Count a file as deleted only if the previous snapshot of its name had it (closes #304)

A backup counted as deleted every file in the local index under the
source path that the walk did not find. That took in files the
snapshot excludes but another snapshot backs up, and files removed long
ago, which every later backup, and the first backup of another name
over the same path, reported as deleted again.

The backup now counts only the files that the most recent completed
snapshot of the same name lists, the walk did not find, and are gone
from disk. A file that is excluded, or inside an excluded directory, is
not counted, nor is one the walk could not reach under --skip-errors.

The snapshots row stores no deleted figure; only the backup's output
changes.

Model: opus-5-5

ARCHITECTURE.md

@@ -279,8 +279,8 @@ Key methods:
 - `Scan(ctx, path, snapshotID)` → Main scan operation
 
 Scan phases:
-1. **Phase 0**: Detect deleted files from previous snapshots
-2. **Phase 1**: Walk directory, identify files needing processing
+1. **Phase 1**: Walk directory, identify files needing processing
+2. **Phase 1b**: Count as deleted the files that the previous snapshot of the same name lists, the walk did not find, and are gone from disk; a file that is excluded, or inside an excluded directory, is not counted
 3. **Phase 2**: Process files (chunk → pack → upload)
 
 #### SnapshotManager
@@ -320,13 +320,13 @@ CreateSnapshot(opts)
     │       │
     │       ├─► scanner.Scan(ctx, path, snapshotID)
     │       │       │
-    │       │       ├─► Phase 0: detectDeletedFiles()
-    │       │       │
     │       │       ├─► Phase 1: scanPhase()
     │       │       │       Walk directory
     │       │       │       Check file metadata changes
     │       │       │       Build list of files to process
     │       │       │
+    │       │       ├─► Phase 1b: detectDeletedFiles()
+    │       │       │
     │       │       └─► Phase 2: processPhase()
     │       │               For each file:
     │       │                   chunker.ChunkReaderStreaming()

README.md

@@ -271,17 +271,8 @@ existing file. Created with mode `0600` since it will contain credentials.
 **`config set`**: Set a scalar config value by dotted YAML path
 (e.g. `vaultik config set compression_level 9`,
 `vaultik config set storage_url "file:///mnt/backups"`). Comments and
-formatting in the file are preserved. Missing keys along the path are
-created: as a list when the next path element is a number (so
-`vaultik config set age_recipients.0 age1...` works on a file without
-`age_recipients`), otherwise as a map. If the config loads, a change
-after which it would not, such as `vaultik config set compression_level 99`,
-is refused and the file is left unchanged. A config that does not load,
-such as the one `config init` writes before `storage_url` is set or one
-with a `${ENV:...}` reference to a variable not set in this shell, is
-checked one setting at a time: only a change after which the changed
-setting cannot be read, such as one giving it the wrong type (a single
-value where a list belongs or a word where a number belongs), is refused.
+formatting in the file are preserved; intermediate maps are created as
+needed.
 
 **`snapshot create`**: Perform incremental backup of configured snapshots.
 * Optional snapshot names argument to create specific snapshots (default: all)
@@ -422,12 +413,11 @@ under `blobs/` whose name is not a blob hash is not counted as a blob,
 since `prune` never deletes it.
 * `--json`: Output as JSON
 
-**`remote nuke`**: Delete every object under `metadata/` and `blobs/` on
-the backup destination store, whatever its name, leaving the bucket prefix
-empty. Destructive and irreversible. This is the single supported way to
-wipe the entire destination store. If a listing afterwards still finds
-anything there, the command names each object left and exits non-zero;
-running it again deletes what is left.
+**`remote nuke`**: Delete every snapshot's metadata and every blob from the
+backup destination store, leaving the bucket prefix empty. Destructive and
+irreversible. This is the single supported way to wipe the entire
+destination store. If anything cannot be deleted, the command exits
+non-zero; running it again deletes what is left.
 * `--force`: Required to confirm destruction.
 
 **`database delete`**: Delete the local SQLite state database file

internal/cli/config.go

@@ -8,7 +8,6 @@ import (
 	"os/exec"
 	"path/filepath"
 	"reflect"
-	"slices"
 	"strconv"
 	"strings"
 	"unicode/utf8"
@@ -45,9 +44,6 @@ var (
 	errNeedNumericIndex = errors.New("key is a list; use a numeric index")
 	errIndexOutOfRange  = errors.New("index out of range")
 	errNotMapOrList     = errors.New("key is not a map or list")
-	errWouldNotLoad     = errors.New(
-		"vaultik would not load the config after this change, " +
-			"so the file was not changed")
 )
 
 const defaultConfigTemplate = `# vaultik configuration
@@ -395,17 +391,8 @@ func newConfigSetCommand() *cobra.Command {
 		Use:   "set <key> <value>",
 		Short: "Set a config value by dotted path (e.g. compression_level 5)",
 		Long: `Sets a scalar config value addressed by dotted YAML path and writes
-the file back, preserving comments and formatting. Missing keys along
-the path are created: as a list when the next path element is a
-number, otherwise as a map.
-
-If the config loads, a change after which it would not, such as
-compression_level 99, is refused and the file is left unchanged. A
-config that does not load, such as the one config init writes before
-storage_url is set or one with a ${ENV:...} reference to a variable
-not set here, is checked one setting at a time: only a change after
-which the changed setting cannot be read, such as one giving it the
-wrong type, is refused.
+the file back, preserving comments and formatting. Intermediate maps
+are created as needed.
 
 Examples:
   vaultik config set storage_url "file:///mnt/backups"
@@ -435,14 +422,7 @@ func writeConfigSet(out *ui.Writer, path, key, value string) error {
 		return err
 	}
 
-	oldData, err := marshalConfigYAML(root)
-	if err != nil {
-		return fmt.Errorf("marshaling config: %w", err)
-	}
-
-	keys := strings.Split(key, ".")
-
-	err = yamlPathSet(root, keys, value)
+	err = yamlPathSet(root, strings.Split(key, "."), value)
 	if err != nil {
 		return err
 	}
@@ -452,21 +432,6 @@ func writeConfigSet(out *ui.Writer, path, key, value string) error {
 		return fmt.Errorf("marshaling config: %w", err)
 	}
 
-	setting, err := yamlPathOnly(root, keys)
-	if err != nil {
-		return err
-	}
-
-	settingData, err := marshalConfigYAML(setting)
-	if err != nil {
-		return fmt.Errorf("marshaling config: %w", err)
-	}
-
-	err = checkConfigChange(oldData, data, settingData)
-	if err != nil {
-		return fmt.Errorf("%w: %w", errWouldNotLoad, err)
-	}
-
 	err = os.WriteFile(path, data, configFileMode)
 	if err != nil {
 		return fmt.Errorf("writing config file: %w", err)
@@ -488,58 +453,6 @@ func writeConfigSet(out *ui.Writer, path, key, value string) error {
 	return nil
 }
 
-// checkConfigChange returns the reason vaultik would not load newData, the
-// config after a change, if the change brings that failure in. If oldData,
-// the config before it, loads, the new one must load too. A config that
-// does not load, such as one still being filled in or one with a ${...}
-// reference that cannot be filled in here, is checked one setting at a
-// time: settingData, the changed setting on its own, must decode into the
-// config type.
-func checkConfigChange(oldData, newData, settingData []byte) error {
-	oldCfg, err := config.Parse(oldData)
-	if err == nil && oldCfg.Validate() == nil {
-		newCfg, err := config.Parse(newData)
-		if err != nil {
-			return err
-		}
-
-		return newCfg.Validate()
-	}
-
-	_, err = config.Parse(settingData)
-
-	return err
-}
-
-// yamlPathOnly returns a document holding only the value at the dotted key
-// path in root, inside the maps and lists that lead to it there.
-func yamlPathOnly(root *yaml.Node, keys []string) (*yaml.Node, error) {
-	node, err := yamlPathGet(root, keys)
-	if err != nil {
-		return nil, err
-	}
-
-	for i, key := range slices.Backward(keys) {
-		parent, err := yamlPathGet(root, keys[:i])
-		if err != nil {
-			return nil, err
-		}
-
-		if parent.Kind == yaml.SequenceNode {
-			node = &yaml.Node{
-				Kind: yaml.SequenceNode, Content: []*yaml.Node{node},
-			}
-		} else {
-			keyNode := &yaml.Node{Kind: yaml.ScalarNode, Value: key}
-			node = &yaml.Node{
-				Kind: yaml.MappingNode, Content: []*yaml.Node{keyNode, node},
-			}
-		}
-	}
-
-	return &yaml.Node{Kind: yaml.DocumentNode, Content: []*yaml.Node{node}}, nil
-}
-
 // marshalConfigYAML renders a config document tree with 2-space indentation,
 // matching defaultConfigTemplate. yaml.Marshal defaults to 4 spaces, which
 // would reindent the whole file on the first `config set` despite the promise
@@ -646,8 +559,8 @@ func yamlPathGet(root *yaml.Node, keys []string) (*yaml.Node, error) {
 	return node, nil
 }
 
-// yamlPathSet navigates a dotted key path, creating missing keys as needed,
-// and sets the final key to the given scalar value. Numeric path
+// yamlPathSet navigates a dotted key path, creating intermediate maps as
+// needed, and sets the final key to the given scalar value. Numeric path
 // components index into sequences; an index equal to the sequence length
 // appends a new element (e.g. "age_recipients.1" on a 1-element list).
 func yamlPathSet(root *yaml.Node, keys []string, value string) error {
@@ -660,12 +573,12 @@ func yamlPathSet(root *yaml.Node, keys []string, value string) error {
 		node = node.Content[0]
 	}
 
-	for i := range keys {
+	for i, key := range keys {
 		last := i == len(keys)-1
 
 		switch node.Kind {
 		case yaml.MappingNode:
-			node = yamlSetInMapping(node, keys, i, value, last)
+			node = yamlSetInMapping(node, key, value, last)
 		case yaml.SequenceNode:
 			next, err := yamlSetInSequence(node, keys, i, value, last)
 			if err != nil {
@@ -734,16 +647,14 @@ func yamlField(typ reflect.Type, key string) (reflect.StructField, bool) {
 	return reflect.StructField{}, false
 }
 
-// yamlSetInMapping resolves (creating if needed) the value node for the
-// path element keys[i] within a mapping node, setting it to value when it
-// is the final path element, and returns the node to descend into.
-func yamlSetInMapping(
-	node *yaml.Node, keys []string, i int, value string, last bool,
-) *yaml.Node {
+// yamlSetInMapping resolves (creating if needed) the value node for key
+// within a mapping node, setting it to value when it is the final path
+// element, and returns the node to descend into.
+func yamlSetInMapping(node *yaml.Node, key, value string, last bool) *yaml.Node {
 	var valueNode *yaml.Node
 
 	for j := 0; j+1 < len(node.Content); j += 2 {
-		if node.Content[j].Value == keys[i] {
+		if node.Content[j].Value == key {
 			valueNode = node.Content[j+1]
 
 			break
@@ -751,8 +662,13 @@ func yamlSetInMapping(
 	}
 
 	if valueNode == nil {
-		keyNode := &yaml.Node{Kind: yaml.ScalarNode, Value: keys[i]}
-		valueNode = newPathNode(keys, i, value)
+		keyNode := &yaml.Node{Kind: yaml.ScalarNode, Value: key}
+
+		valueNode = &yaml.Node{Kind: yaml.MappingNode}
+		if last {
+			valueNode = &yaml.Node{Kind: yaml.ScalarNode, Value: value}
+		}
+
 		node.Content = append(node.Content, keyNode, valueNode)
 	} else if last {
 		setScalar(valueNode, value)
@@ -780,7 +696,12 @@ func yamlSetInSequence(
 	}
 
 	if idx == len(node.Content) {
-		node.Content = append(node.Content, newPathNode(keys, i, value))
+		newNode := &yaml.Node{Kind: yaml.MappingNode}
+		if last {
+			newNode = &yaml.Node{Kind: yaml.ScalarNode, Value: value}
+		}
+
+		node.Content = append(node.Content, newNode)
 	} else if last {
 		setScalar(node.Content[idx], value)
 	}
@@ -788,22 +709,6 @@ func yamlSetInSequence(
 	return node.Content[idx], nil
 }
 
-// newPathNode returns the node to create for the missing path element
-// keys[i]: the value when it is the final path element, otherwise an empty
-// list when the next path element is a number and an empty map when not.
-func newPathNode(keys []string, i int, value string) *yaml.Node {
-	if i == len(keys)-1 {
-		return &yaml.Node{Kind: yaml.ScalarNode, Value: value}
-	}
-
-	_, err := strconv.Atoi(keys[i+1])
-	if err == nil {
-		return &yaml.Node{Kind: yaml.SequenceNode}
-	}
-
-	return &yaml.Node{Kind: yaml.MappingNode}
-}
-
 // setScalar overwrites a node in place with a plain scalar value.
 func setScalar(n *yaml.Node, value string) {
 	n.Kind = yaml.ScalarNode

internal/cli/config_test.go

@@ -58,17 +58,14 @@ func TestDefaultConfigTemplateParses(t *testing.T) {
 	}
 }
 
-// testRecipient is a valid age public key.
-const testRecipient = "age1278m9q7dp3chsh2dcy82qk27v047zywyvtxwnj4cvt0z65jw6a7q5dqhfj"
-
 // TestConfigSetRecipientOnFreshConfig follows the README quickstart: on the
 // file `config init` writes, `config set age_recipients.0` and
 // `config set storage_url` give a config that loads with that recipient.
-// Neither is refused, although the config does not load until both are set;
-// once it loads, a recipient that is not a valid key is.
 func TestConfigSetRecipientOnFreshConfig(t *testing.T) {
 	t.Parallel()
 
+	const recipient = "age1278m9q7dp3chsh2dcy82qk27v047zywyvtxwnj4cvt0z65jw6a7q5dqhfj"
+
 	path := filepath.Join(t.TempDir(), "config.yml")
 
 	err := os.WriteFile(path, []byte(defaultConfigTemplate), configFileMode)
@@ -78,7 +75,7 @@ func TestConfigSetRecipientOnFreshConfig(t *testing.T) {
 
 	out := ui.NewWithColor(&bytes.Buffer{}, false)
 
-	err = writeConfigSet(out, path, "age_recipients.0", testRecipient)
+	err = writeConfigSet(out, path, "age_recipients.0", recipient)
 	if err != nil {
 		t.Fatalf("config set age_recipients.0: %v", err)
 	}
@@ -93,211 +90,8 @@ func TestConfigSetRecipientOnFreshConfig(t *testing.T) {
 		t.Fatalf("config.Load: %v", err)
 	}
 
-	if len(cfg.AgeRecipients) != 1 || cfg.AgeRecipients[0] != testRecipient {
-		t.Errorf("age_recipients = %v, want [%s]", cfg.AgeRecipients, testRecipient)
-	}
-
-	err = writeConfigSet(out, path, "age_recipients.0", "notakey")
-	if err == nil || !strings.Contains(err.Error(), "not a valid recipient") {
-		t.Errorf("config set age_recipients.0 notakey gives error %v, "+
-			"want one saying it is not a valid recipient", err)
-	}
-
-	_, err = config.Load(path)
-	if err != nil {
-		t.Errorf("config.Load after the refused change: %v", err)
-	}
-}
-
-// configWithoutRecipients loads, but has no age_recipients key and no
-// snapshot named work.
-const configWithoutRecipients = `storage_url: file:///mnt/backups
-snapshots:
-  home:
-    paths:
-      - "~"
-`
-
-// configWithUnsetReference loads only where VAULTIK_TEST_UNSET_SECRET is
-// set, as a backup job's environment might set it. No test sets it.
-const configWithUnsetReference = configWithoutRecipients + `s3:
-  secret_access_key: ${ENV:VAULTIK_TEST_UNSET_SECRET}
-`
-
-// configWithLevelReference returns configWithoutRecipients with a ${FILE:...}
-// reference on compression_level to a file holding 9, so that the config
-// loads once the reference is filled in.
-func configWithLevelReference(t *testing.T) string {
-	t.Helper()
-
-	levelPath := filepath.Join(t.TempDir(), "level")
-
-	err := os.WriteFile(levelPath, []byte("9"), configFileMode)
-	if err != nil {
-		t.Fatalf("write level: %v", err)
-	}
-
-	return configWithoutRecipients +
-		"compression_level: ${FILE:" + levelPath + "}\n"
-}
-
-// TestConfigSetIndexUnderMissingKey checks that a list index under a key
-// the file does not have creates a list, and that the result loads.
-func TestConfigSetIndexUnderMissingKey(t *testing.T) {
-	t.Parallel()
-
-	tests := []struct {
-		key   string
-		value string
-		field func(cfg *config.Config) []string
-	}{
-		{"age_recipients.0", testRecipient,
-			func(cfg *config.Config) []string { return cfg.AgeRecipients }},
-		{"snapshots.work.paths.0", "/srv/work",
-			func(cfg *config.Config) []string { return cfg.Snapshots["work"].Paths }},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.key, func(t *testing.T) {
-			t.Parallel()
-
-			path := filepath.Join(t.TempDir(), "config.yml")
-
-			err := os.WriteFile(path, []byte(configWithoutRecipients), configFileMode)
-			if err != nil {
-				t.Fatalf("write config: %v", err)
-			}
-
-			err = writeConfigSet(ui.NewWithColor(&bytes.Buffer{}, false),
-				path, tt.key, tt.value)
-			if err != nil {
-				t.Fatalf("config set %s: %v", tt.key, err)
-			}
-
-			cfg, err := config.Load(path)
-			if err != nil {
-				t.Fatalf("config.Load: %v", err)
-			}
-
-			got := tt.field(cfg)
-			if len(got) != 1 || got[0] != tt.value {
-				t.Errorf("%s gives %v, want [%s]", tt.key, got, tt.value)
-			}
-		})
-	}
-}
-
-// TestConfigSetKeepsFileThatWouldNotLoad checks that config set refuses a
-// change after which the config would not load, with an error giving the
-// reason, and leaves the file as it was. On the file `config init` writes,
-// which does not load until storage_url is set, and on one that cannot be
-// read here, only a value of the wrong type is refused.
-func TestConfigSetKeepsFileThatWouldNotLoad(t *testing.T) {
-	t.Parallel()
-
-	levelReference := configWithLevelReference(t)
-
-	tests := []struct {
-		config string
-		key    string
-		value  string
-		reason string
-	}{
-		// Index 1 of the empty list the missing key gives.
-		{configWithoutRecipients, "age_recipients.1", testRecipient,
-			"index out of range"},
-		// A list set to a single value.
-		{configWithoutRecipients, "snapshots.home.paths", "/srv",
-			"into []string"},
-		{configWithoutRecipients, "chunk_size", "fast",
-			"invalid size format"},
-		// Values of the right type that fail validation.
-		{configWithoutRecipients, "compression_level", "99",
-			"compression_level must be between 1 and 19"},
-		{configWithoutRecipients, "chunk_size", "1KB",
-			"chunk_size must be at least 1MB"},
-		// With its reference filled in, the config loads.
-		{levelReference, "blob_size_limit", "1MB",
-			"blob_size_limit must be at least"},
-		// The type check on a config that does not load yet.
-		{defaultConfigTemplate, "snapshots.apps.paths", "/srv",
-			"into []string"},
-		// The type check on a config that cannot be read here.
-		{configWithUnsetReference, "snapshots.home.paths", "/x",
-			"cannot unmarshal !!str `/x`"},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.key+" "+tt.value, func(t *testing.T) {
-			t.Parallel()
-
-			path := filepath.Join(t.TempDir(), "config.yml")
-
-			err := os.WriteFile(path, []byte(tt.config), configFileMode)
-			if err != nil {
-				t.Fatalf("write config: %v", err)
-			}
-
-			err = writeConfigSet(ui.NewWithColor(&bytes.Buffer{}, false),
-				path, tt.key, tt.value)
-			if err == nil || !strings.Contains(err.Error(), tt.reason) {
-				t.Errorf("config set %s %s gives error %v, want one saying %q",
-					tt.key, tt.value, err, tt.reason)
-			}
-
-			data, err := os.ReadFile(path) //nolint:gosec // G304: test-controlled path
-			if err != nil {
-				t.Fatalf("read config: %v", err)
-			}
-
-			if string(data) != tt.config {
-				t.Errorf("config set %s changed the file to:\n%s",
-					tt.key, data)
-			}
-		})
-	}
-}
-
-// TestConfigSetRefusesOnlyItsOwnFailure checks that setting another key
-// works on a config with a ${...} reference on compression_level, which
-// loads because loading fills the reference in, on one whose
-// compression_level already fails to load, and on one with a reference
-// that cannot be filled in here.
-func TestConfigSetRefusesOnlyItsOwnFailure(t *testing.T) {
-	t.Parallel()
-
-	configs := map[string]string{
-		"reference":       configWithLevelReference(t),
-		"failing":         configWithoutRecipients + "compression_level: fast\n",
-		"unset reference": configWithUnsetReference,
-	}
-
-	for name, configYAML := range configs {
-		t.Run(name, func(t *testing.T) {
-			t.Parallel()
-
-			path := filepath.Join(t.TempDir(), "config.yml")
-
-			err := os.WriteFile(path, []byte(configYAML), configFileMode)
-			if err != nil {
-				t.Fatalf("write config: %v", err)
-			}
-
-			err = writeConfigSet(ui.NewWithColor(&bytes.Buffer{}, false),
-				path, "hostname", "myhost")
-			if err != nil {
-				t.Fatalf("config set hostname: %v", err)
-			}
-
-			data, err := os.ReadFile(path) //nolint:gosec // G304: test-controlled path
-			if err != nil {
-				t.Fatalf("read config: %v", err)
-			}
-
-			if !strings.Contains(string(data), "hostname: myhost") {
-				t.Errorf("config set hostname wrote:\n%s", data)
-			}
-		})
+	if len(cfg.AgeRecipients) != 1 || cfg.AgeRecipients[0] != recipient {
+		t.Errorf("age_recipients = %v, want [%s]", cfg.AgeRecipients, recipient)
 	}
 }
 

internal/config/config.go

@@ -4,7 +4,6 @@
 package config
 
 import (
-	"bytes"
 	"errors"
 	"fmt"
 	"os"
@@ -234,48 +233,14 @@ func New(path Path) (*Config, error) {
 	return cfg, nil
 }
 
-// Load reads the configuration file at path, parses it with Parse, warns
-// when others can read the file, and validates the configuration.
-// Returns an error if the file cannot be read, parsed, or if validation
-// fails.
+// Load reads and parses the configuration file from the specified path.
+// It applies default values for optional fields, performs environment variable
+// substitution using smartconfig, and validates the configuration.
+// The configuration file should be in YAML format. Returns an error if the file
+// cannot be read, parsed, or if validation fails.
 func Load(path string) (*Config, error) {
-	data, err := os.ReadFile(path) //nolint:gosec // G304: config path is operator-supplied
-	if err != nil {
-		return nil, fmt.Errorf("failed to load config file: %w", err)
-	}
-
-	cfg, err := Parse(data)
-	if err != nil {
-		return nil, err
-	}
-
-	// Check config file permissions (warn if world or group readable)
-	//nolint:gosec // G703: config path is operator-supplied by design
-	info, statErr := os.Stat(path)
-	if statErr == nil {
-		mode := info.Mode().Perm()
-		if mode&0044 != 0 { // group or world readable
-			log.Warn(cfg.readableByOthersWarning(),
-				"path", path,
-				"mode", fmt.Sprintf("%04o", mode),
-				"recommendation", "chmod 600 "+path)
-		}
-	}
-
-	err = cfg.Validate()
-	if err != nil {
-		return nil, fmt.Errorf("invalid config: %w", err)
-	}
-
-	return cfg, nil
-}
-
-// Parse reads YAML config data as Load does, without validating it. It
-// applies default values for optional fields, fills in ${...} references
-// using smartconfig, and expands ~ in paths.
-func Parse(data []byte) (*Config, error) {
 	// Load config using smartconfig for interpolation
-	sc, err := smartconfig.NewFromReader(bytes.NewReader(data))
+	sc, err := smartconfig.NewFromConfigPath(path)
 	if err != nil {
 		return nil, fmt.Errorf("failed to load config file: %w", err)
 	}
@@ -337,6 +302,24 @@ func Parse(data []byte) (*Config, error) {
 		cfg.S3.Region = "us-east-1"
 	}
 
+	// Check config file permissions (warn if world or group readable)
+	//nolint:gosec // G703: config path is operator-supplied by design
+	info, statErr := os.Stat(path)
+	if statErr == nil {
+		mode := info.Mode().Perm()
+		if mode&0044 != 0 { // group or world readable
+			log.Warn(cfg.readableByOthersWarning(),
+				"path", path,
+				"mode", fmt.Sprintf("%04o", mode),
+				"recommendation", "chmod 600 "+path)
+		}
+	}
+
+	err = cfg.Validate()
+	if err != nil {
+		return nil, fmt.Errorf("invalid config: %w", err)
+	}
+
 	return cfg, nil
 }
 

internal/database/files.go

@@ -267,6 +267,45 @@ func (r *FileRepository) ListUnderPath(
 	return files, rows.Err()
 }
 
+// ListUnderPathInSnapshot returns the files that ListUnderPath returns
+// for path and that the snapshot lists, in no particular order.
+func (r *FileRepository) ListUnderPathInSnapshot(
+	ctx context.Context, path, snapshotID string,
+) ([]*File, error) {
+	path = strings.TrimRight(path, "/")
+	dirPrefix := path + "/"
+
+	query := `
+		SELECT f.id, f.path, f.source_path, f.mtime, f.mtime_nsec, f.size,
+			f.mode, f.uid, f.gid, f.link_target
+		FROM files f
+		JOIN snapshot_files sf ON sf.file_id = f.id
+		WHERE sf.snapshot_id = ?
+		  AND (f.path = ? OR substr(f.path, 1, length(?)) = ?)
+	`
+
+	rows, err := r.db.conn.QueryContext(ctx, query,
+		snapshotID, path, dirPrefix, dirPrefix)
+	if err != nil {
+		return nil, fmt.Errorf("querying files: %w", err)
+	}
+
+	defer func() { _ = rows.Close() }()
+
+	var files []*File
+
+	for rows.Next() {
+		file, err := r.scanFileRows(rows)
+		if err != nil {
+			return nil, fmt.Errorf("scanning file: %w", err)
+		}
+
+		files = append(files, file)
+	}
+
+	return files, rows.Err()
+}
+
 // ListIDsWithChunksNotInUploadedBlobs returns the IDs of the files whose
 // path starts with prefix and that list at least one chunk held by no
 // blob whose upload has completed (uploaded_ts set). A new snapshot

internal/database/files_test.go

@@ -212,6 +212,65 @@ func TestFileRepositoryListUnderPath(t *testing.T) {
 	}
 }
 
+// ListUnderPathInSnapshot leaves out files outside path and files the
+// snapshot does not list, though another snapshot lists them.
+func TestFileRepositoryListUnderPathInSnapshot(t *testing.T) {
+	t.Parallel()
+
+	db, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+	files := database.NewFileRepository(db)
+	snapshots := database.NewSnapshotRepository(db)
+
+	listed := map[string][]string{
+		"one": {"/src/a.txt", "/src2/c.txt"},
+		"two": {"/src/b.txt"},
+	}
+
+	for snapshotID, paths := range listed {
+		err := snapshots.Create(ctx, nil, &database.Snapshot{
+			ID:        types.SnapshotID(snapshotID),
+			Hostname:  "host",
+			StartedAt: time.Now(),
+		})
+		if err != nil {
+			t.Fatalf("failed to create snapshot %s: %v", snapshotID, err)
+		}
+
+		for _, path := range paths {
+			err := files.Create(ctx, nil, &database.File{
+				Path:  types.FilePath(path),
+				MTime: time.Now().Truncate(time.Second),
+				Mode:  0644,
+			})
+			if err != nil {
+				t.Fatalf("failed to create %s: %v", path, err)
+			}
+
+			err = snapshots.AddFile(ctx, nil, snapshotID, path)
+			if err != nil {
+				t.Fatalf("failed to add %s to %s: %v", path, snapshotID, err)
+			}
+		}
+	}
+
+	found, err := files.ListUnderPathInSnapshot(ctx, "/src", "one")
+	if err != nil {
+		t.Fatalf("failed to list files: %v", err)
+	}
+
+	got := make([]string, 0, len(found))
+	for _, f := range found {
+		got = append(got, f.Path.String())
+	}
+
+	if !slices.Equal(got, []string{"/src/a.txt"}) {
+		t.Errorf("got %q, want only /src/a.txt", got)
+	}
+}
+
 func TestFileRepositorySymlink(t *testing.T) {
 	t.Parallel()
 

internal/snapshot/module.go

@@ -16,6 +16,9 @@ type ScannerParams struct {
 	Fs             afero.Fs
 	Exclude        []string // Exclude patterns (combined global + snapshot-specific)
 	SkipErrors     bool     // Skip file read errors (log loudly but continue)
+	// PreviousSnapshotID is the most recent completed snapshot of the
+	// same name, "" for none.
+	PreviousSnapshotID string
 }
 
 // Module exports backup functionality as an fx module.
@@ -55,6 +58,7 @@ func provideScannerFactory(
 			UI:                 params.UI,
 			Exclude:            excludes,
 			SkipErrors:         params.SkipErrors,
+			PreviousSnapshotID: params.PreviousSnapshotID,
 		})
 	}
 }

internal/snapshot/scanner.go

@@ -58,6 +58,10 @@ type Scanner struct {
 	compressionLevel int
 	ageRecipient     string
 	snapshotID       string // Current snapshot being processed
+	// previousSnapshotID is the most recent completed snapshot of the
+	// same name, "" for none. Only a file it lists can be counted as
+	// deleted.
+	previousSnapshotID string
 	// currentSourcePath is the source directory being scanned, stored with
 	// each file record.
 	currentSourcePath string
@@ -129,6 +133,9 @@ type ScannerConfig struct {
 	// SkipErrors skips files that cannot be opened or read (log loudly but
 	// continue); packer, database, encryption, and upload errors still abort.
 	SkipErrors bool
+	// PreviousSnapshotID is the most recent completed snapshot of the
+	// same name, "" for none.
+	PreviousSnapshotID string
 }
 
 // ScanResult contains the results of a scan operation. Files and bytes
@@ -207,6 +214,7 @@ func NewScanner(cfg ScannerConfig) *Scanner {
 		compiledExclude:    compiledExclude,
 		progress:           progress,
 		skipErrors:         cfg.SkipErrors,
+		previousSnapshotID: cfg.PreviousSnapshotID,
 		ui:                 uiw,
 		pendingChunkHashes: make(map[string]struct{}),
 	}
@@ -258,8 +266,9 @@ func (s *Scanner) Scan(
 
 	filesToProcess := scanResult.FilesToProcess
 
-	// Phase 1b: Detect deleted files by comparing DB against scanned files
-	err = s.detectDeletedFilesFromMap(ctx, knownFiles, existingFiles, result)
+	// Phase 1b: Detect deleted files by comparing the previous snapshot
+	// of this name against scanned files
+	err = s.detectDeletedFiles(ctx, path, existingFiles, result)
 	if err != nil {
 		return nil, fmt.Errorf("detecting deleted files: %w", err)
 	}
@@ -439,9 +448,8 @@ func (s *Scanner) summarizeScanPhase(
 }
 
 // loadKnownFiles loads the known files at and beneath path from the
-// database into a map for fast lookup. Every loaded file the scan does
-// not find is counted as deleted. This avoids per-file database queries
-// during the scan phase.
+// database into a map for fast lookup. This avoids per-file database
+// queries during the scan phase.
 func (s *Scanner) loadKnownFiles(
 	ctx context.Context, path string,
 ) (map[string]*database.File, error) {
@@ -1954,21 +1962,29 @@ func (s *Scanner) queueFileForBatchInsert(
 	})
 }
 
-// detectDeletedFilesFromMap finds files that existed in previous snapshots
-// but no longer exist. Uses pre-loaded maps to avoid any filesystem or
-// database access.
-func (s *Scanner) detectDeletedFilesFromMap(
+// detectDeletedFiles counts as deleted each file at or beneath path that
+// the previous snapshot of this name lists, the walk did not find, and
+// is gone from disk. A file that is excluded, or inside an excluded
+// directory, is not counted: the walk skips it whether or not it is
+// still on disk.
+func (s *Scanner) detectDeletedFiles(
 	ctx context.Context,
-	knownFiles map[string]*database.File,
+	path string,
 	existingFiles map[string]struct{},
 	result *ScanResult,
 ) error {
-	if len(knownFiles) == 0 {
+	if s.previousSnapshotID == "" {
 		return nil
 	}
 
-	// Check each known file against the enumerated set (no filesystem access needed)
-	for path, file := range knownFiles {
+	previousFiles, err := s.repos.Files.ListUnderPathInSnapshot(
+		ctx, path, s.previousSnapshotID)
+	if err != nil {
+		return fmt.Errorf("listing files of snapshot %s: %w",
+			s.previousSnapshotID, err)
+	}
+
+	for _, file := range previousFiles {
 		// Check context cancellation periodically
 		select {
 		case <-ctx.Done():
@@ -1976,13 +1992,22 @@ func (s *Scanner) detectDeletedFilesFromMap(
 		default:
 		}
 
-		// Check if the file exists in our enumerated set
-		if _, exists := existingFiles[path]; !exists {
-			// File has been deleted
+		filePath := file.Path.String()
+
+		_, exists := existingFiles[filePath]
+		if exists || s.excludedOrInExcludedDir(filePath, path) {
+			continue
+		}
+
+		// Under --skip-errors the walk also misses what it cannot reach,
+		// such as the files in a directory it cannot open.
+		if !s.goneFromDisk(filePath) {
+			continue
+		}
+
 		result.FilesDeleted++
 		result.BytesDeleted += file.Size
-			log.Debug("Detected deleted file", "path", path, "size", file.Size)
-		}
+		log.Debug("Detected deleted file", "path", filePath, "size", file.Size)
 	}
 
 	if result.FilesDeleted > 0 {
@@ -1993,6 +2018,34 @@ func (s *Scanner) detectDeletedFilesFromMap(
 	return nil
 }
 
+// excludedOrInExcludedDir reports whether filePath, which is at or
+// beneath rootPath, or any directory between rootPath and it, matches an
+// exclude pattern. A pattern such as */.local/share/Trash matches the
+// directory but not the files inside it, which the walk skips too.
+func (s *Scanner) excludedOrInExcludedDir(filePath, rootPath string) bool {
+	for p := filePath; len(p) > len(rootPath); p = filepath.Dir(p) {
+		if s.shouldExclude(p, rootPath) {
+			return true
+		}
+	}
+
+	return false
+}
+
+// goneFromDisk reports whether looking filePath up on disk finds that
+// it does not exist. Like the walk, it does not follow a symlink, so a
+// symlink whose target is gone is still on disk.
+func (s *Scanner) goneFromDisk(filePath string) bool {
+	var err error
+	if lstater, ok := s.fs.(afero.Lstater); ok {
+		_, _, err = lstater.LstatIfPossible(filePath)
+	} else {
+		_, err = s.fs.Stat(filePath)
+	}
+
+	return errors.Is(err, os.ErrNotExist)
+}
+
 // wrapPermissionError augments permission errors with platform-specific
 // remediation instructions. On macOS, TCC-protected directories (Calendars,
 // Reminders, Photos, etc.) return EPERM unless the running application has

internal/vaultik/fault_injection_test.go

@@ -672,6 +672,7 @@ func faultScannerFactory(
 			UI:                 params.UI,
 			Exclude:            params.Exclude,
 			SkipErrors:         params.SkipErrors,
+			PreviousSnapshotID: params.PreviousSnapshotID,
 		})
 	}
 }

internal/vaultik/nuke_remote_test.go

@@ -18,8 +18,7 @@ import (
 // TestNukeRemoteLeavesNoFiles checks that remote nuke leaves no file
 // under a file:// destination, including the `.partial` files uploads
 // killed part-way leave next to a snapshot's metadata and next to where a
-// blob would have been, a snapshot's database whose manifest was never
-// uploaded, and a file under blobs/ whose name is not a blob hash.
+// blob would have been.
 func TestNukeRemoteLeavesNoFiles(t *testing.T) {
 	log.Initialize(log.Config{})
 	t.Parallel()
@@ -39,9 +38,6 @@ func TestNukeRemoteLeavesNoFiles(t *testing.T) {
 			"db.zst.age-123456.partial"),
 		filepath.Join(storeDir, "blobs", hash[:2], hash[2:4],
 			hash+"-123456.partial"),
-		filepath.Join(storeDir, "metadata",
-			snapshot.RemoteSnapshotKey("no-manifest"), "db.zst.age"),
-		filepath.Join(storeDir, "blobs", "0b", "01", ".DS_Store"),
 	}
 
 	for _, leftover := range leftovers {
@@ -104,34 +100,6 @@ func TestNukeRemoteFailsWhenADeleteFails(t *testing.T) {
 	}
 }
 
-// TestNukeRemoteNamesWhatIsLeft checks that remote nuke, when an object
-// it does not recognise cannot be deleted, does not report the store
-// empty but names that object and fails.
-func TestNukeRemoteNamesWhatIsLeft(t *testing.T) {
-	log.Initialize(log.Config{})
-	t.Parallel()
-
-	ctx := context.Background()
-	storeDir := filepath.Join(t.TempDir(), "store")
-	v, _, out := backUpToFileDestination(ctx, t, storeDir)
-
-	const leftKey = "blobs/0b/01/.DS_Store"
-
-	leftPath := filepath.Join(storeDir, filepath.FromSlash(leftKey))
-	require.NoError(t, os.MkdirAll(filepath.Dir(leftPath), 0o750))
-	require.NoError(t, os.WriteFile(leftPath, []byte("finder"), 0o600))
-
-	store := faultstore.New(v.Storage)
-	store.OnDelete = func(key string) bool { return key == leftKey }
-	v.Storage = store
-
-	require.Error(t, v.NukeRemote(true))
-
-	assert.Contains(t, out.String(), leftKey)
-	assert.NotContains(t, out.String(), "now empty")
-	assert.Contains(t, out.String(), "vaultik remote nuke --force")
-}
-
 // TestNukeRemoteRefusesAnotherDestinationWithoutRetryAdvice checks that
 // remote nuke, when the local index belongs to a different destination
 // than the configured one, fails without advising to run nuke again:

internal/vaultik/prune.go

@@ -22,11 +22,6 @@ var errNukeRequiresForce = errors.New(
 // errBlobDeleteFailed reports unreferenced blobs prune could not delete.
 var errBlobDeleteFailed = errors.New("blob(s) could not be deleted")
 
-// errObjectsLeft reports objects remote nuke still finds on the backup
-// destination store after deleting.
-var errObjectsLeft = errors.New(
-	"object(s) still on the backup destination store")
-
 // 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.
@@ -40,11 +35,10 @@ const metadataDirName = "metadata"
 // (blobs/<aa>/<bb>/<hash>).
 const blobKeyParts = 4
 
-// NukeRemote deletes every object under metadata/ and blobs/ in remote
-// storage, whatever its name, along with any object an upload cut off
-// part-way left under a temporary `.partial` name. It returns
-// successfully only when a listing afterwards finds nothing left there,
-// and the next backup then starts from scratch.
+// NukeRemote deletes every snapshot's metadata and every blob from remote
+// storage, along with any object an upload cut off part-way left under a
+// temporary `.partial` name. After this returns successfully the bucket
+// prefix is empty and the next backup starts from scratch.
 //
 // Refuses to run unless force is true. The caller is responsible for
 // confirming with the user.
@@ -74,8 +68,7 @@ func (v *Vaultik) NukeRemote(force bool) error {
 }
 
 // emptyDestinationStore does the deleting for NukeRemote and stops at
-// the first step that fails. It also fails when objects are still
-// listed at the end, naming each one.
+// the first step that fails.
 func (v *Vaultik) emptyDestinationStore() error {
 	v.UI.Beginf("Removing all snapshot metadata from backup destination store.")
 
@@ -84,62 +77,25 @@ func (v *Vaultik) emptyDestinationStore() error {
 		return fmt.Errorf("removing all snapshots: %w", err)
 	}
 
-	v.UI.Beginf("Removing everything still present in backup destination store.")
+	v.UI.Beginf("Removing any blobs still present in backup destination store.")
 
-	var left []string
-
-	for _, prefix := range []string{"metadata/", "blobs/"} {
-		keys, err := v.deleteEverythingUnder(prefix)
+	err = v.PruneBlobs(&PruneOptions{Force: true})
 	if err != nil {
-			return err
+		return fmt.Errorf("pruning blobs: %w", err)
 	}
 
-		left = append(left, keys...)
+	// The file and rclone listings skip `.partial` objects, so the two
+	// steps above never delete them.
+	for _, prefix := range []string{"metadata/", "blobs/"} {
+		err = v.Storage.DeletePartialUploads(v.ctx, prefix)
+		if err != nil {
+			return fmt.Errorf("deleting partial uploads: %w", err)
 		}
-
-	for _, key := range left {
-		v.UI.Warningf("Still on the backup destination store: %s", key)
-	}
-
-	if len(left) > 0 {
-		return fmt.Errorf("%d %w", len(left), errObjectsLeft)
 	}
 
 	return nil
 }
 
-// deleteEverythingUnder deletes every object under prefix, whatever its
-// name, and returns the keys a listing afterwards still finds. A delete
-// that fails is logged and the others still run; that object then
-// shows up in the listing afterwards.
-func (v *Vaultik) deleteEverythingUnder(prefix string) ([]string, error) {
-	keys, err := v.Storage.List(v.ctx, prefix)
-	if err != nil {
-		return nil, fmt.Errorf("listing %s: %w", prefix, err)
-	}
-
-	for _, key := range keys {
-		err = v.Storage.Delete(v.ctx, key)
-		if err != nil {
-			log.Error("Failed to delete object", "key", key, "error", err)
-		}
-	}
-
-	// The file and rclone listings skip `.partial` objects, so the
-	// deletes above never reach them.
-	err = v.Storage.DeletePartialUploads(v.ctx, prefix)
-	if err != nil {
-		return nil, fmt.Errorf("deleting partial uploads: %w", err)
-	}
-
-	left, err := v.Storage.List(v.ctx, prefix)
-	if err != nil {
-		return nil, fmt.Errorf("listing %s: %w", prefix, err)
-	}
-
-	return left, nil
-}
-
 // PruneBlobsResult contains the result of a blob prune operation
 //
 //nolint:tagliatelle // snake_case is the established JSON output format

internal/vaultik/snapshot.go

@@ -243,12 +243,18 @@ func (v *Vaultik) createNamedSnapshot(
 		return err
 	}
 
+	previousSnapshotID, err := v.previousSnapshotID(snapName)
+	if err != nil {
+		return err
+	}
+
 	scanner := v.ScannerFactory(snapshot.ScannerParams{
 		EnableProgress:     !opts.Cron,
 		UI:                 v.UI,
 		Fs:                 v.Fs,
 		Exclude:            v.Config.GetExcludes(snapName),
 		SkipErrors:         opts.SkipErrors,
+		PreviousSnapshotID: previousSnapshotID,
 	})
 
 	snapshotID, err := v.SnapshotManager.CreateSnapshotWithName(
@@ -283,6 +289,24 @@ func (v *Vaultik) createNamedSnapshot(
 	return nil
 }
 
+// previousSnapshotID returns the ID of the most recent completed snapshot
+// named snapName in the local index, or "" when there is none.
+func (v *Vaultik) previousSnapshotID(snapName string) (string, error) {
+	snapshots, err := v.Repositories.Snapshots.ListRecent(v.ctx, listRecentLimit)
+	if err != nil {
+		return "", fmt.Errorf("listing snapshots: %w", err)
+	}
+
+	for _, s := range snapshots {
+		if s.CompletedAt != nil &&
+			parseSnapshotName(s.ID.String(), s.Hostname.String()) == snapName {
+			return s.ID.String(), nil
+		}
+	}
+
+	return "", nil
+}
+
 // resolveSnapshotPaths resolves source directories to absolute paths
 // with symlink resolution.
 func (v *Vaultik) resolveSnapshotPaths(snapName string) ([]string, error) {

internal/vaultik/snapshot_deleted_count_test.go

@@ -0,0 +1,225 @@
+package vaultik_test
+
+import (
+	"bytes"
+	"context"
+	"fmt"
+	"os"
+	"path/filepath"
+	"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/ui"
+	"sneak.berlin/go/vaultik/internal/vaultik"
+)
+
+// These tests cover https://git.eeqj.de/sneak/vaultik/issues/304: a
+// backup counts a file as deleted only when the previous snapshot of
+// the same name had it and it is gone, and never counts an excluded
+// file.
+
+// deletedCountEnv is a backup setup over the source directory src whose
+// user-facing output is kept in out. Each test configures its snapshots
+// with setSnapshot.
+type deletedCountEnv struct {
+	v   *vaultik.Vaultik
+	out *bytes.Buffer
+	src string
+}
+
+// newDeletedCountEnv writes files, keyed by path relative to src.
+func newDeletedCountEnv(t *testing.T, files map[string][]byte) *deletedCountEnv {
+	t.Helper()
+
+	ctx := context.Background()
+	fs := afero.NewOsFs()
+	tempDir := t.TempDir()
+	srcDir := filepath.Join(tempDir, "src")
+
+	for rel, content := range files {
+		path := filepath.Join(srcDir, rel)
+		require.NoError(t, fs.MkdirAll(filepath.Dir(path), 0o755))
+		require.NoError(t, afero.WriteFile(fs, path, content, 0o644))
+	}
+
+	cfg := faultTestConfig()
+	cfg.IndexPath = filepath.Join(tempDir, "index.sqlite")
+	cfg.Snapshots = map[string]config.SnapshotConfig{}
+
+	store, err := storage.NewFileStorer(filepath.Join(tempDir, "remote"))
+	require.NoError(t, err)
+
+	db, err := database.New(ctx, cfg.IndexPath)
+	require.NoError(t, err)
+	t.Cleanup(func() { _ = db.Close() })
+
+	repos := database.NewRepositories(db)
+	out := &bytes.Buffer{}
+	v := newBackupVaultik(ctx, cfg, store, repos, db, fs)
+	v.UI = ui.NewWithColor(out, false)
+
+	return &deletedCountEnv{v: v, out: out, src: srcDir}
+}
+
+// setSnapshot configures the snapshot name to back up the path rel
+// beneath src, with the given excludes.
+func (e *deletedCountEnv) setSnapshot(name, rel string, exclude ...string) {
+	e.v.Config.Snapshots[name] = config.SnapshotConfig{
+		Paths:   []string{filepath.Join(e.src, rel)},
+		Exclude: exclude,
+	}
+}
+
+// backUp runs a backup of the named snapshot and returns its output.
+func (e *deletedCountEnv) backUp(t *testing.T, name string) string {
+	t.Helper()
+
+	e.out.Reset()
+	require.NoError(t, e.v.CreateSnapshot(&vaultik.SnapshotCreateOptions{
+		Snapshots: []string{name},
+	}))
+
+	return e.out.String()
+}
+
+// A file this snapshot excludes is not counted as deleted: neither one
+// that another snapshot backs up, nor one that the previous snapshot of
+// this name had before the exclude was added.
+func TestBackupDoesNotCountExcludedFileAsDeleted(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"top.txt":       []byte("top"),
+		"cache/tmp.bin": []byte("cache"),
+		"photos/a.jpg":  []byte("photo a"),
+		"photos/b.jpg":  []byte("photo b"),
+		"photos/c.jpg":  []byte("photo c"),
+	})
+	env.setSnapshot("photos", "photos")
+	env.setSnapshot("home", "", "/photos")
+
+	env.backUp(t, "photos")
+	assert.Contains(t, env.backUp(t, "home"), filesLine(2, 2, 0))
+
+	env.setSnapshot("home", "", "/photos", "/cache")
+	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
+}
+
+// A file inside a directory that an exclude added after a backup
+// matches is not counted as deleted, though the pattern matches only the
+// directory.
+func TestBackupDoesNotCountFileInExcludedDirectoryAsDeleted(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"top.txt":                         []byte("top"),
+		"user/.local/share/Trash/old.txt": []byte("old"),
+	})
+	env.setSnapshot("home", "")
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(2, 2, 0))
+
+	env.setSnapshot("home", "", "*/.local/share/Trash")
+	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
+}
+
+// Under --skip-errors a file inside a directory that the walk cannot
+// open is not counted as deleted: it is still on disk.
+func TestBackupDoesNotCountFileInUnopenableDirectoryAsDeleted(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"top.txt":           []byte("top"),
+		"locked/inside.txt": []byte("inside"),
+	})
+	env.setSnapshot("home", "")
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(2, 2, 0))
+
+	// A directory's mode does not lock out root, who runs the tests, so
+	// opening the directory is made to fail instead.
+	env.v.Fs = &openFailFs{
+		path: filepath.Join(env.src, "locked"),
+		err:  os.ErrPermission,
+	}
+
+	env.out.Reset()
+	require.NoError(t, env.v.CreateSnapshot(&vaultik.SnapshotCreateOptions{
+		SkipErrors: true,
+		Snapshots:  []string{"home"},
+	}))
+	assert.Contains(t, env.out.String(), filesLine(1, 0, 1))
+}
+
+// A backup counts only files that the previous snapshot of its own name
+// had, not one that a later snapshot of another name over the same path
+// had and that is since removed.
+func TestBackupIgnoresSnapshotOfAnotherName(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"kept.txt": []byte("kept"),
+	})
+	env.setSnapshot("home", "")
+	env.setSnapshot("other", "")
+
+	env.backUp(t, "home")
+
+	// Snapshot start times are kept in whole seconds: wait so that other's
+	// snapshot is strictly the most recent.
+	time.Sleep(time.Second)
+
+	extra := filepath.Join(env.src, "extra.txt")
+	require.NoError(t, os.WriteFile(extra, []byte("extra"), 0o600))
+	env.backUp(t, "other")
+	require.NoError(t, os.Remove(extra))
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
+}
+
+// A file removed from disk is counted as deleted by the next backup of
+// the snapshot that had it, and not by any later backup of that
+// snapshot, nor by the first backup of another name over the same path.
+func TestBackupCountsDeletedFileOnce(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	aContent := bytes.Repeat([]byte("a"), 1000)
+	bContent := bytes.Repeat([]byte("b"), 2000)
+	keptContent := bytes.Repeat([]byte("k"), 500)
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"a.txt":    aContent,
+		"b.txt":    bContent,
+		"kept.txt": keptContent,
+	})
+	env.setSnapshot("home", "")
+	env.setSnapshot("other", "")
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(3, 3, 0))
+
+	require.NoError(t, os.Remove(filepath.Join(env.src, "a.txt")))
+	require.NoError(t, os.Remove(filepath.Join(env.src, "b.txt")))
+
+	summary := env.backUp(t, "home")
+	assert.Contains(t, summary,
+		"Files: 1 examined, 0 backed up, 1 unchanged, 2 deleted.")
+	assert.Contains(t, summary,
+		fmt.Sprintf("Data: %s total (%s backed up), %s deleted.",
+			env.v.UI.Size(int64(len(keptContent))), env.v.UI.Size(0),
+			env.v.UI.Size(int64(len(aContent)+len(bContent)))))
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
+	assert.Contains(t, env.backUp(t, "other"), filesLine(1, 0, 1))
+}