultik) listUniqueSnapshotIDs() ([]string, error) {
 		}
 	}
 
-	return snapshotIDs, nil
+	return snapshotIDs
 }
 
-// listAllRemoteBlobs returns a map of all blob hashes to their sizes in remote storage
-func (v *Vaultik) listAllRemoteBlobs() (map[string]int64, error) {
+// listAllRemoteBlobs returns a map of all blob hashes in remote storage
+// to their listing entries.
+func (v *Vaultik) listAllRemoteBlobs() (map[string]storage.ObjectInfo, error) {
 	log.Info("Listing all blobs in storage")
 
-	allBlobs := make(map[string]int64)
+	allBlobs := make(map[string]storage.ObjectInfo)
 	blobObjectCh := v.Storage.ListStream(v.ctx, "blobs/")
 
 	for object := range blobObjectCh {
@@ -372,7 +490,7 @@ func (v *Vaultik) listAllRemoteBlobs() (map[string]int64, error) {
 			continue
 		}
 
-		allBlobs[parts[3]] = object.Size
+		allBlobs[parts[3]] = object
 	}
 
 	log.Info("Found blobs in storage", "count", len(allBlobs))
@@ -380,30 +498,135 @@ func (v *Vaultik) listAllRemoteBlobs() (map[string]int64, error) {
 	return allBlobs, nil
 }
 
-// findUnreferencedBlobs returns blob hashes not referenced by any
-// manifest and their total size.
+// findUnreferencedBlobs returns the hashes of the blobs no manifest
+// references that are older than the prune grace period, and their total
+// size. It also returns how many unreferenced blobs it left out for
+// being newer than that, or of unknown age because the listing gave no
+// time for them.
 func (v *Vaultik) findUnreferencedBlobs(
-	allBlobs map[string]int64, referenced map[string]bool,
-) ([]string, int64) {
+	allBlobs map[string]storage.ObjectInfo, referenced map[string]bool,
+) ([]string, int64, int) {
 	var (
 		unreferenced []string
 		totalSize    int64
+		tooNew       int
 	)
 
-	for hash, size := range allBlobs {
-		if !referenced[hash] {
-			unreferenced = append(unreferenced, hash)
-			totalSize += size
+	cutoff := time.Now().UTC().Add(-v.Config.PruneGracePeriod)
+
+	for hash, blob := range allBlobs {
+		if referenced[hash] {
+			continue
+		}
+
+		if blob.ModTime.IsZero() || blob.ModTime.After(cutoff) {
+			tooNew++
+
+			continue
+		}
+
+		unreferenced = append(unreferenced, hash)
+		totalSize += blob.Size
+	}
+
+	return unreferenced, totalSize, tooNew
+}
+
+// findMetadataDirsWithoutManifest returns the remote key of each
+// directory under metadata/ that has no manifest.json.zst, such as one a
+// backup leaves when its manifest upload fails after db.zst.age was
+// uploaded. It leaves out a directory a local snapshot record claims,
+// and one holding an object newer than the prune grace period, or of
+// unknown age because the listing gave no time for it: a backup still
+// running may be writing there. A name that is not a remote key is
+// never returned.
+func (v *Vaultik) findMetadataDirsWithoutManifest(
+	metadataObjects []storage.ObjectInfo,
+) ([]string, error) {
+	localIDs, err := v.localSnapshotIDs()
+	if err != nil {
+		return nil, fmt.Errorf("listing local snapshots: %w", err)
+	}
+
+	keep := make(map[string]bool, len(localIDs))
+	for _, id := range localIDs {
+		keep[snapshot.RemoteSnapshotKey(id)] = true
+	}
+
+	cutoff := time.Now().UTC().Add(-v.Config.PruneGracePeriod)
+	listed := make(map[string]bool)
+
+	for _, object := range metadataObjects {
+		parts := strings.Split(object.Key, "/")
+		if len(parts) < metadataKeyParts || !isBlobHash(parts[1]) {
+			continue
+		}
+
+		remoteKey := parts[1]
+		listed[remoteKey] = true
+
+		if parts[2] == "manifest.json.zst" ||
+			object.ModTime.IsZero() || object.ModTime.After(cutoff) {
+			keep[remoteKey] = true
 		}
 	}
 
-	return unreferenced, totalSize
+	var remoteKeys []string
+
+	for remoteKey := range listed {
+		if !keep[remoteKey] {
+			remoteKeys = append(remoteKeys, remoteKey)
+		}
+	}
+
+	sort.Strings(remoteKeys)
+
+	return remoteKeys, nil
+}
+
+// deleteMetadataDirs deletes everything in the given directories under
+// metadata/ and counts in the result the directories deleted and those
+// it could not delete.
+func (v *Vaultik) deleteMetadataDirs(
+	remoteKeys []string, result *PruneBlobsResult,
+) {
+	for _, remoteKey := range remoteKeys {
+		_, err := v.deleteRemoteSnapshotByKey(remoteKey)
+		if err != nil {
+			log.Error("Failed to delete metadata directory with no manifest",
+				"remote_key", remoteKey, "error", err)
+
+			result.MetadataDirsFailed++
+
+			continue
+		}
+
+		log.Info("Deleted metadata directory with no manifest",
+			"remote_key", remoteKey)
+
+		result.MetadataDirsDeleted++
+	}
+}
+
+// reportBlobsTooNew says how many unreferenced blobs prune kept for being
+// newer than the grace period or of unknown age. Under --json the
+// document carries the count instead.
+func (v *Vaultik) reportBlobsTooNew(tooNew int, opts *PruneOptions) {
+	if tooNew == 0 || opts.JSON {
+		return
+	}
+
+	v.UI.Infof("Kept %d unreferenced blob(s) newer than "+
+		"prune_grace_period (%s), or of unknown age: a backup still "+
+		"running may need them.",
+		tooNew, v.Config.PruneGracePeriod)
 }
 
 // deleteUnreferencedBlobs deletes the given blobs from storage and
 // populates the result.
 func (v *Vaultik) deleteUnreferencedBlobs(
-	unreferencedBlobs []string, allBlobs map[string]int64, result *PruneBlobsResult,
+	unreferencedBlobs []string, allBlobs map[string]storage.ObjectInfo,
+	result *PruneBlobsResult,
 ) {
 	log.Info("Deleting unreferenced blobs")
 
@@ -418,7 +641,7 @@ func (v *Vaultik) deleteUnreferencedBlobs(
 		}
 
 		result.BlobsDeleted++
-		result.BytesFreed += allBlobs[hash]
+		result.BytesFreed += allBlobs[hash].Size
 
 		if (i+1)%progressLogEvery == 0 || i == len(unreferencedBlobs)-1 {
 			log.Info("Deletion progress",

internal/vaultik/prune_grace_period_test.go

@@ -0,0 +1,166 @@
+package vaultik_test
+
+import (
+	"bytes"
+	"context"
+	"encoding/json"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+	"time"
+
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"sneak.berlin/go/vaultik/internal/config"
+	"sneak.berlin/go/vaultik/internal/database"
+	"sneak.berlin/go/vaultik/internal/log"
+	"sneak.berlin/go/vaultik/internal/storage"
+	"sneak.berlin/go/vaultik/internal/storage/faultstore"
+	"sneak.berlin/go/vaultik/internal/ui"
+	"sneak.berlin/go/vaultik/internal/vaultik"
+)
+
+// TestPruneDuringBackupKeepsItsBlobs runs a prune from another host
+// sharing the destination store at the moment a backup has uploaded its
+// blobs but not yet its manifest, so no manifest lists those blobs. The
+// prune must leave them, and the backup must then restore.
+func TestPruneDuringBackupKeepsItsBlobs(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	fs := afero.NewOsFs()
+	tempDir := t.TempDir()
+	dataDir := filepath.Join(tempDir, "src")
+	storeDir := t.TempDir()
+	restoreDir := filepath.Join(tempDir, "restored")
+	dbPath := filepath.Join(tempDir, "index.sqlite")
+
+	ctx := context.Background()
+	cfg := faultTestConfig()
+	testFiles := writeFaultSourceTree(t, fs, dataDir)
+
+	inner, err := storage.NewFileStorer(storeDir)
+	require.NoError(t, err)
+
+	otherHostCfg := faultTestConfig()
+	otherHostCfg.PruneGracePeriod = time.Hour
+	otherHost := newReaderVaultik(ctx, otherHostCfg, inner, nil, fs)
+
+	var (
+		pruned   bool
+		pruneErr error
+	)
+
+	store := faultstore.New(inner)
+	store.OnPut = func(key string) faultstore.PutAction {
+		if strings.HasSuffix(key, "/manifest.json.zst") {
+			pruned = true
+			pruneErr = otherHost.PruneBlobs(&vaultik.PruneOptions{Force: true})
+		}
+
+		return faultstore.PutNormal
+	}
+
+	db, err := database.New(ctx, dbPath)
+	require.NoError(t, err)
+
+	repos := database.NewRepositories(db)
+
+	id := fullFaultBackup(ctx, t, fs, store, cfg, repos, dataDir, dbPath, "shared")
+	require.NoError(t, db.Close())
+
+	require.True(t, pruned, "the prune must run before the manifest upload")
+	require.NoError(t, pruneErr)
+
+	v := newReaderVaultik(ctx, cfg, inner, nil, fs)
+	require.NoError(t, v.Restore(&vaultik.RestoreOptions{
+		SnapshotID: id,
+		TargetDir:  restoreDir,
+		Verify:     true,
+	}), "a prune during the backup must not delete the backup's blobs")
+
+	assertRestoredTree(t, fs, restoreDir, testFiles)
+}
+
+// TestPruneKeepsUnreferencedBlobWithNoTime checks that a blob no
+// manifest lists, whose listing gives no modification time (as an S3
+// listing entry without LastModified does), is kept and counted with
+// the blobs too new to delete: its age is unknown.
+func TestPruneKeepsUnreferencedBlobWithNoTime(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newListEnv(t)
+
+	// Written into the mock store's map directly rather than through
+	// Put, so its listing gives no time.
+	blobKey := "blobs/" + testBlobHashA[:2] + "/" + testBlobHashA[2:4] +
+		"/" + testBlobHashA
+	env.store.data[blobKey] = []byte("blob")
+
+	require.NoError(t, env.v.PruneBlobs(&vaultik.PruneOptions{JSON: true}))
+
+	assert.True(t, env.store.hasKey(blobKey),
+		"a blob of unknown age must be kept")
+
+	var result vaultik.PruneBlobsResult
+
+	require.NoError(t, json.Unmarshal(env.stdout.Bytes(), &result))
+	assert.Equal(t, 0, result.BlobsDeleted)
+	assert.Equal(t, 1, result.BlobsTooNew)
+}
+
+// TestPruneDeletesUnreferencedBlobOlderThanGracePeriod checks that the
+// grace period only delays deletion: a blob no manifest lists is deleted
+// once it is older than the grace period, and kept and counted until
+// then.
+func TestPruneDeletesUnreferencedBlobOlderThanGracePeriod(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	ctx := context.Background()
+	storeDir := t.TempDir()
+
+	store, err := storage.NewFileStorer(storeDir)
+	require.NoError(t, err)
+
+	oldKey := "blobs/" + testBlobHashA[:2] + "/" + testBlobHashA[2:4] +
+		"/" + testBlobHashA
+	newKey := "blobs/" + testBlobHashB[:2] + "/" + testBlobHashB[2:4] +
+		"/" + testBlobHashB
+
+	for _, key := range []string{oldKey, newKey} {
+		require.NoError(t, store.Put(ctx, key, strings.NewReader("blob")))
+	}
+
+	gracePeriod := time.Hour
+	beforeGracePeriod := time.Now().Add(-gracePeriod - time.Minute)
+	require.NoError(t, os.Chtimes(filepath.Join(storeDir, oldKey),
+		beforeGracePeriod, beforeGracePeriod))
+
+	stdout := &bytes.Buffer{}
+	v := &vaultik.Vaultik{
+		Config:  &config.Config{PruneGracePeriod: gracePeriod},
+		Storage: store,
+		Stdout:  stdout,
+		UI:      ui.NewWithColor(stdout, false),
+	}
+	v.SetContext(ctx)
+
+	require.NoError(t, v.PruneBlobs(&vaultik.PruneOptions{JSON: true}))
+
+	_, err = store.Stat(ctx, oldKey)
+	require.ErrorIs(t, err, storage.ErrNotFound,
+		"a blob older than the grace period must be deleted")
+
+	_, err = store.Stat(ctx, newKey)
+	require.NoError(t, err, "a blob newer than the grace period must be kept")
+
+	var result vaultik.PruneBlobsResult
+
+	require.NoError(t, json.Unmarshal(stdout.Bytes(), &result))
+	assert.Equal(t, 1, result.BlobsDeleted)
+	assert.Equal(t, 1, result.BlobsTooNew)
+}

internal/vaultik/prune_metadata_dir_test.go

@@ -0,0 +1,225 @@
+package vaultik_test
+
+import (
+	"bytes"
+	"context"
+	"encoding/json"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"sneak.berlin/go/vaultik/internal/config"
+	"sneak.berlin/go/vaultik/internal/log"
+	"sneak.berlin/go/vaultik/internal/snapshot"
+	"sneak.berlin/go/vaultik/internal/storage"
+	"sneak.berlin/go/vaultik/internal/storage/faultstore"
+	"sneak.berlin/go/vaultik/internal/ui"
+	"sneak.berlin/go/vaultik/internal/vaultik"
+)
+
+// metadataObjectKey returns the key of the named file in the metadata
+// directory of the snapshot with the given human ID.
+func metadataObjectKey(snapshotID, name string) string {
+	return "metadata/" + snapshot.RemoteSnapshotKey(snapshotID) + "/" + name
+}
+
+// TestPruneDeletesMetadataDirWithoutManifestOlderThanGracePeriod checks
+// that prune deletes a directory under metadata/ holding only
+// db.zst.age, as a backup leaves when its manifest upload fails, once it
+// is older than the grace period, and keeps one newer than that. A
+// directory with a manifest is never deleted, however old.
+func TestPruneDeletesMetadataDirWithoutManifestOlderThanGracePeriod(
+	t *testing.T,
+) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	ctx := context.Background()
+	storeDir := t.TempDir()
+
+	store, err := storage.NewFileStorer(storeDir)
+	require.NoError(t, err)
+
+	const (
+		oldID      = "testhost_home_2026-01-01T00:00:00Z"
+		newID      = "testhost_home_2026-01-02T00:00:00Z"
+		completeID = "testhost_home_2026-01-03T00:00:00Z"
+	)
+
+	oldDB := metadataObjectKey(oldID, "db.zst.age")
+	newDB := metadataObjectKey(newID, "db.zst.age")
+	completeDB := metadataObjectKey(completeID, "db.zst.age")
+	completeManifest := metadataObjectKey(completeID, "manifest.json.zst")
+
+	manifest, err := snapshot.EncodeManifest(&snapshot.Manifest{
+		SnapshotID: snapshot.RemoteSnapshotKey(completeID),
+	}, 3)
+	require.NoError(t, err)
+
+	for _, key := range []string{oldDB, newDB, completeDB} {
+		require.NoError(t, store.Put(ctx, key, strings.NewReader("db")))
+	}
+
+	require.NoError(t, store.Put(ctx, completeManifest,
+		bytes.NewReader(manifest)))
+
+	gracePeriod := time.Hour
+	beforeGracePeriod := time.Now().Add(-gracePeriod - time.Minute)
+
+	for _, key := range []string{oldDB, completeDB, completeManifest} {
+		require.NoError(t, os.Chtimes(filepath.Join(storeDir, key),
+			beforeGracePeriod, beforeGracePeriod))
+	}
+
+	stdout := &bytes.Buffer{}
+	v := &vaultik.Vaultik{
+		Config:  &config.Config{PruneGracePeriod: gracePeriod},
+		Storage: store,
+		Stdout:  stdout,
+		UI:      ui.NewWithColor(stdout, false),
+	}
+	v.SetContext(ctx)
+
+	require.NoError(t, v.PruneBlobs(&vaultik.PruneOptions{JSON: true}))
+
+	_, err = store.Stat(ctx, oldDB)
+	require.ErrorIs(t, err, storage.ErrNotFound,
+		"a directory with no manifest older than the grace period "+
+			"must be deleted")
+
+	for _, key := range []string{newDB, completeDB, completeManifest} {
+		_, err = store.Stat(ctx, key)
+		require.NoError(t, err, "%s must be kept", key)
+	}
+
+	var result vaultik.PruneBlobsResult
+
+	require.NoError(t, json.Unmarshal(stdout.Bytes(), &result))
+	assert.Equal(t, 1, result.MetadataDirsDeleted)
+}
+
+// TestPruneKeepsMetadataDirClaimedUnknownAgeOrNotRemoteKey checks that
+// prune --force keeps a directory under metadata/ with no manifest when a
+// local snapshot record claims it, when the listing gives no time for an
+// object in it, or when its name is not a remote key. A fourth such
+// directory is named, deleted and reported, although there are no
+// unreferenced blobs to delete.
+func TestPruneKeepsMetadataDirClaimedUnknownAgeOrNotRemoteKey(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	ctx := context.Background()
+	env := newListEnv(t)
+
+	const (
+		claimedID = "testhost_home_2026-01-01T00:00:00Z"
+		leftID    = "testhost_home_2026-01-03T00:00:00Z"
+	)
+
+	env.addLocal(t, claimedID, time.Now().Add(-time.Hour))
+
+	claimedDB := metadataObjectKey(claimedID, "db.zst.age")
+	unknownAgeDB := metadataObjectKey("testhost_home_2026-01-02T00:00:00Z",
+		"db.zst.age")
+	leftDB := metadataObjectKey(leftID, "db.zst.age")
+	notRemoteKeyDB := "metadata/not-a-remote-key/db.zst.age"
+
+	for _, key := range []string{claimedDB, leftDB, notRemoteKeyDB} {
+		require.NoError(t, env.store.Put(ctx, key, strings.NewReader("db")))
+	}
+
+	// Written into the mock store's map directly rather than through
+	// Put, so its listing gives no time.
+	env.store.data[unknownAgeDB] = []byte("db")
+
+	require.NoError(t, env.v.PruneBlobs(&vaultik.PruneOptions{Force: true}))
+
+	assert.True(t, env.store.hasKey(claimedDB),
+		"a directory a local snapshot record claims must be kept")
+	assert.True(t, env.store.hasKey(unknownAgeDB),
+		"a directory holding an object of unknown age must be kept")
+	assert.True(t, env.store.hasKey(notRemoteKeyDB),
+		"a directory whose name is not a remote key must be kept")
+	assert.False(t, env.store.hasKey(leftDB),
+		"a directory with no manifest, unclaimed and old, must be deleted")
+
+	output := env.stdout.String()
+
+	assert.Contains(t, output, "Found 1 metadata director(ies) left by "+
+		"backups that stopped before their manifest:")
+	assert.Contains(t, output,
+		"metadata/"+snapshot.RemoteSnapshotKey(leftID)+"/")
+	assert.NotContains(t, output, "not-a-remote-key")
+	assert.Contains(t, output,
+		"Deleted 1 metadata director(ies) with no manifest.")
+	assert.NotContains(t, output, "No unreferenced blobs to remove.")
+}
+
+// TestPruneDeclinedKeepsMetadataDirWithoutManifest checks that the prompt
+// names a directory under metadata/ with no manifest that prune is about
+// to delete, and that answering no keeps it.
+func TestPruneDeclinedKeepsMetadataDirWithoutManifest(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newListEnv(t)
+
+	const leftID = "testhost_home_2026-01-01T00:00:00Z"
+
+	leftDB := metadataObjectKey(leftID, "db.zst.age")
+	require.NoError(t, env.store.Put(context.Background(), leftDB,
+		strings.NewReader("db")))
+
+	env.v.Stdin = strings.NewReader("n\n")
+
+	require.NoError(t, env.v.PruneBlobs(&vaultik.PruneOptions{}))
+
+	assert.True(t, env.store.hasKey(leftDB),
+		"a declined prune must keep the directory")
+
+	output := env.stdout.String()
+
+	assert.Contains(t, output,
+		"  metadata/"+snapshot.RemoteSnapshotKey(leftID)+"/\n")
+	assert.Contains(t, output, "Delete 1 metadata director(ies)? [y/N] ")
+	assert.Contains(t, output, "Cancelled")
+	assert.NotContains(t, output, "Deleted")
+}
+
+// TestPruneFailedMetadataDirDeleteReturnsError checks that prune --json
+// counts a directory under metadata/ with no manifest that it cannot
+// delete, and then returns an error, so the command exits non-zero.
+func TestPruneFailedMetadataDirDeleteReturnsError(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newListEnv(t)
+
+	leftDB := metadataObjectKey("testhost_home_2026-01-01T00:00:00Z",
+		"db.zst.age")
+	require.NoError(t, env.store.Put(context.Background(), leftDB,
+		strings.NewReader("db")))
+
+	store := faultstore.New(env.store)
+	store.OnDelete = func(key string) bool {
+		return strings.HasPrefix(key, "metadata/")
+	}
+	env.v.Storage = store
+
+	err := env.v.PruneBlobs(&vaultik.PruneOptions{JSON: true})
+
+	require.ErrorContains(t, err,
+		"1 metadata director(ies) with no manifest could not be deleted")
+	assert.True(t, env.store.hasKey(leftDB))
+
+	var result vaultik.PruneBlobsResult
+
+	require.NoError(t, json.Unmarshal(env.stdout.Bytes(), &result),
+		"stdout must hold the JSON document, got:\n%s", env.stdout.String())
+	assert.Equal(t, 1, result.MetadataDirsFailed)
+	assert.Equal(t, 0, result.MetadataDirsDeleted)
+}

internal/vaultik/remove_snapshot_test.go

@@ -26,11 +26,14 @@ import (
 type testStorer struct {
 	mu   sync.Mutex
 	data map[string][]byte
+	// putTimes holds when Put stored each object; ListStream reports it.
+	putTimes map[string]time.Time
 }
 
 func newTestStorer() *testStorer {
 	return &testStorer{
-		data: make(map[string][]byte),
+		data:     make(map[string][]byte),
+		putTimes: make(map[string]time.Time),
 	}
 }
 
@@ -44,6 +47,7 @@ func (s *testStorer) Put(_ context.Context, key string, reader io.Reader) error
 	}
 
 	s.data[key] = data
+	s.putTimes[key] = time.Now().UTC()
 
 	return nil
 }
@@ -87,6 +91,7 @@ func (s *testStorer) Delete(_ context.Context, key string) error {
 	defer s.mu.Unlock()
 
 	delete(s.data, key)
+	delete(s.putTimes, key)
 
 	return nil
 }
@@ -120,8 +125,9 @@ func (s *testStorer) ListStream(
 		for key, data := range s.data {
 			if prefix == "" || strings.HasPrefix(key, prefix) {
 				ch <- storage.ObjectInfo{
-					Key:  key,
-					Size: int64(len(data)),
+					Key:     key,
+					Size:    int64(len(data)),
+					ModTime: s.putTimes[key],
 				}
 			}
 		}

internal/vaultik/snapshot.go

@@ -1301,7 +1301,7 @@ const pruneCommandHint = "vaultik prune"
 // snapshotRemoveCommandHint is the command suggested, with the
 // snapshot's ID, when a remove could not reach the destination store:
 // running it again removes the snapshot's metadata there, which
-// `vaultik prune` never does.
+// `vaultik prune` never does while the manifest is there.
 const snapshotRemoveCommandHint = "vaultik snapshot remove"
 
 // RemoveSnapshot removes a snapshot from the local index database and,
@@ -1504,7 +1504,8 @@ func (v *Vaultik) confirmRemoveSnapshot(snapshotID string, opts *RemoveOptions)
 // the local index, its removal there has already happened, so a failure
 // is only a warning telling the user to run `vaultik snapshot remove`
 // for the snapshot again once the destination store is reachable
-// (`vaultik prune` never removes snapshot metadata).
+// (`vaultik prune` never removes snapshot metadata that has its
+// manifest).
 func (v *Vaultik) removeSnapshotRemote(
 	snapshotID string, inLocalIndex bool, markerErr error,
 	opts *RemoveOptions,