Keep unreferenced blobs newer than prune_grace_period (closes #387)

A backup uploads its blobs before the manifest that lists them, and the
process lock is per user per machine, so a prune from another host or
user sharing the destination deleted a running backup's blobs; that
backup still reported success and could not be restored.

Prune now deletes an unreferenced blob only once it is older than the new
config key prune_grace_period (default 24h), and reports how many it kept
(blobs_too_new under --json). The storage listing now carries each
object's modification time. remote nuke is unchanged. The README says what
the lock covers and that a shared destination relies on the grace period
or needs one prefix per host.

Model: opus-5-5

README.md

@@ -96,6 +96,12 @@ 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, so it must be longer than the longest backup
+run; otherwise 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 +198,17 @@ 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 before the manifest that lists them, so a
+prune from elsewhere at that moment finds blobs no snapshot lists. It
+deletes such a blob only once it is older than `prune_grace_period`
+(default `24h`), which therefore must be longer than the longest backup run
+of any host or user sharing the destination. `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
@@ -296,7 +312,8 @@ value where a list belongs or a word where a number belongs), is refused.
 * `--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
+  remove orphaned blobs older than `prune_grace_period` from remote storage,
+  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
@@ -423,9 +440,12 @@ 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
+set and delete any blob not in that set that is older than
-manifests — network cost scales with the number of snapshots. `snapshot
+`prune_grace_period` (default `24h`). A newer one is kept and counted: it
-create --prune` runs the same cleanup automatically; this is the
+may belong to a backup still running, on this host or another sharing the
+destination store, that has not yet uploaded its manifest. 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),
@@ -436,6 +456,8 @@ exits non-zero.
 * `--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` is counted in
+  `blobs_too_new` and not in `blobs_found`.
 
 **`info`**: Display system configuration, storage settings, encryption
 recipients, and local database statistics.
@@ -510,6 +532,12 @@ 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, so it must be longer than the longest backup
+run; otherwise 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 +624,8 @@ 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`
 
 ### chunking and deduplication
 
@@ -641,6 +670,7 @@ 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. A backup uploads its blobs 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)). A duration such as `36h` or `90m`; `0s` deletes such blobs at once |
 | `hostname` | system hostname | Hostname used in snapshot IDs |
 | `index_path` | platform data dir | Local SQLite index path |
 

config.example.yml

@@ -328,6 +328,15 @@ 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
+# A backup uploads its blobs before the manifest that lists them, so on a
+# destination shared between hosts or users this must be longer than the
+# longest backup run
+# 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 +228,8 @@ 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
 
 ### 6. Incomplete Snapshot Cleanup
 

docs/REPOSTRUCTURE.md

@@ -166,7 +166,7 @@ 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
 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`). A backup uploads its blobs 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. `remote nuke` has no such check
 
 ## Restoration Requirements
 

internal/cli/config.go

@@ -239,6 +239,13 @@ storage_url: ""
 # Default: 3
 # compression_level: 3
 
+# How old a blob that no snapshot lists must be before prune deletes it.
+# A backup uploads its blobs before the manifest that lists them, so on a
+# destination shared between hosts or users this must be longer than the
+# longest backup run. 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/prune.go

@@ -20,7 +20,10 @@ 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.
 
 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

@@ -132,8 +132,8 @@ on Linux), then /etc/vaultik/config.yml.`,
 		"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 "+
+			"orphaned blobs older than prune_grace_period (not after a "+
-			"files)")
+			"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
@@ -187,6 +189,13 @@ 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. A backup lists its blobs in a manifest only
+	// once it has uploaded them all, so a younger one 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 +297,7 @@ func Parse(data []byte) (*Config, error) {
 		ChunkSize:        defaultChunkSize,
 		IndexPath:        filepath.Join(xdg.DataHome, appName, "index.sqlite"),
 		CompressionLevel: defaultCompressionLevel,
+		PruneGracePeriod: defaultPruneGracePeriod,
 		S3:               S3Config{PartSize: defaultS3PartSize},
 	}
 

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"
@@ -302,6 +303,9 @@ func IsNotFound(err error) bool {
 type ObjectInfo struct {
 	Key  string
 	Size int64
+	// ModTime is the object's LastModified time. Only ListObjectsStream
+	// sets it.
+	ModTime time.Time
 	Err     error
 }
 
@@ -345,6 +349,7 @@ func (c *Client) ListObjectsStream(
 					ch <- ObjectInfo{
 						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
+// prefix filtering, the modification time ListStream reports, overwrite,
-// Get and Stat. Each section takes its own fresh backend instance, so the
+// delete, delete-of-missing, and not-found on Get and Stat. Each section
-// order of sections never matters and no section sees another's objects.
+// 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

@@ -237,6 +237,7 @@ func (f *FileStorer) ListStream(ctx context.Context, prefix string) <-chan Objec
 				ch <- ObjectInfo{
 					Key:     relPath,
 					Size:    info.Size(),
+					ModTime: info.ModTime(),
 				}
 			}
 

internal/storage/rclone.go

@@ -213,6 +213,7 @@ func (r *RcloneStorer) ListStream(
 				ch <- ObjectInfo{
 					Key:     key,
 					Size:    obj.Size(),
+					ModTime: obj.ModTime(ctx),
 				}
 			}
 		})

internal/storage/s3.go

@@ -91,6 +91,7 @@ func (s *S3Storer) ListStream(ctx context.Context, prefix string) <-chan ObjectI
 			ch <- ObjectInfo{
 				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.
@@ -27,6 +28,9 @@ type ProgressCallback func(bytesTransferred int64) error
 type ObjectInfo struct {
 	Key  string // Object key/path
 	Size int64  // Size in bytes
+	// 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)
 }
 
@@ -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

@@ -5,8 +5,10 @@ import (
 	"errors"
 	"fmt"
 	"strings"
+	"time"
 
 	"sneak.berlin/go/vaultik/internal/log"
+	"sneak.berlin/go/vaultik/internal/storage"
 )
 
 // PruneOptions contains options for the prune command
@@ -163,6 +165,9 @@ 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. BlobsFound does not include them.
+	BlobsTooNew int `json:"blobs_too_new"`
 }
 
 // Prune removes orphaned data from the local index database AND
@@ -208,9 +213,19 @@ 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)}
+	result := &PruneBlobsResult{
+		BlobsFound:  len(unreferencedBlobs),
+		BlobsTooNew: tooNew,
+	}
+
+	if tooNew > 0 && !opts.JSON {
+		v.UI.Infof("Kept %d unreferenced blob(s) newer than "+
+			"prune_grace_period (%s): a backup still running may need them.",
+			tooNew, v.Config.PruneGracePeriod)
+	}
 
 	if len(unreferencedBlobs) == 0 {
 		log.Info("No unreferenced blobs found")
@@ -344,11 +359,12 @@ func (v *Vaultik) listUniqueSnapshotIDs() ([]string, error) {
 	return snapshotIDs, nil
 }
 
-// listAllRemoteBlobs returns a map of all blob hashes to their sizes in remote storage
+// listAllRemoteBlobs returns a map of all blob hashes in remote storage
-func (v *Vaultik) listAllRemoteBlobs() (map[string]int64, error) {
+// 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 +388,7 @@ 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 +396,44 @@ func (v *Vaultik) listAllRemoteBlobs() (map[string]int64, error) {
 	return allBlobs, nil
 }
 
-// findUnreferencedBlobs returns blob hashes not referenced by any
+// findUnreferencedBlobs returns the hashes of the blobs no manifest
-// manifest and their total size.
+// 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.
 func (v *Vaultik) findUnreferencedBlobs(
-	allBlobs map[string]int64, referenced map[string]bool,
+	allBlobs map[string]storage.ObjectInfo, referenced map[string]bool,
-) ([]string, int64) {
+) ([]string, int64, int) {
 	var (
 		unreferenced []string
 		totalSize    int64
+		tooNew       int
 	)
 
-	for hash, size := range allBlobs {
+	cutoff := time.Now().UTC().Add(-v.Config.PruneGracePeriod)
-		if !referenced[hash] {
+
-			unreferenced = append(unreferenced, hash)
+	for hash, blob := range allBlobs {
-			totalSize += size
+		if referenced[hash] {
-		}
+			continue
 		}
 
-	return unreferenced, totalSize
+		if blob.ModTime.After(cutoff) {
+			tooNew++
+
+			continue
+		}
+
+		unreferenced = append(unreferenced, hash)
+		totalSize += blob.Size
+	}
+
+	return unreferenced, totalSize, tooNew
 }
 
 // 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 +448,7 @@ 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 +1,138 @@
+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)
+}
+
+// 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)
+}