Walk an operand nested on another filesystem with -x (closes #106)

With -x, an operand under another operand is kept and walked on its
own when the walk of the deepest kept operand above it cannot reach
it: some directory from it (from its directory, for a regular file) up
to but not including that operand is on a different filesystem than
that operand. Below a kept operand, the rule keeping records under a
directory -x did not enter covers only directories its own walk did
not enter, so records of files gone from it are deleted.

The new tests stub the devices and share their scan steps with the
test for #99. Comments and
README sentences on operands dropped before the walk now also hold
with -x.

Model: opus-5-5

README.md

@@ -271,16 +271,21 @@ All three subcommands operate on a single SQLite database file:
   error (exit 1) telling the user to run `scan` first.
 - Only one `scan` runs against a database at a time. For its whole run, `scan`
   holds an exclusive `flock(2)` lock on a lock file beside the database, named
-  by appending `.lock` to the database path (`/var/lib/sfdupes/db.sqlite.lock`
+  by appending `.lock` to the database's path with symlinks resolved
-  by default), taken before it walks the filesystem or opens the database. A
+  (`/var/lib/sfdupes/db.sqlite.lock` by default), taken before it walks the
-  second `scan` against the same database does not wait: it fails at once with a
+  filesystem or opens the database. Every path to one database, through a
-  one-line error naming the lock file and exits 1, without walking anything or
+  symlink to the file or to a directory above it, names the same lock file. Just
-  opening the database, and the running scan carries on. The lock file is
+  before it takes the lock, `scan` creates the database file, empty, if it is
-  created on first use, open to its owner only, and left in place: a leftover
+  missing (through a symlink at the database path, it creates the symlink's
-  file blocks nothing, because the lock ends with the process holding it however
+  target), so the lock file is named the same way before the first scan sets up
-  it ends, a fatal error or an interrupt included, and deleting the file while a
+  the database as after. A second `scan` against the same database does not
-  scan runs would let a second scan start. `report` and `trees` never take the
+  wait: it fails at once with a one-line error naming the lock file and exits 1,
-  lock, so they run during a scan.
+  without walking anything or opening the database, and the running scan carries
+  on. The lock file is created on first use, open to its owner only, and left in
+  place: a leftover file blocks nothing, because the lock ends with the process
+  holding it however it ends, a fatal error or an interrupt included, and
+  deleting the file while a scan runs would let a second scan start. `report`
+  and `trees` never take the lock, so they run during a scan.
 - While `scan` runs, the database is in WAL journal mode with a busy timeout, so
   running a report while a cron `scan` is in progress is safe. The filesystem is
   authoritative; the database is an eventually-consistent reflection of it.
@@ -314,7 +319,8 @@ All three subcommands operate on a single SQLite database file:
     CREATE TABLE files (
         path       BLOB PRIMARY KEY,  -- absolute path, raw bytes
         size       INTEGER NOT NULL,  -- bytes, from lstat
-        mtime   INTEGER NOT NULL,  -- Unix seconds, from lstat
+        mtime      INTEGER NOT NULL,  -- whole Unix seconds of the mtime, from lstat
+        mtime_nsec INTEGER NOT NULL,  -- nanoseconds within that second, 0 to 999999999
         head       TEXT NOT NULL,     -- lowercase-hex SHA-256; first 64 KiB, or whole file under 10 MiB
         tail       TEXT NOT NULL,     -- lowercase-hex SHA-256; last 64 KiB, or whole file under 10 MiB
         content    TEXT NOT NULL      -- lowercase-hex SHA-256, whole file or samples
@@ -323,18 +329,22 @@ All three subcommands operate on a single SQLite database file:
     ```
 
     Paths are stored as BLOBs because Unix paths are raw bytes, not guaranteed
-    UTF-8. `mtime` is used only for change detection; it is not part of the
+    UTF-8. `mtime` and `mtime_nsec` hold the file's mtime to the nanosecond:
-    duplicate key. For a file under 10 MiB `head`, `tail`, and `content` all
+    `mtime` the whole Unix seconds, rounded down, and `mtime_nsec` the
-    hold the whole-file hash (that range is hashed in full, with no end
+    nanoseconds past that second. Split this way they hold any mtime a
-    windows); for a larger file `head` and `tail` hold the first- and last-64
+    filesystem can record, one before 1678 or after 2262 included, which a
-    KiB hashes and `content` the whole-file or sampled hash. All three are empty
+    single 64-bit count of nanoseconds cannot. They are used only for change
-    strings when the file has never been hashed because its size was unique as
+    detection and are not part of the duplicate key. For a file under 10 MiB
-    of the last scan that covered it. For a file of 10 MiB or more, `content`
+    `head`, `tail`, and `content` all hold the whole-file hash (that range is
-    stays empty until the content phase of a scan (see "`scan` mode" below) has
+    hashed in full, with no end windows); for a larger file `head` and `tail`
-    read the file. A record with an empty `content` is never part of a duplicate
+    hold the first- and last-64 KiB hashes and `content` the whole-file or
-    group, though it still defines the file for tree reconstruction. The
+    sampled hash. All three are empty strings when the file has never been
-    `files_signature` index lets SQLite group the records by signature for
+    hashed because its size was unique as of the last scan that covered it. For
-    `report` without sorting the whole table.
+    a file of 10 MiB or more, `content` stays empty until the content phase of a
+    scan (see "`scan` mode" below) has read the file. A record with an empty
+    `content` is never part of a duplicate group, though it still defines the
+    file for tree reconstruction. The `files_signature` index lets SQLite group
+    the records by signature for `report` without sorting the whole table.
 
 ### Duplicate detection
 
@@ -388,7 +398,11 @@ results do not depend on the working directory. All operands belong to a single
 scan and are enumerated concurrently: every operand seeds the shared walk worker
 pool. Overlapping operands are harmless — an operand that duplicates another or
 lies under another is dropped before walking, so every file is reached exactly
-once and produces one database record.
+once and produces one database record. With `-x`, though, an operand under
+another one is kept and walked on its own when any directory from it (from its
+directory, for a regular file) up to but not including the operand covering it
+is on a different filesystem than that operand, because that operand's walk does
+not enter such a directory and so does not reach it.
 
 An operand that is a symlink (never followed, not even as an operand), socket,
 FIFO, or device node, or a directory named `.zfs`, is not scanned. `scan` prints
@@ -397,9 +411,8 @@ drops it from the scanned operands before reading the database. Another operand
 beneath it is still scanned. The records stored beneath it are not deleted: they
 are treated like any other record outside the scanned operands, including the
 content-phase exception below. If it lies under another operand, they are under
-that operand instead, and are deleted like any other record there that this scan
+that operand instead, and are treated like any other record there. This is not
-did not verify. This is not an error: a scan whose every operand is dropped
+an error: a scan whose every operand is dropped walks nothing and exits 0.
-walks nothing and exits 0.
 
 `scan` synchronizes the database with the filesystem state under the scanned
 operands:
@@ -421,6 +434,9 @@ operands:
   once its size, `head`, and `tail` match another record's.
 - A file whose mtime is newer than recorded, or whose size differs, is processed
   as if new: re-hashed, or recorded without hashes, per the shared-size rule.
+  Change detection compares the mtime to the nanosecond, as finely as the
+  filesystem records it, so a same-size rewrite counts as a change whenever the
+  filesystem gives it a later mtime than recorded, even within the same second.
 - A database record whose path lies under one of the scanned operands but was
   not successfully processed this run is deleted. This removes records for
   deleted files. It also removes records for paths that failed to stat or hash
@@ -434,6 +450,12 @@ operands:
   a `content` hash is read for one, wherever it lies, once its size, `head`, and
   `tail` match another record's. If that file is gone or has changed since its
   record was written, the record is left as it is.
+- With `-x`, a record below a directory the walk did not enter because that
+  directory is on another filesystem than its operand counts as outside the
+  scanned operands: it is not deleted, and its size joins the size census. A
+  filesystem mounted under an operand can therefore be scanned on its own
+  schedule into the same database. Records below an operand at or inside such a
+  directory are not kept this way, since that operand's own walk verifies them.
 
 `scan` runs **four sequential phases over the whole scan**. Parallelism lives
 inside each phase; batched database writes begin during the hash phase:
@@ -500,15 +522,19 @@ Rules for the walk:
 - Filesystem boundaries are crossed by default. With `-x` (long form
   `--one-file-system`, following the GNU `du`/`rsync` convention), never descend
   into a directory on a different filesystem than its `PATH` operand; each
-  operand is bounded by its own filesystem.
+  operand is bounded by its own filesystem. The records below such a directory,
+  unless they lie below an operand at or inside that directory, count as outside
+  the scanned operands, as described in "`scan` mode" above: they are not
+  deleted, and their sizes join the size census.
 - On any per-path error (permission denied, file vanished between passes,
   unreadable): print a one-line warning to stderr, skip the path, and continue.
   Per-file errors never abort the run; the final summary reports how many were
   skipped. As specified above, a skipped path that has a database record from an
   earlier scan loses that record, unless it failed only in the content phase, or
-  is an operand dropped before the database was read that lies under no other
+  is an operand dropped before the database was read whose record counts as
-  operand; an unreadable directory subtree likewise loses its records (accepted:
+  outside the scanned operands; an unreadable directory subtree likewise loses
-  the database mirrors what the latest scan could actually verify).
+  its records (accepted: the database mirrors what the latest scan could
+  actually verify).
 
 Concurrency: the walk phase (which also stats files), the hash phase, and the
 content phase each use a worker pool of `--workers` workers (default

TODO.md

@@ -29,6 +29,36 @@
 
 # Completed Steps
 
+- with `-x`, an operand under another operand is walked on its own instead of
+  being dropped when a directory from it (from its directory, for a regular
+  file) up to but not including that operand is on a different filesystem than
+  that operand, whose walk then cannot reach it, and the records of files gone
+  from below it are deleted (2026-10-14,
+  https://git.eeqj.de/sneak/sfdupes/issues/106)
+
+- with `-x`, `scan` keeps the records below a directory on another filesystem
+  under its operand, and counts their sizes in the size census, instead of
+  deleting them (2026-10-14, https://git.eeqj.de/sneak/sfdupes/issues/99)
+
+- the hash and content phases open each file without blocking and check that it
+  is still a regular file, so one replaced by a FIFO or device node after it was
+  statted is warned about and skipped instead of hanging the scan (2026-10-14,
+  https://git.eeqj.de/sneak/sfdupes/issues/100)
+
+- the scan lock file is named from the database's path with symlinks resolved,
+  after `scan` creates the database file if it is missing, so a scan through a
+  symlink to the database fails while another scan holds the lock (2026-10-14,
+  https://git.eeqj.de/sneak/sfdupes/issues/101)
+
+- on a terminal, a warning for the last file of a phase no longer erases the
+  phase's finished bar: the bar is drawn again below the warning (2026-10-14,
+  https://git.eeqj.de/sneak/sfdupes/issues/102)
+
+- `scan` records mtime to the nanosecond, as whole seconds in `mtime` plus
+  `mtime_nsec`, and compares it at that resolution, so a same-size rewrite
+  within the same second is re-hashed (2026-10-07,
+  https://git.eeqj.de/sneak/sfdupes/issues/12)
+
 - cut the narration from `TODO.md` Completed Steps and from the comments in
   `script/` and both Dockerfiles; §Workflow now branches from and merges to
   `next` (2026-10-04, https://git.eeqj.de/sneak/sfdupes/issues/49)

db.go

@@ -11,6 +11,7 @@ import (
 	"path/filepath"
 	"slices"
 	"strconv"
+	"time"
 
 	"golang.org/x/sys/unix"
 	// The pure-Go SQLite driver, registered as "sqlite"; keeps cgo
@@ -34,18 +35,25 @@ const schemaVersion = 1
 // scan.
 const dbDirPerm = 0o755
 
+// dbFilePerm is the mode for a database file created by scan, the mode
+// SQLite gives a database file it creates.
+const dbFilePerm = 0o644
+
 // lockFilePerm is the mode for the scan lock file. Anyone who can open
 // the file can hold the lock and keep every scan from running, so it
 // is open to its owner only.
 const lockFilePerm = 0o600
 
 // createTableSQL is the schema applied to a fresh database. Paths are
-// BLOBs because Unix paths are raw bytes, not guaranteed UTF-8.
+// BLOBs because Unix paths are raw bytes, not guaranteed UTF-8. mtime
+// holds whole Unix seconds and mtime_nsec the nanoseconds within that
+// second.
 const createTableSQL = `
 CREATE TABLE files (
     path       BLOB PRIMARY KEY,
     size       INTEGER NOT NULL,
     mtime      INTEGER NOT NULL,
+    mtime_nsec INTEGER NOT NULL,
     head       TEXT NOT NULL,
     tail       TEXT NOT NULL,
     content    TEXT NOT NULL
@@ -61,10 +69,11 @@ CREATE INDEX files_signature ON files (size, head, tail, content)
 // upsertSQL inserts one file record, replacing any existing record for
 // the same path.
 const upsertSQL = `
-INSERT INTO files (path, size, mtime, head, tail, content)
+INSERT INTO files (path, size, mtime, mtime_nsec, head, tail, content)
-VALUES (?, ?, ?, ?, ?, ?)
+VALUES (?, ?, ?, ?, ?, ?, ?)
 ON CONFLICT (path) DO UPDATE SET
     size = excluded.size, mtime = excluded.mtime,
+    mtime_nsec = excluded.mtime_nsec,
     head = excluded.head, tail = excluded.tail,
     content = excluded.content
 `
@@ -135,19 +144,37 @@ func openDB(path, params string) (*sql.DB, error) {
 
 // lockScanDatabase takes the lock that keeps a second scan off the
 // database at path: an exclusive flock(2) on the file beside it named
-// path with ".lock" appended, created along with the database's parent
+// by the database's path with symlinks resolved and ".lock" appended,
-// directory if missing. A lock held by another scan fails at once
+// so every path to one database names the same lock file. If missing,
-// instead of waiting. The lock lasts until the returned file is closed
+// the database's parent directory and an empty database file are
-// or the process ends. The file is never deleted: a scan that deleted
+// created first, so the lock file is named the same way before the
-// it would let the next scan lock a new file while another still holds
+// database is set up as after. A lock held by another scan fails at
-// the old one.
+// once instead of waiting. The lock lasts until the returned file is
+// closed or the process ends. The lock file is never deleted: a scan
+// that deleted it would let the next scan lock a new file while
+// another still holds the old one.
 func lockScanDatabase(path string) (*os.File, error) {
 	err := os.MkdirAll(filepath.Dir(path), dbDirPerm)
 	if err != nil {
 		return nil, fmt.Errorf("create database directory: %w", err)
 	}
 
-	lockPath := path + ".lock"
+	// Like SQLite, this follows a symlink at path and creates its
+	// target. SQLite opens an empty file as a new database.
+	//nolint:gosec // the operator chooses the database path
+	dbFile, err := os.OpenFile(path, os.O_RDWR|os.O_CREATE, dbFilePerm)
+	if err != nil {
+		return nil, fmt.Errorf("create database: %w", err)
+	}
+
+	_ = dbFile.Close()
+
+	resolved, err := filepath.EvalSymlinks(path)
+	if err != nil {
+		return nil, fmt.Errorf("resolve database path: %w", err)
+	}
+
+	lockPath := resolved + ".lock"
 
 	//nolint:gosec // the operator chooses the database path
 	f, err := os.OpenFile(lockPath, os.O_RDWR|os.O_CREATE, lockFilePerm)
@@ -356,8 +383,8 @@ func userVersion(ctx context.Context, db *sql.DB) (int, error) {
 // which is the order of the primary key, so SQLite does not sort.
 func loadFileRows(ctx context.Context, db *sql.DB, fn func(r scanRec)) error {
 	rows, err := db.QueryContext(ctx,
-		"SELECT path, size, mtime, head, tail, content FROM files "+
+		"SELECT path, size, mtime, mtime_nsec, head, tail, content "+
-			"ORDER BY path")
+			"FROM files ORDER BY path")
 	if err != nil {
 		return fmt.Errorf("read records: %w", err)
 	}
@@ -367,16 +394,18 @@ func loadFileRows(ctx context.Context, db *sql.DB, fn func(r scanRec)) error {
 	for rows.Next() {
 		var (
 			path      []byte
+			sec, nsec int64
 			r         scanRec
 		)
 
-		err = rows.Scan(&path, &r.size, &r.mtime, &r.head, &r.tail,
+		err = rows.Scan(&path, &r.size, &sec, &nsec, &r.head, &r.tail,
 			&r.content)
 		if err != nil {
 			return fmt.Errorf("read record: %w", err)
 		}
 
 		r.path = string(path)
+		r.mtime = time.Unix(sec, nsec)
 		fn(r)
 	}
 
@@ -466,10 +495,10 @@ func loadDupeRows(ctx context.Context, db *sql.DB,
 // values, and skipping the hash columns keeps the scan's in-memory
 // index small on multi-million-file databases.
 func loadFileMeta(ctx context.Context, db *sql.DB,
-	fn func(path string, size, mtime int64, hashed bool),
+	fn func(path string, size int64, mtime time.Time, hashed bool),
 ) error {
 	rows, err := db.QueryContext(ctx,
-		"SELECT path, size, mtime, head <> '' FROM files")
+		"SELECT path, size, mtime, mtime_nsec, head <> '' FROM files")
 	if err != nil {
 		return fmt.Errorf("read records: %w", err)
 	}
@@ -479,16 +508,16 @@ func loadFileMeta(ctx context.Context, db *sql.DB,
 	for rows.Next() {
 		var (
 			path            []byte
-			size, mtime int64
+			size, sec, nsec int64
 			hashed          int64
 		)
 
-		err = rows.Scan(&path, &size, &mtime, &hashed)
+		err = rows.Scan(&path, &size, &sec, &nsec, &hashed)
 		if err != nil {
 			return fmt.Errorf("read record: %w", err)
 		}
 
-		fn(string(path), size, mtime, hashed != 0)
+		fn(string(path), size, time.Unix(sec, nsec), hashed != 0)
 	}
 
 	err = rows.Err()
@@ -507,7 +536,7 @@ func loadFileMeta(ctx context.Context, db *sql.DB,
 // memory; the rows come ordered by size, head, and tail, so each
 // group's rows arrive together.
 const contentCandidatesSQL = `
-SELECT f.path, f.size, f.mtime, f.head, f.tail, f.content <> ''
+SELECT f.path, f.size, f.mtime, f.mtime_nsec, f.head, f.tail, f.content <> ''
 FROM files AS f
 JOIN (
     SELECT size, head, tail
@@ -534,16 +563,19 @@ func loadContentCandidates(ctx context.Context, db *sql.DB,
 	for rows.Next() {
 		var (
 			path      []byte
+			sec, nsec int64
 			r         scanRec
 			hashed    int64
 		)
 
-		err = rows.Scan(&path, &r.size, &r.mtime, &r.head, &r.tail, &hashed)
+		err = rows.Scan(&path, &r.size, &sec, &nsec, &r.head, &r.tail,
+			&hashed)
 		if err != nil {
 			return fmt.Errorf("read record: %w", err)
 		}
 
 		r.path = string(path)
+		r.mtime = time.Unix(sec, nsec)
 		fn(r, hashed != 0)
 	}
 
@@ -627,8 +659,8 @@ func execUpserts(ctx context.Context, tx *sql.Tx, upserts []scanRec,
 	defer func() { _ = st.Close() }()
 
 	for _, r := range upserts {
-		_, err = st.ExecContext(ctx,
+		_, err = st.ExecContext(ctx, []byte(r.path), r.size,
-			[]byte(r.path), r.size, r.mtime, r.head, r.tail, r.content)
+			r.mtime.Unix(), r.mtime.Nanosecond(), r.head, r.tail, r.content)
 		if err != nil {
 			return fmt.Errorf("upsert %s: %w", r.path, err)
 		}

db_test.go

@@ -10,13 +10,22 @@ import (
 	"slices"
 	"strings"
 	"testing"
+	"time"
 )
 
-// testDBPath returns a database path inside a fresh temp dir.
+// testDBPath returns a database path inside a fresh temp dir, with
+// symlinks resolved as the scan lock resolves them, so the lock file
+// is this path plus ".lock" even where the temp dir is reached through
+// a symlink.
 func testDBPath(t *testing.T) string {
 	t.Helper()
 
-	return filepath.Join(t.TempDir(), "db.sqlite")
+	dir, err := filepath.EvalSymlinks(t.TempDir())
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	return filepath.Join(dir, "db.sqlite")
 }
 
 // openTestDB creates a fresh scan database in a temp dir.
@@ -260,10 +269,13 @@ func TestApplyChangesRoundTrip(t *testing.T) {
 	// written.
 	recs := []scanRec{
 		{
-			size: 2, mtime: 20, head: "h2", tail: "t2", content: "c2",
+			size: 2, mtime: time.Unix(20, 999_999_999), head: "h2", tail: "t2",
-			path: "/a/tab\tnew\nline",
+			content: "c2", path: "/a/tab\tnew\nline",
+		},
+		{
+			size: 1, mtime: time.Unix(10, 0), head: "h1", tail: "t1",
+			content: "c1", path: "/a/x",
 		},
-		{size: 1, mtime: 10, head: "h1", tail: "t1", content: "c1", path: "/a/x"},
 	}
 
 	err := applyChanges(t.Context(), db, recs, nil,
@@ -281,7 +293,8 @@ func TestApplyChangesRoundTrip(t *testing.T) {
 	// An upsert for an existing path updates in place; a delete
 	// removes exactly its path.
 	upd := scanRec{
-		size: 3, mtime: 30, head: "h3", tail: "t3", content: "c3", path: "/a/x",
+		size: 3, mtime: time.Unix(30, 0), head: "h3", tail: "t3", content: "c3",
+		path: "/a/x",
 	}
 
 	err = applyChanges(t.Context(), db, []scanRec{upd},
@@ -308,7 +321,7 @@ func TestApplyChangesBatching(t *testing.T) {
 	recs := make([]scanRec, 0, n)
 	for i := range n {
 		recs = append(recs, scanRec{
-			size: int64(i), mtime: 1, head: "h", tail: "t",
+			size: int64(i), mtime: time.Unix(1, 0), head: "h", tail: "t",
 			path: fmt.Sprintf("/batch/%07d", i),
 		})
 	}

main_test.go

@@ -822,7 +822,7 @@ func holdScanLock(t *testing.T, path string) {
 
 func TestRunSecondScanFails(t *testing.T) {
 	// README §Database: while one scan holds the lock, a second scan
-	// fails at once, naming the lock file, without creating the
+	// fails at once, naming the lock file, without opening the
 	// database.
 	path := testDBPath(t)
 	t.Setenv(databaseEnv, path)
@@ -848,10 +848,99 @@ func TestRunSecondScanFails(t *testing.T) {
 		t.Errorf("stdout = %q, want nothing (data only)", got)
 	}
 
-	_, err := os.Stat(path)
+	// Taking the lock created the database file, empty; opening it as
-	if !errors.Is(err, fs.ErrNotExist) {
+	// a database would have written to it.
-		t.Errorf("stat %s = %v, want the database not created", path, err)
+	info, err := os.Stat(path)
+	if err != nil {
+		t.Fatal(err)
 	}
+
+	if info.Size() != 0 {
+		t.Errorf("database size = %d, want 0 (not opened)", info.Size())
+	}
+}
+
+// assertSecondScanFails runs a scan against the database
+// SFDUPES_DATABASE names while the test holds the lock on it. It fails
+// the test unless that scan fails at once, naming the lock file beside
+// path, the database's real path.
+func assertSecondScanFails(t *testing.T, path string) {
+	t.Helper()
+
+	var stderr bytes.Buffer
+
+	code := run([]string{cmdScan, t.TempDir()}, io.Discard, &stderr)
+	if code != exitFatal {
+		t.Errorf("run(scan) = %d, want %d", code, exitFatal)
+	}
+
+	want := "sfdupes: another scan is running (lock held on " +
+		path + ".lock)\n"
+	if got := stderr.String(); got != want {
+		t.Errorf("stderr = %q, want %q", got, want)
+	}
+}
+
+func TestRunSecondScanThroughSymlinkFails(t *testing.T) {
+	// README §Database: every path to one database names the same lock
+	// file, so while a scan holds it through one path, a scan through
+	// another fails, naming the lock file beside the database's real
+	// path.
+	t.Run("symlink to the database", func(t *testing.T) {
+		path := testDBPath(t)
+		t.Setenv(databaseEnv, path)
+
+		scanFixture(t)
+
+		link := filepath.Join(t.TempDir(), "link.sqlite")
+
+		err := os.Symlink(path, link)
+		if err != nil {
+			t.Fatal(err)
+		}
+
+		holdScanLock(t, path)
+		t.Setenv(databaseEnv, link)
+		assertSecondScanFails(t, path)
+	})
+
+	t.Run("symlink to its directory, no database yet", func(t *testing.T) {
+		path := testDBPath(t)
+		link := filepath.Join(t.TempDir(), "link")
+
+		err := os.Symlink(filepath.Dir(path), link)
+		if err != nil {
+			t.Fatal(err)
+		}
+
+		holdScanLock(t, path)
+		t.Setenv(databaseEnv, filepath.Join(link, filepath.Base(path)))
+		assertSecondScanFails(t, path)
+	})
+
+	t.Run("symlink whose target does not exist yet", func(t *testing.T) {
+		path := testDBPath(t)
+		link := filepath.Join(t.TempDir(), "link.sqlite")
+
+		err := os.Symlink(path, link)
+		if err != nil {
+			t.Fatal(err)
+		}
+
+		// The first scan takes the lock through the link before the
+		// database exists, then creates the database through it.
+		holdScanLock(t, link)
+
+		db, err := openScanDatabase(t.Context(), link)
+		if err != nil {
+			t.Fatal(err)
+		}
+
+		closeScanDatabase(t.Context(), db, link)
+
+		t.Setenv(databaseEnv, link)
+		assertSecondScanFails(t, path)
+	})
 }
 
 func TestRunScanReleasesLock(t *testing.T) {

progress.go

@@ -139,6 +139,13 @@ func (p *progress) warnf(format string, args ...any) {
 	}
 
 	fmt.Fprintln(os.Stderr, msg)
+
+	// The library never draws a finished bar again, so the warning for
+	// a pass's last item would erase it for good: draw its last frame
+	// again below the warning.
+	if p.bar != nil && p.bar.IsFinished() {
+		fmt.Fprint(os.Stderr, p.bar.String())
+	}
 }
 
 // finish terminates the pass's display. A bar whose pass stopped short

progress_test.go

@@ -187,3 +187,25 @@ func TestBarStoppedShortKeepsCount(t *testing.T) {
 		t.Errorf("terminal shows %q, want a count of 2 of 10", shown)
 	}
 }
+
+// TestWarningAfterLastItemKeepsBar checks that a warning printed after
+// a pass's last item, as for a failed read of the last file, leaves the
+// pass's finished bar on the terminal below the warning.
+//
+//nolint:paralleltest // captureStderr replaces the process-wide os.Stderr
+func TestWarningAfterLastItemKeepsBar(t *testing.T) {
+	stderr := captureStderr(t)
+	p := &progress{
+		label: "hash", total: 2, start: time.Now(),
+		bar: newBar("hash", 2),
+	}
+
+	p.increment()
+	p.increment()
+	p.warnf("warning")
+	p.finish()
+
+	if shown := lastFrame(stderr()); !strings.Contains(shown, "(2/2,") {
+		t.Errorf("terminal shows %q, want a count of 2 of 2", shown)
+	}
+}

report.go

@@ -7,6 +7,7 @@ import (
 	"io"
 	"os"
 	"strings"
+	"time"
 )
 
 // ioBufSize is the buffer size for the buffered stdout writers.
@@ -21,7 +22,7 @@ const minGroupSize = 2
 // only and used by scan for change detection.
 type scanRec struct {
 	size    int64
-	mtime   int64
+	mtime   time.Time
 	head    string
 	tail    string
 	content string

report_test.go

@@ -11,6 +11,7 @@ import (
 	"slices"
 	"strings"
 	"testing"
+	"time"
 )
 
 // awkwardDir is a directory name holding every byte the reports escape.
@@ -313,8 +314,14 @@ func TestDupeGroupsMtimeExcluded(t *testing.T) {
 	// mtime is informational only; records differing only in mtime
 	// still group together.
 	recs := []scanRec{
-		{size: 9, mtime: 100, head: "h", tail: "t", content: "c", path: "/m/1"},
+		{
-		{size: 9, mtime: 200, head: "h", tail: "t", content: "c", path: "/m/2"},
+			size: 9, mtime: time.Unix(100, 0), head: "h", tail: "t",
+			content: "c", path: "/m/1",
+		},
+		{
+			size: 9, mtime: time.Unix(200, 0), head: "h", tail: "t",
+			content: "c", path: "/m/2",
+		},
 	}
 
 	groups := dupeGroupsOf(t, recs)

scan.go

@@ -17,6 +17,7 @@ import (
 	"strings"
 	"sync"
 	"syscall"
+	"time"
 )
 
 // The duplicate ladder (see hashSignature and README "Duplicate
@@ -68,7 +69,7 @@ var errInterrupted = errors.New("scan interrupted")
 type fileRec struct {
 	path  string
 	size  int64
-	mtime int64
+	mtime time.Time
 	dev   uint64
 	ino   uint64
 }
@@ -79,7 +80,7 @@ type fileRec struct {
 // they would dominate the scan's memory.
 type fileMeta struct {
 	size   int64
-	mtime  int64
+	mtime  time.Time
 	hashed bool
 }
 
@@ -202,10 +203,16 @@ func resolveRoots(roots []string) ([]string, error) {
 }
 
 // pruneRoots drops operands already covered by another operand:
-// duplicates and any operand lying under another one. Every remaining
+// duplicates and any operand lying under another one. With -x, an
-// file is then reachable through exactly one root, so walked paths are
+// operand under another one is kept when the walk of the deepest kept
-// unique without keeping a scan-wide set of every path seen.
+// operand above it cannot reach it: when device puts any directory from
-func pruneRoots(roots []string) []string {
+// it (from its directory, for a regular file) up to but not including
+// that operand on a different filesystem than that operand. Every
+// remaining file is then reachable through exactly one root, so walked
+// paths are unique without keeping a scan-wide set of every path seen.
+func pruneRoots(roots []string, oneFS bool,
+	device func(path string) (uint64, bool),
+) []string {
 	// Shorter-first ordering guarantees an ancestor is kept before any
 	// operand under it is considered.
 	sorted := slices.Clone(roots)
@@ -220,14 +227,58 @@ func pruneRoots(roots []string) []string {
 	kept := make([]string, 0, len(sorted))
 
 	for _, r := range sorted {
-		if !underAnyRoot(r, kept) {
+		above := deepestRoot(r, kept)
+		if above == "" {
 			kept = append(kept, r)
+
+			continue
+		}
+
+		// Without -x, and always for a duplicate, r is dropped.
+		if !oneFS || above == r {
+			continue
+		}
+
+		aboveDev, aboveOK := device(above)
+		if !aboveOK {
+			continue
+		}
+
+		// The walk of above enters a directory only when it is on
+		// above's filesystem, and then reaches every regular file in it
+		// whatever device the file reports, so for a regular-file
+		// operand the directories checked start at its directory.
+		dir := r
+
+		fi, err := os.Lstat(r)
+		if err == nil && fi.Mode().IsRegular() {
+			dir = filepath.Dir(r)
+		}
+
+		for ; dir != above; dir = filepath.Dir(dir) {
+			dev, ok := device(dir)
+			if ok && dev != aboveDev {
+				kept = append(kept, r)
+
+				break
+			}
 		}
 	}
 
 	return kept
 }
 
+// deviceOfPath returns the filesystem device ID of the file at path,
+// when lstat succeeds and the platform exposes one.
+func deviceOfPath(path string) (uint64, bool) {
+	fi, err := os.Lstat(path)
+	if err != nil {
+		return 0, false
+	}
+
+	return deviceOfInfo(fi)
+}
+
 // scanStats summarizes one scan's database synchronization for the
 // final stderr summary, or for the line an interrupted scan prints.
 type scanStats struct {
@@ -287,21 +338,22 @@ func syncScan(ctx context.Context, db *sql.DB, roots []string,
 // size, head, and tail match another record's). Records outside the
 // roots are never touched, except that the content phase fills in
 // their content hash. Operands the walk cannot start from are dropped
-// first, so the records beneath them count as outside the roots unless
+// first, so the records beneath them are treated as if those operands
-// they lie under another root.
+// had not been given.
 func (s *scanState) runPhases(ctx context.Context, roots []string,
 	workers int, oneFS bool,
 ) error {
 	// Types are checked before pruning so that an operand under a
 	// dropped one is still scanned, not dropped as lying under it.
-	roots = pruneRoots(s.walkableRoots(roots))
+	roots = pruneRoots(s.walkableRoots(roots), oneFS, deviceOfPath)
 
 	err := s.loadIndex(ctx, roots)
 	if err != nil {
 		return err
 	}
 
-	changed, unhashed := s.walkPhase(startWalk(ctx, roots, oneFS, workers))
+	changed, unhashed := s.walkPhase(
+		startWalk(ctx, roots, oneFS, workers), roots)
 
 	// A cancelled walk stops early, so its size census covers only part
 	// of the roots, and every file it never reached would look vanished
@@ -329,10 +381,10 @@ func (s *scanState) runPhases(ctx context.Context, roots []string,
 // walkableRoots returns the operands the walk can start from: regular
 // files, and directories not named .zfs. Every other operand is warned
 // about, counted as skipped, and dropped. A dropped operand is no
-// longer a root, so the records stored beneath it count as outside the
+// longer a root, so the records stored beneath it are treated as if it
-// roots and are not deleted as unverified, unless it lies under another
+// had not been given: those under no other root count as outside the
-// root. An operand that fails lstat here is kept, and the walk warns
+// roots and are not deleted as unverified. An operand that fails lstat
-// about it.
+// here is kept, and the walk warns about it.
 func (s *scanState) walkableRoots(roots []string) []string {
 	kept := make([]string, 0, len(roots))
 
@@ -369,7 +421,7 @@ func (s *scanState) loadIndex(ctx context.Context, roots []string) error {
 	s.existing = make(map[string]fileMeta)
 
 	return loadFileMeta(ctx, s.db,
-		func(path string, size, mtime int64, hashed bool) {
+		func(path string, size int64, mtime time.Time, hashed bool) {
 			prog.increment()
 
 			if underAnyRoot(path, roots) {
@@ -390,15 +442,27 @@ func (s *scanState) loadIndex(ctx context.Context, roots []string) error {
 // (the content phase may still fill in its content hash). It returns
 // the new-or-changed files and the unchanged files whose records lack
 // hashes; both remain candidates until the census decides whether
-// their sizes are shared.
+// their sizes are shared. A record below a directory -x did not enter
+// counts as outside the roots: it is not deleted, and its size joins
+// the census. That does not hold below a root at or inside that
+// directory, since that root's own walk verifies the records below it.
 func (s *scanState) walkPhase(
-	events <-chan walkEvent,
+	events <-chan walkEvent, roots []string,
 ) ([]fileRec, []fileRec) {
 	prog := newProgress("walk", -1)
 
-	var changed, unhashed []fileRec
+	var (
+		changed, unhashed []fileRec
+		otherFSDirs       []string
+	)
 
 	for ev := range events {
+		if ev.otherFSDir != "" {
+			otherFSDirs = append(otherFSDirs, ev.otherFSDir)
+
+			continue
+		}
+
 		if ev.fail {
 			s.st.skipped++
 
@@ -415,7 +479,7 @@ func (s *scanState) walkPhase(
 		old, ok := s.existing[ev.rec.path]
 
 		switch {
-		case !ok || old.size != ev.rec.size || old.mtime < ev.rec.mtime:
+		case !ok || old.size != ev.rec.size || mtimeAfter(ev.rec.mtime, old.mtime):
 			changed = append(changed, ev.rec)
 		case old.hashed:
 			delete(s.existing, ev.rec.path)
@@ -428,6 +492,19 @@ func (s *scanState) walkPhase(
 
 	prog.finish()
 
+	for path, old := range s.existing {
+		// Kept only when a directory -x did not enter lies below the
+		// deepest root above the record. A root at or below that
+		// directory was walked on its own and did not find the file.
+		// Both contain the record, so the longer path is the deeper.
+		otherFSDir := deepestRoot(path, otherFSDirs)
+		if len(otherFSDir) > len(deepestRoot(path, roots)) {
+			delete(s.existing, path)
+
+			s.sizes = append(s.sizes, old.size)
+		}
+	}
+
 	return changed, unhashed
 }
 
@@ -807,7 +884,7 @@ func unchangedFile(r scanRec) (fileRec, bool, error) {
 	}
 
 	if !fi.Mode().IsRegular() || fi.Size() != r.size ||
-		fi.ModTime().Unix() > r.mtime {
+		mtimeAfter(fi.ModTime(), r.mtime) {
 		return fileRec{}, false, nil
 	}
 
@@ -818,6 +895,16 @@ func unchangedFile(r scanRec) (fileRec, bool, error) {
 	}, true, nil
 }
 
+// mtimeAfter reports whether mtime a is later than mtime b.
+// Not a.After(b): time.Time wraps an mtime past year 292 billion; Unix() undoes it.
+func mtimeAfter(a, b time.Time) bool {
+	if a.Unix() != b.Unix() {
+		return a.Unix() > b.Unix()
+	}
+
+	return a.Nanosecond() > b.Nanosecond()
+}
+
 // underAnyRoot reports whether path is any of the roots or lies under
 // one of them.
 func underAnyRoot(path string, roots []string) bool {
@@ -845,6 +932,20 @@ func underRoot(path, root string) bool {
 	return strings.HasPrefix(path, prefix)
 }
 
+// deepestRoot returns the longest of the roots that path is or lies
+// under, or "" when it lies under none.
+func deepestRoot(path string, roots []string) string {
+	deepest := ""
+
+	for _, root := range roots {
+		if underRoot(path, root) && len(root) > len(deepest) {
+			deepest = root
+		}
+	}
+
+	return deepest
+}
+
 // dirJob is one directory awaiting traversal by the walk workers. It
 // carries its operand's filesystem device so -x can stop at
 // filesystem boundaries.
@@ -855,19 +956,23 @@ type dirJob struct {
 }
 
 // walkEvent is one walk result delivered to the walk phase: a regular
-// file's statted record, or a warning when fail is set.
+// file's statted record, a warning when fail is set, or, when
+// otherFSDir is set, a directory -x did not enter because it is on
+// another filesystem than its operand.
 type walkEvent struct {
 	rec        fileRec
 	warn       string
 	fail       bool
+	otherFSDir string
 }
 
 // startWalk seeds every root into the shared walk worker pool and
 // returns the event stream: one record per regular file, one warning
-// event per per-path error. The channel is closed when the walk
+// event per per-path error, and one event per directory -x did not
-// completes, and also when ctx is cancelled — every goroutine in the
+// enter. The channel is closed when the walk completes, and also when
-// pool abandons its blocking send in that case, so the consumer sees a
+// ctx is cancelled — every goroutine in the pool abandons its blocking
-// truncated but properly terminated stream instead of a stalled one.
+// send in that case, so the consumer sees a truncated but properly
+// terminated stream instead of a stalled one.
 func startWalk(ctx context.Context, roots []string, oneFS bool,
 	workers int,
 ) <-chan walkEvent {
@@ -934,7 +1039,8 @@ func operandWarning(root string, fi fs.FileInfo) string {
 // operand becomes an initial job. walkableRoots has already dropped
 // every other operand. One that has changed into something else since
 // is warned about and skipped here; it is still a root, so the records
-// stored beneath it are deleted as unverified.
+// stored beneath it, other than those under another root, are deleted
+// as unverified.
 func seedRoot(ctx context.Context, root string,
 	events chan<- walkEvent,
 ) []dirJob {
@@ -966,7 +1072,7 @@ func seedRoot(ctx context.Context, root string,
 	sendEvent(ctx, events, walkEvent{rec: fileRec{
 		path:  root,
 		size:  fi.Size(),
-		mtime: fi.ModTime().Unix(),
+		mtime: fi.ModTime(),
 		dev:   dev,
 		ino:   ino,
 	}})
@@ -1124,7 +1230,7 @@ func emitFile(ctx context.Context, p string, e fs.DirEntry,
 	sendEvent(ctx, events, walkEvent{rec: fileRec{
 		path:  p,
 		size:  info.Size(),
-		mtime: info.ModTime().Unix(),
+		mtime: info.ModTime(),
 		dev:   dev,
 		ino:   ino,
 	}})
@@ -1133,7 +1239,9 @@ func emitFile(ctx context.Context, p string, e fs.DirEntry,
 // subdirJob applies the descent rules to directory p: never enter
 // .zfs (ZFS snapshot pseudo-dirs would list every file once per
 // snapshot), and with -x never enter a directory on a different
-// filesystem than its operand.
+// filesystem than its operand, sending an event that names it so the
+// scan keeps the records below it, except those below an operand at or
+// inside it.
 func subdirJob(ctx context.Context, p string, e fs.DirEntry,
 	parent dirJob, oneFS bool, events chan<- walkEvent,
 ) (dirJob, bool) {
@@ -1157,6 +1265,8 @@ func subdirJob(ctx context.Context, p string, e fs.DirEntry,
 	}
 
 	if dev, ok := deviceOfInfo(info); ok && dev != parent.rootDev {
+		sendEvent(ctx, events, walkEvent{otherFSDir: p})
+
 		return dirJob{}, false
 	}
 
@@ -1298,6 +1408,38 @@ func hashWorker(ctx context.Context, jobs <-chan []fileRec,
 	}
 }
 
+// errNotRegular reports a path that is no longer a regular file when it
+// is opened to be read.
+var errNotRegular = errors.New("not a regular file")
+
+// openRegularFile opens path for reading and returns it only if it is
+// still a regular file, since the path may have been replaced after it
+// was statted. O_NONBLOCK keeps the open of a FIFO or a device node
+// from waiting forever, and fstat then rejects it. Reads of a regular
+// file ignore O_NONBLOCK.
+func openRegularFile(path string) (*os.File, error) {
+	//nolint:gosec // hashing operator-supplied paths is the tool's purpose
+	f, err := os.OpenFile(path, os.O_RDONLY|syscall.O_NONBLOCK, 0)
+	if err != nil {
+		return nil, err
+	}
+
+	fi, err := f.Stat()
+	if err != nil {
+		_ = f.Close()
+
+		return nil, err
+	}
+
+	if !fi.Mode().IsRegular() {
+		_ = f.Close()
+
+		return nil, errNotRegular
+	}
+
+	return f, nil
+}
+
 // emptyHash is the lowercase-hex SHA-256 of the empty input: the head,
 // tail, and content hash of every zero-length file.
 const emptyHash = "e3b0c44298fc1c149afbf4c8996fb924" +
@@ -1320,8 +1462,7 @@ func hashSignature(path string, size int64) (string, string, string, error) {
 		return emptyHash, emptyHash, emptyHash, nil
 	}
 
-	//nolint:gosec // hashing operator-supplied paths is the tool's purpose
+	f, err := openRegularFile(path)
-	f, err := os.Open(path)
 	if err != nil {
 		return "", "", "", err
 	}
@@ -1352,8 +1493,7 @@ func hashSignature(path string, size int64) (string, string, string, error) {
 // tail are returned empty, because the content phase keeps the ones its
 // records already hold.
 func hashContentOnly(path string, size int64) (string, string, string, error) {
-	//nolint:gosec // hashing operator-supplied paths is the tool's purpose
+	f, err := openRegularFile(path)
-	f, err := os.Open(path)
 	if err != nil {
 		return "", "", "", err
 	}

scan_test.go

@@ -20,6 +20,8 @@ import (
 	"syscall"
 	"testing"
 	"time"
+
+	"golang.org/x/sys/unix"
 )
 
 // writeFile creates a file with the given content and returns its path.
@@ -581,6 +583,65 @@ func TestScanContentHashedStalePartners(t *testing.T) {
 	}
 }
 
+// TestScanContentSameSecondRewrite is TestScanContentStalePartners for
+// a stored file rewritten in place at the same size with an mtime later
+// in the same second than recorded: the file counts as changed, so
+// neither it nor its match inside the operand is read.
+func TestScanContentSameSecondRewrite(t *testing.T) {
+	t.Parallel()
+
+	db := openTestDB(t)
+	dirA := t.TempDir()
+	changed := sparseFileWithoutMatch(t, dirA, "changed", headTailMin)
+
+	first := time.Date(2026, 1, 2, 3, 4, 5, 100_000_000, time.UTC)
+
+	err := os.Chtimes(changed, first, first)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	syncTree(t, db, dirA)
+
+	before := dbRecords(t, db)
+
+	// Rewrite one byte in place, keeping the size.
+	pokeAt(t, changed, headTailMin/2, []byte{1})
+
+	later := first.Add(500 * time.Millisecond)
+
+	err = os.Chtimes(changed, later, later)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	dirB := t.TempDir()
+	sparseFile(t, dirB, "changed-copy", headTailMin)
+
+	st := syncTree(t, db, dirB)
+	if st != (scanStats{walked: 1, added: 1}) {
+		t.Errorf("stats = %+v, want 1 added and nothing skipped", st)
+	}
+
+	recs := dbRecords(t, db)
+	for _, r := range recs {
+		if r.content != "" {
+			t.Errorf("%s: content = %q, want none: its only match is stale",
+				r.path, r.content)
+		}
+	}
+
+	for _, old := range before {
+		if r := recordByPath(t, recs, old.path); r != old {
+			t.Errorf("record = %+v, want it left as %+v", r, old)
+		}
+	}
+
+	if groups := dupeGroups(t, db); len(groups) != 0 {
+		t.Errorf("groups = %+v, want none", groups)
+	}
+}
+
 // TestScanContentReadFailure checks that a failed content read is
 // counted as skipped and leaves the record without a content hash, and
 // that a later scan tries the read again.
@@ -783,8 +844,8 @@ func TestWalk(t *testing.T) {
 			t.Errorf("%s: size = %d, want 1..3", r.path, r.size)
 		}
 
-		if r.mtime <= 0 {
+		if r.mtime.Unix() <= 0 {
-			t.Errorf("%s: mtime = %d, want positive", r.path, r.mtime)
+			t.Errorf("%s: mtime = %v, want after 1970", r.path, r.mtime)
 		}
 	}
 }
@@ -936,7 +997,7 @@ func dirEntryFor(t *testing.T, dir, name string) fs.DirEntry {
 }
 
 // callSubdirJob runs subdirJob against e under parent, collecting any
-// warning events it emits (subdirJob emits at most one).
+// events it emits (subdirJob emits at most one).
 func callSubdirJob(t *testing.T, p string, e fs.DirEntry,
 	parent dirJob, oneFS bool,
 ) (dirJob, bool, []walkEvent) {
@@ -1014,8 +1075,15 @@ func TestSubdirJobOneFilesystem(t *testing.T) {
 				t.Fatalf("accepted = %v, want %v", ok, tc.wantOK)
 			}
 
-			if len(evs) != 0 {
+			// A refused descent names the directory, so the scan keeps
-				t.Fatalf("unexpected events: %+v", evs)
+			// the records below it.
+			var wantEvs []walkEvent
+			if !ok {
+				wantEvs = []walkEvent{{otherFSDir: sub}}
+			}
+
+			if !slices.Equal(evs, wantEvs) {
+				t.Fatalf("events = %+v, want %+v", evs, wantEvs)
 			}
 
 			// The accepted job must carry the operand's device down, or -x
@@ -1067,6 +1135,296 @@ func TestSubdirJobStatError(t *testing.T) {
 	}
 }
 
+// syncOneFilesystem scans roots into db with -x and returns the scan
+// stats. Every device pruneRoots looks up, and the device each
+// operand's walk compares its subdirectories with, comes from devices
+// instead of from lstat, so a test can put a path on a filesystem that
+// no directory here is on. Unlike runPhases, it skips walkableRoots,
+// the check for a cancelled walk, and the content phase.
+func syncOneFilesystem(t *testing.T, db *sql.DB, roots []string,
+	devices map[string]uint64,
+) scanStats {
+	t.Helper()
+
+	device := func(path string) (uint64, bool) {
+		dev, ok := devices[path]
+
+		return dev, ok
+	}
+
+	roots = pruneRoots(roots, true, device)
+
+	ctx := t.Context()
+	s := &scanState{db: db}
+
+	err := s.loadIndex(ctx, roots)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	jobs, subdirs, events := startWalkWorkers(ctx, 2, true)
+
+	// seedRoot emits a regular-file operand itself and returns a job
+	// only for a directory operand.
+	var initial []dirJob
+
+	for _, root := range roots {
+		for _, job := range seedRoot(ctx, root, events) {
+			job.rootDev = devices[root]
+			initial = append(initial, job)
+		}
+	}
+
+	dispatchDirs(ctx, initial, jobs, subdirs)
+
+	changed, unhashed := s.walkPhase(events, roots)
+	s.partition(changed, unhashed)
+
+	err = s.hashPhase(ctx, 2)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	err = s.updatePhase(ctx)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	return s.st
+}
+
+// TestScanOneFilesystemKeepsOtherFilesystemRecords checks that with -x a
+// record below a directory the walk does not enter, because it is on
+// another filesystem than its operand, counts as outside the operands:
+// it is not deleted, and its size joins the size census. The record of
+// a gone file that is not below that directory is still deleted, even
+// when its path begins with the directory's name. The operand is given
+// a device that no directory here is on, so no second real filesystem
+// is needed.
+func TestScanOneFilesystemKeepsOtherFilesystemRecords(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+
+	// A scan without -x records the file below mnt, and mnt2, which is
+	// beside mnt, not below it.
+	mounted := writeFile(t, dir, "mnt/f", pattern(1, 100))
+	gone := writeFile(t, dir, "mnt2", pattern(3, 50))
+	syncTree(t, db, dir)
+
+	err := os.Remove(gone)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	// The same size as mnt/f, so it is hashed only if mnt/f's size is
+	// in the census.
+	added := writeFile(t, dir, "added", pattern(2, 100))
+
+	info, err := os.Lstat(dir)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	dev, ok := deviceOfInfo(info)
+	if !ok {
+		t.Skip("platform exposes no device id")
+	}
+
+	syncOneFilesystem(t, db, []string{dir}, map[string]uint64{dir: dev + 1})
+
+	recs := dbRecords(t, db)
+	recordByPath(t, recs, mounted)
+
+	if recordByPath(t, recs, added).head == "" {
+		t.Errorf("%s not hashed: the census lacks the size of %s",
+			added, mounted)
+	}
+
+	if slices.Contains(recordPaths(recs), gone) {
+		t.Errorf("record for %s kept: the file is gone and not below mnt",
+			gone)
+	}
+}
+
+// TestScanOneFilesystemWalksNestedOperand checks that with -x an
+// operand under another one, on a different filesystem than it, is
+// walked on its own: a file added below it is recorded, and the record
+// of a file gone from below it is deleted. A record below a directory
+// that its own walk does not enter is still kept. Each operand is given
+// a device that no directory here is on, so neither walk enters a
+// subdirectory.
+func TestScanOneFilesystemWalksNestedOperand(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+
+	// A scan without -x records both files below mnt.
+	gone := writeFile(t, dir, "mnt/gone", pattern(1, 10))
+	kept := writeFile(t, dir, "mnt/sub/kept", pattern(2, 20))
+	syncTree(t, db, dir)
+
+	err := os.Remove(gone)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	added := writeFile(t, dir, "mnt/added", pattern(3, 30))
+
+	info, err := os.Lstat(dir)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	dev, ok := deviceOfInfo(info)
+	if !ok {
+		t.Skip("platform exposes no device id")
+	}
+
+	mnt := filepath.Join(dir, "mnt")
+	syncOneFilesystem(t, db, []string{dir, mnt},
+		map[string]uint64{dir: dev + 1, mnt: dev + 2})
+
+	paths := recordPaths(dbRecords(t, db))
+
+	if !slices.Contains(paths, added) {
+		t.Errorf("no record for %s: the walk did not reach %s", added, mnt)
+	}
+
+	if slices.Contains(paths, gone) {
+		t.Errorf("record for %s kept: the file is gone", gone)
+	}
+
+	if !slices.Contains(paths, kept) {
+		t.Errorf("record for %s deleted: the walk of %s did not enter %s",
+			kept, mnt, filepath.Dir(kept))
+	}
+}
+
+// TestScanOneFilesystemWalksOperandBelowOtherFilesystem checks that
+// with -x an operand on the same filesystem as the operand covering it
+// is walked on its own when a directory between them is on another
+// filesystem, since the walk of the covering operand does not enter
+// that directory: a file added below the nested operand is recorded,
+// and the record of a file gone from below it is deleted. A record
+// below that directory but outside the nested operand is still kept.
+// Both operands are given one device that no directory here is on,
+// while mnt keeps its own.
+func TestScanOneFilesystemWalksOperandBelowOtherFilesystem(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+
+	// A scan without -x records both files below mnt.
+	gone := writeFile(t, dir, "mnt/back/gone", pattern(1, 10))
+	kept := writeFile(t, dir, "mnt/kept", pattern(2, 20))
+	syncTree(t, db, dir)
+
+	err := os.Remove(gone)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	added := writeFile(t, dir, "mnt/back/added", pattern(3, 30))
+
+	info, err := os.Lstat(dir)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	dev, ok := deviceOfInfo(info)
+	if !ok {
+		t.Skip("platform exposes no device id")
+	}
+
+	mnt := filepath.Join(dir, "mnt")
+	back := filepath.Join(mnt, "back")
+	syncOneFilesystem(t, db, []string{dir, back},
+		map[string]uint64{dir: dev + 1, mnt: dev, back: dev + 1})
+
+	paths := recordPaths(dbRecords(t, db))
+
+	if !slices.Contains(paths, added) {
+		t.Errorf("no record for %s: the walk did not reach %s", added, back)
+	}
+
+	if slices.Contains(paths, gone) {
+		t.Errorf("record for %s kept: the file is gone", gone)
+	}
+
+	if !slices.Contains(paths, kept) {
+		t.Errorf("record for %s deleted: the walk of %s did not enter %s",
+			kept, dir, mnt)
+	}
+}
+
+// TestScanOneFilesystemRecordsNestedFileOnce checks that with -x a
+// regular-file operand under another operand is dropped when the file
+// reports a different device than that operand but its directory does
+// not, as a file bind-mounted into the tree does: the walk of the other
+// operand enters the directory and reaches the file, so the file is
+// recorded once.
+func TestScanOneFilesystemRecordsNestedFileOnce(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	file := writeFile(t, dir, "sub/f", pattern(1, 10))
+
+	info, err := os.Lstat(dir)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	dev, ok := deviceOfInfo(info)
+	if !ok {
+		t.Skip("platform exposes no device id")
+	}
+
+	st := syncOneFilesystem(t, db, []string{dir, file}, map[string]uint64{
+		dir: dev, filepath.Dir(file): dev, file: dev + 1,
+	})
+
+	if st.added != 1 {
+		t.Errorf("%s recorded %d times, want once", file, st.added)
+	}
+}
+
+// TestScanOneFilesystemWalksNestedFileOperand checks that with -x a
+// regular-file operand under another operand is kept when its directory
+// is on a different filesystem than that operand: the walk of the other
+// operand does not enter the directory, so the file is recorded once,
+// as its own operand. The other operand is given a device that no
+// directory here is on.
+func TestScanOneFilesystemWalksNestedFileOperand(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	file := writeFile(t, dir, "sub/f", pattern(1, 10))
+
+	info, err := os.Lstat(dir)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	dev, ok := deviceOfInfo(info)
+	if !ok {
+		t.Skip("platform exposes no device id")
+	}
+
+	st := syncOneFilesystem(t, db, []string{dir, file}, map[string]uint64{
+		dir: dev + 1, filepath.Dir(file): dev,
+	})
+
+	if st.added != 1 {
+		t.Errorf("%s recorded %d times, want once", file, st.added)
+	}
+}
+
 // buildSmokeTree recreates the README smoke-test filesystem layout
 // with deterministic content and returns the tree root.
 func buildSmokeTree(t *testing.T) string {
@@ -1285,11 +1643,172 @@ func TestSyncScanMtimeBump(t *testing.T) {
 		t.Fatalf("mtime-bump stats = %+v, want 1 updated", st)
 	}
 
-	if r := recordByPath(t, dbRecords(t, db), a); r.mtime != future.Unix() {
+	if r := recordByPath(t, dbRecords(t, db), a); !r.mtime.Equal(future) {
-		t.Fatalf("mtime = %d, want %d", r.mtime, future.Unix())
+		t.Fatalf("mtime = %v, want %v", r.mtime, future)
 	}
 }
 
+// assertWholeFileHashed fails unless the record for path holds the
+// whole-file hash of data as its head, tail, and content.
+func assertWholeFileHashed(t *testing.T, db *sql.DB, path string,
+	data []byte,
+) {
+	t.Helper()
+
+	r := recordByPath(t, dbRecords(t, db), path)
+	if want := hexSum(data); r.head != want || r.tail != want ||
+		r.content != want {
+		t.Fatalf("head, tail, content = %q, %q, %q, want %q for each",
+			r.head, r.tail, r.content, want)
+	}
+}
+
+// TestSyncScanSameSecondRewrite rewrites a file in place at the same
+// size with an mtime later in the same second as the recorded one: the
+// next scan must notice the change and re-hash the file.
+func TestSyncScanSameSecondRewrite(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	a := writeFile(t, dir, "a.bin", pattern(1, 500))
+
+	// b.bin shares the size of a.bin, so a.bin is hashed.
+	writeFile(t, dir, "b.bin", pattern(2, 500))
+
+	first := time.Date(2026, 1, 2, 3, 4, 5, 100_000_000, time.UTC)
+
+	err := os.Chtimes(a, first, first)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	syncTree(t, db, dir)
+
+	rewritten := pattern(3, 500)
+	writeFile(t, dir, "a.bin", rewritten)
+
+	later := first.Add(500 * time.Millisecond)
+
+	err = os.Chtimes(a, later, later)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	st := syncTree(t, db, dir)
+	if st != (scanStats{walked: 2, updated: 1, unchanged: 1}) {
+		t.Fatalf("rescan stats = %+v, want 1 updated 1 unchanged", st)
+	}
+
+	assertWholeFileHashed(t, db, a, rewritten)
+}
+
+// TestSyncScanOperandSameSecondRewrite is TestSyncScanSameSecondRewrite
+// for files given to scan as operands, which scan stats without reading
+// their directory.
+func TestSyncScanOperandSameSecondRewrite(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	a := writeFile(t, dir, "a.bin", pattern(1, 500))
+
+	// b.bin shares the size of a.bin, so a.bin is hashed.
+	b := writeFile(t, dir, "b.bin", pattern(2, 500))
+
+	first := time.Date(2026, 1, 2, 3, 4, 5, 100_000_000, time.UTC)
+
+	err := os.Chtimes(a, first, first)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	syncTree(t, db, a, b)
+
+	rewritten := pattern(3, 500)
+	writeFile(t, dir, "a.bin", rewritten)
+
+	later := first.Add(500 * time.Millisecond)
+
+	err = os.Chtimes(a, later, later)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	st := syncTree(t, db, a, b)
+	if st != (scanStats{walked: 2, updated: 1, unchanged: 1}) {
+		t.Fatalf("rescan stats = %+v, want 1 updated 1 unchanged", st)
+	}
+
+	assertWholeFileHashed(t, db, a, rewritten)
+}
+
+// TestSyncScanRewriteAfter2262 runs assertLateRewriteRehashed with an
+// mtime after 2262, a time too late to count in nanoseconds in an int64.
+func TestSyncScanRewriteAfter2262(t *testing.T) {
+	t.Parallel()
+
+	assertLateRewriteRehashed(t, time.Date(2300, 1, 2, 3, 4, 5, 0, time.UTC))
+}
+
+// TestSyncScanRewritePastTimeLimit runs assertLateRewriteRehashed with an
+// mtime one second past the latest a time.Time holds without wrapping it
+// to a time far in the past.
+func TestSyncScanRewritePastTimeLimit(t *testing.T) {
+	t.Parallel()
+
+	assertLateRewriteRehashed(t, time.Unix(9223371974719179008, 0))
+}
+
+// assertLateRewriteRehashed scans a directory, rewrites a file in it in
+// place at the same size, sets its mtime to late, and fails unless the
+// next scan re-hashes the file. It skips where late does not fit the
+// platform's timespec or the filesystem does not store it.
+func assertLateRewriteRehashed(t *testing.T, late time.Time) {
+	t.Helper()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	a := writeFile(t, dir, "a.bin", pattern(1, 500))
+
+	// b.bin shares the size of a.bin, so a.bin is hashed.
+	writeFile(t, dir, "b.bin", pattern(2, 500))
+
+	syncTree(t, db, dir)
+
+	rewritten := pattern(3, 500)
+	writeFile(t, dir, "a.bin", rewritten)
+
+	// os.Chtimes cannot set such a time: it converts through UnixNano.
+	ts, err := unix.TimeToTimespec(late)
+	if err != nil {
+		t.Skipf("an mtime %d seconds after 1970 does not fit this platform's "+
+			"timespec: %v", late.Unix(), err)
+	}
+
+	err = unix.UtimesNano(a, []unix.Timespec{ts, ts})
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	fi, err := os.Lstat(a)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	if fi.ModTime().Unix() != late.Unix() {
+		t.Skipf("the filesystem stored the mtime as %d seconds after 1970, "+
+			"not %d", fi.ModTime().Unix(), late.Unix())
+	}
+
+	st := syncTree(t, db, dir)
+	if st != (scanStats{walked: 2, updated: 1, unchanged: 1}) {
+		t.Fatalf("rescan stats = %+v, want 1 updated 1 unchanged", st)
+	}
+
+	assertWholeFileHashed(t, db, a, rewritten)
+}
+
 func TestSyncScanAddRemove(t *testing.T) {
 	t.Parallel()
 
@@ -1335,9 +1854,7 @@ func TestSyncScanSizeChange(t *testing.T) {
 
 	writeFile(t, dir, "f", pattern(1, 200))
 
-	mt := time.Unix(old.mtime, 0)
+	err := os.Chtimes(p, old.mtime, old.mtime)
-
-	err := os.Chtimes(p, mt, mt)
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -1577,6 +2094,54 @@ func TestScanHardlinkRunFailsTogether(t *testing.T) {
 	}
 }
 
+// TestHashPhaseSkipsFileReplacedByFIFO replaces a walked regular file
+// with a FIFO before the hash phase reads it. Opening a FIFO that has
+// no writer waits for one, so a blocking open would hang the phase. The
+// path must be warned about once and skipped, with no record written.
+//
+//nolint:paralleltest // captureStderr replaces the process-wide os.Stderr
+func TestHashPhaseSkipsFileReplacedByFIFO(t *testing.T) {
+	stderr := captureStderr(t)
+	dir := t.TempDir()
+	p := writeFile(t, dir, "a.bin", pattern(1, 300))
+
+	walked, _ := collectWalk(t, []string{dir}, false, 1)
+
+	err := os.Remove(p)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	err = unix.Mkfifo(p, 0o600)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	s := &scanState{db: openTestDB(t), toHash: walked}
+
+	err = s.hashPhase(t.Context(), 1)
+	if err != nil {
+		t.Fatalf("hashPhase = %v, want nil", err)
+	}
+
+	if s.st.skipped != 1 || len(s.batch) != 0 {
+		t.Errorf("skipped = %d, records = %d, want 1 skipped and none",
+			s.st.skipped, len(s.batch))
+	}
+
+	warning := "hash " + p + ": not a regular file\n"
+	if got := stderr(); strings.Count(got, warning) != 1 {
+		t.Errorf("stderr = %q, want %q once", got, warning)
+	}
+
+	// The content phase opens files the same way.
+	_, _, content, err := hashContentOnly(p, headTailMin)
+	if content != "" || !errors.Is(err, errNotRegular) {
+		t.Errorf("hashContentOnly on a FIFO = %q, %v; want no hash and %v",
+			content, err, errNotRegular)
+	}
+}
+
 // injectedWriteFailure is the message the injected database trigger
 // aborts with, so the test can recognize its own failure in the error
 // the scan reports.
@@ -1770,14 +2335,43 @@ func TestHashRuns(t *testing.T) {
 func TestPruneRoots(t *testing.T) {
 	t.Parallel()
 
+	const pqRoot = "/p/q"
+
+	// /p/q is on another filesystem than /p; /p/q/r is on the same one as
+	// /p/q, /p/s as /p, and /p/t has no known device.
+	devices := map[string]uint64{"/p": 1, pqRoot: 2, "/p/q/r": 2, "/p/s": 1}
+	device := func(path string) (uint64, bool) {
+		dev, ok := devices[path]
+
+		return dev, ok
+	}
+
 	// Duplicates and operands under other operands are dropped; /cc is
 	// not under /c (sibling with a shared prefix).
-	got := pruneRoots([]string{"/a/b", "/a", "/c", "/a", "/a/b/c", "/cc"})
+	got := pruneRoots([]string{"/a/b", "/a", "/c", "/a", "/a/b/c", "/cc"},
+		false, device)
 
 	want := []string{"/a", "/c", "/cc"}
 	if !slices.Equal(got, want) {
 		t.Fatalf("pruneRoots = %q, want %q", got, want)
 	}
+
+	nested := []string{"/p/q/r", pqRoot, "/p", "/p", "/p/s", "/p/t"}
+
+	got = pruneRoots(nested, false, device)
+
+	want = []string{"/p"}
+	if !slices.Equal(got, want) {
+		t.Fatalf("pruneRoots without -x = %q, want %q", got, want)
+	}
+
+	// With -x, /p/q, on another filesystem than /p, is kept as well.
+	got = pruneRoots(nested, true, device)
+
+	want = []string{"/p", pqRoot}
+	if !slices.Equal(got, want) {
+		t.Fatalf("pruneRoots with -x = %q, want %q", got, want)
+	}
 }
 
 func TestReportsNeverTouchFilesystem(t *testing.T) {