Leave removed copies out of report and trees (closes #173)

A deleted duplicate stayed in both reports until a scan covered it, and
a missing scan operand is a fatal error. report now runs lstat on each
path of a possible duplicate group and drops paths that are gone; trees
does the same for the directory at the top of each copy, never the
files inside. A group left with one copy is not reported. Only "does not
exist" and "not a directory" count as gone, so a permission error keeps
the copy for an unprivileged user. README says a stale report is fixed
by scanning again.

Model: opus-5-5

Makefile

@@ -4,7 +4,7 @@ export CGO_ENABLED = 0
 
 BINARY := sfdupes
 VERSION := $(shell git describe --tags --always --dirty 2>/dev/null || echo dev)
-LDFLAGS := -X main.Version=$(VERSION)
+LDFLAGS := -X sneak.berlin/go/sfdupes/internal/sfdupes.Version=$(VERSION)
 
 .PHONY: sfdupes build bootstrap setup test lint fmt fmt-check check docker hooks clean
 
@@ -14,7 +14,7 @@ LDFLAGS := -X main.Version=$(VERSION)
 # Default target: build the binary. Phony so go build (which has its
 # own build cache) always decides what to recompile.
 sfdupes:
-	go build -ldflags "$(LDFLAGS)" -o $(BINARY)
+	go build -ldflags "$(LDFLAGS)" -o $(BINARY) ./cmd/sfdupes
 
 build: sfdupes
 

cmd/sfdupes/main.go

@@ -0,0 +1,29 @@
+// Command sfdupes quickly identifies candidate duplicate files across
+// very large filesystems without reading every byte of every file.
+// Files are considered duplicates when their sizes are equal and they
+// agree on three SHA-256 hashes: of the first 64 KiB, of the last 64
+// KiB, and of the content. The content hash covers the whole file under
+// 100 MiB, and 1 MiB at each gigabyte at 100 MiB or more, so a large
+// file is never read in full. scan maintains a persistent SQLite
+// database of file signatures (SFDUPES_DATABASE, default
+// /var/lib/sfdupes/db.sqlite) that the other subcommands read.
+//
+// Usage:
+//
+//	sfdupes scan [--workers N] [-x] [--no-default-excludes] PATH...
+//	sfdupes report > dupes.tsv
+//	sfdupes trees > dupetrees.tsv
+//	sfdupes info
+//	sfdupes dwim
+//	sfdupes --version
+//
+// See README.md for the complete specification.
+package main
+
+import (
+	"os"
+
+	"sneak.berlin/go/sfdupes/internal/sfdupes"
+)
+
+func main() { os.Exit(sfdupes.Main()) }

internal/sfdupes/cancel_test.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes //nolint:testpackage // cancels the unexported runScan and hashWorker
 
 import (
 	"context"

internal/sfdupes/cli.go

@@ -1,23 +1,6 @@
-// Command sfdupes quickly identifies candidate duplicate files across
-// very large filesystems without reading every byte of every file.
-// Files are considered duplicates when their sizes are equal and they
-// agree on three SHA-256 hashes: of the first 64 KiB, of the last 64
-// KiB, and of the content. The content hash covers the whole file under
-// 100 MiB, and 1 MiB at each gigabyte at 100 MiB or more, so a large
-// file is never read in full. scan maintains a persistent SQLite
-// database of file signatures (SFDUPES_DATABASE, default
-// /var/lib/sfdupes/db.sqlite) that the other subcommands read.
-//
-// Usage:
-//
-//	sfdupes scan [--workers N] [-x] [--no-default-excludes] PATH...
-//	sfdupes report > dupes.tsv
-//	sfdupes trees > dupetrees.tsv
-//	sfdupes info
-//	sfdupes --version
-//
-// See README.md for the complete specification.
-package main
+// Package sfdupes implements the sfdupes command and the database its
+// subcommands share.
+package sfdupes
 
 import (
 	"context"
@@ -45,6 +28,7 @@ const (
 	cmdReport = "report"
 	cmdTrees  = "trees"
 	cmdInfo   = "info"
+	cmdDwim   = "dwim"
 )
 
 // errNoSubcommand is returned by the root command when it is invoked
@@ -84,20 +68,22 @@ func buildVersion(linkerVersion string, info *debug.BuildInfo) string {
 	return info.Main.Version
 }
 
-func main() {
+// Main runs the command line in os.Args and returns the process exit
+// code.
+func Main() int {
 	// Once the reader of a stdout pipe has gone, as in "sfdupes report |
 	// head", the Go runtime ends the process with SIGPIPE on the next
 	// write instead of returning an error (README "Error handling").
 	// Registering for SIGPIPE with os/signal would change that.
-	os.Exit(run(os.Args[1:], os.Stdout, os.Stderr))
+	return run(os.Args[1:], os.Stdout, os.Stderr)
 }
 
 // run executes args against the command tree and returns the process
 // exit code. It is the program's single exit point: the subcommands
 // return their errors instead of exiting, so every deferred cleanup —
 // above all closing the database, which checkpoints the SQLite WAL —
-// runs before the process ends. The report, trees and info subcommands
-// write their data to stdout.
+// runs before the process ends. The report, trees, info and dwim
+// subcommands write their data to stdout.
 func run(args []string, stdout, stderr io.Writer) int {
 	// A nil slice makes cobra fall back to os.Args, which would let a
 	// test binary's own flags reach the command tree.
@@ -201,7 +187,16 @@ func newRootCommand(stdout, stderr io.Writer) *cobra.Command {
 		}),
 	}
 
-	root.AddCommand(newScanCommand(), reportCmd, treesCmd, infoCmd)
+	dwimCmd := &cobra.Command{
+		Use:   cmdDwim,
+		Short: "Scan / with the default excludes, then print the duplicate-tree report",
+		Args:  cobra.NoArgs,
+		RunE: runE(func(ctx context.Context, _ []string) error {
+			return runDwim(ctx, "/", stdout)
+		}),
+	}
+
+	root.AddCommand(newScanCommand(), reportCmd, treesCmd, infoCmd, dwimCmd)
 
 	return root
 }

internal/sfdupes/cli_test.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes //nolint:testpackage // drives the unexported run
 
 import (
 	"bytes"
@@ -14,6 +14,8 @@ import (
 	"strconv"
 	"strings"
 	"testing"
+
+	"golang.org/x/sys/unix"
 )
 
 // usageMarker is the first line of cobra's usage text, which a usage
@@ -394,7 +396,7 @@ func TestRunNamesRelativeDatabase(t *testing.T) {
 }
 
 func TestRunUsesDatabaseThroughSymlinkedDirectory(t *testing.T) {
-	// README §Database: the path names the file exactly. With link a
+	// README §Settings: the path names the file exactly. With link a
 	// symlink to the directory real/sub, link/../db.sqlite names
 	// real/db.sqlite, not db.sqlite beside link. Every subcommand must
 	// use that file, relative or absolute, and its first line must name
@@ -620,6 +622,7 @@ func TestRunUsageErrors(t *testing.T) {
 		"report with args":   {[]string{cmdReport, "x"}, usageMarker},
 		"trees with args":    {[]string{cmdTrees, "x"}, usageMarker},
 		"info with args":     {[]string{cmdInfo, "x"}, usageMarker},
+		"dwim with args":     {[]string{cmdDwim, "x"}, usageMarker},
 		"unknown flag":       {[]string{cmdScan, "--nope", "/"}, usageMarker},
 		"unknown subcommand": {[]string{"nope"}, "unknown command"},
 	}
@@ -649,7 +652,7 @@ func TestRunUsageErrors(t *testing.T) {
 }
 
 func TestRunScanRejectsWorkersBelowOne(t *testing.T) {
-	// README §scan mode: --workers below 1 is a usage error reported in
+	// README §Settings: --workers below 1 is a usage error reported in
 	// one line on stderr, before the scan opens the database.
 	for _, workers := range []string{"0", "-1"} {
 		t.Run(workers, func(t *testing.T) {
@@ -687,8 +690,8 @@ func TestRunScanRejectsWorkersBelowOne(t *testing.T) {
 func TestRunHelp(t *testing.T) {
 	t.Parallel()
 
-	// README §Subcommands: help goes to stderr, exits 0, and leaves
-	// stdout empty.
+	// README §Settings: help goes to stderr, exits 0, and leaves stdout
+	// empty.
 	cases := [][]string{{"--help"}, {"-h"}, {cmdScan, "--help"}}
 
 	for _, args := range cases {
@@ -714,8 +717,8 @@ func TestRunHelp(t *testing.T) {
 func TestRunVersion(t *testing.T) {
 	t.Parallel()
 
-	// README §Subcommands: the version is one line on stdout, with
-	// nothing on stderr, and exits 0.
+	// README §Settings: the version is one line on stdout, with nothing
+	// on stderr, and exits 0.
 	info, _ := debug.ReadBuildInfo()
 
 	for _, arg := range []string{"--version", "-v"} {
@@ -774,8 +777,8 @@ func TestBuildVersion(t *testing.T) {
 func TestRunVersionWriteFailureIsFatal(t *testing.T) {
 	t.Parallel()
 
-	// README §Error handling: a stdout write failure exits 1, reported
-	// in one line on stderr.
+	// README §Error handling: a failed write to stdout is a fatal error,
+	// exit 1, reported on stderr starting with "sfdupes:".
 	var stderr bytes.Buffer
 
 	code := run([]string{"--version"}, failingWriter{}, &stderr)
@@ -797,7 +800,7 @@ func TestRunVersionWriteFailureIsFatal(t *testing.T) {
 func scanFixture(t *testing.T) []string {
 	t.Helper()
 
-	dir := t.TempDir()
+	dir := realTempDir(t)
 
 	dupes := []string{
 		writeFile(t, dir, "one/a.bin", pattern(1, 300)),
@@ -867,7 +870,7 @@ func TestRunScanSucceedsDespiteWarnings(t *testing.T) {
 	path := testDBPath(t)
 	t.Setenv(databaseEnv, path)
 
-	dir := t.TempDir()
+	dir := realTempDir(t)
 	writeFile(t, dir, "a.bin", pattern(1, 300))
 
 	// Same size as a.bin, so the scan reads it, and the read fails.
@@ -895,58 +898,278 @@ func TestRunScanSucceedsDespiteWarnings(t *testing.T) {
 	assertNoSidecars(t, path)
 }
 
-func TestRunScanSkipsSymlinkOperand(t *testing.T) {
-	path := testDBPath(t)
-	t.Setenv(databaseEnv, path)
+// realTempDir returns a new temporary directory by its real path, so
+// tests hold where the temporary directory is reached through a
+// symlink.
+func realTempDir(t *testing.T) string {
+	t.Helper()
 
-	dir := t.TempDir()
-	writeFile(t, dir, "target/sub/f", pattern(1, 10))
-
-	link := filepath.Join(dir, "link")
-
-	err := os.Symlink(filepath.Join(dir, "target"), link)
+	dir, err := filepath.EvalSymlinks(t.TempDir())
 	if err != nil {
 		t.Fatal(err)
 	}
 
-	// Scanning a directory through the symlink stores a record beneath
-	// the symlink's own path for a file beneath its target.
-	scanOK(t, filepath.Join(link, "sub"))
-
-	assertOperandSkipped(t, path, link, "symlink",
-		filepath.Join(link, "sub", "f"))
+	return dir
 }
 
+// symlink creates link pointing at target.
+func symlink(t *testing.T, target, link string) {
+	t.Helper()
+
+	err := os.Symlink(target, link)
+	if err != nil {
+		t.Fatal(err)
+	}
+}
+
+// TestRunScanFollowsSymlinkOperand scans link, a symlink to target.
+// The operand is scanned at its real path, and its file is recorded
+// there.
+func TestRunScanFollowsSymlinkOperand(t *testing.T) {
+	path := testDBPath(t)
+	t.Setenv(databaseEnv, path)
+
+	dir := realTempDir(t)
+	f := writeFile(t, dir, "target/sub/f", pattern(1, 10))
+
+	link := filepath.Join(dir, "link")
+	symlink(t, filepath.Join(dir, "target"), link)
+
+	stderr := scanOK(t, link)
+
+	summary := "scan: 1 files seen (1 added, 0 updated, 0 removed, " +
+		"0 unchanged), 0 skipped\n"
+	if !strings.Contains(stderr, summary) {
+		t.Errorf("stderr = %q, want %q", stderr, summary)
+	}
+
+	if got := storedPaths(t, path); !slices.Equal(got, []string{f}) {
+		t.Errorf("records = %q, want %q", got, []string{f})
+	}
+}
+
+// TestRunScanWalksOperandUnderSymlinkOperand scans link and link/sub,
+// with link a symlink to target. Both resolve under target, so
+// target/sub is walked once, as part of target.
 func TestRunScanWalksOperandUnderSymlinkOperand(t *testing.T) {
 	path := testDBPath(t)
 	t.Setenv(databaseEnv, path)
 
-	dir := t.TempDir()
-	writeFile(t, dir, "target/sub/f", pattern(1, 10))
+	dir := realTempDir(t)
+	f := writeFile(t, dir, "target/sub/f", pattern(1, 10))
 
 	link := filepath.Join(dir, "link")
+	symlink(t, filepath.Join(dir, "target"), link)
 
-	err := os.Symlink(filepath.Join(dir, "target"), link)
+	stderr := scanOK(t, link, filepath.Join(link, "sub"))
+
+	summary := "scan: 1 files seen (1 added, 0 updated, 0 removed, " +
+		"0 unchanged), 0 skipped\n"
+	if !strings.Contains(stderr, summary) {
+		t.Errorf("stderr = %q, want %q", stderr, summary)
+	}
+
+	if got := storedPaths(t, path); !slices.Equal(got, []string{f}) {
+		t.Errorf("records = %q, want %q", got, []string{f})
+	}
+}
+
+// TestRunScanWalksSymlinkedOperandBelowOperand is the case of
+// https://git.eeqj.de/sneak/sfdupes/issues/144: scan dir dir/link/sub,
+// with dir/link a symlink to a directory outside dir. The walk of dir
+// does not follow link, so dir/link/sub is walked on its own at its
+// real path, and the record an earlier scan stored there survives.
+func TestRunScanWalksSymlinkedOperandBelowOperand(t *testing.T) {
+	path := testDBPath(t)
+	t.Setenv(databaseEnv, path)
+
+	dir := realTempDir(t)
+	a := writeFile(t, dir, "a", pattern(1, 10))
+
+	outside := realTempDir(t)
+	f := writeFile(t, outside, "sub/f", pattern(2, 10))
+
+	symlink(t, outside, filepath.Join(dir, "link"))
+
+	scanOK(t, filepath.Join(outside, "sub"))
+
+	stderr := scanOK(t, dir, filepath.Join(dir, "link", "sub"))
+
+	summary := "scan: 2 files seen (1 added, 0 updated, 0 removed, " +
+		"1 unchanged), 0 skipped\n"
+	if !strings.Contains(stderr, summary) {
+		t.Errorf("stderr = %q, want %q", stderr, summary)
+	}
+
+	want := []string{a, f}
+	slices.Sort(want)
+
+	if got := storedPaths(t, path); !slices.Equal(got, want) {
+		t.Errorf("records = %q, want %q", got, want)
+	}
+}
+
+// TestRunScanDropsSymlinkOperandInsideOperand scans dir and link, with
+// link, outside dir, a symlink to dir/real. link resolves inside dir,
+// so it is dropped as covered by dir, and its file is recorded once.
+func TestRunScanDropsSymlinkOperandInsideOperand(t *testing.T) {
+	path := testDBPath(t)
+	t.Setenv(databaseEnv, path)
+
+	dir := realTempDir(t)
+	f := writeFile(t, dir, "real/f", pattern(1, 10))
+
+	link := filepath.Join(realTempDir(t), "link")
+	symlink(t, filepath.Join(dir, "real"), link)
+
+	stderr := scanOK(t, dir, link)
+
+	summary := "scan: 1 files seen (1 added, 0 updated, 0 removed, " +
+		"0 unchanged), 0 skipped\n"
+	if !strings.Contains(stderr, summary) {
+		t.Errorf("stderr = %q, want %q", stderr, summary)
+	}
+
+	if got := storedPaths(t, path); !slices.Equal(got, []string{f}) {
+		t.Errorf("records = %q, want %q", got, []string{f})
+	}
+}
+
+// TestRunScanDanglingSymlinkOperandIsFatal scans a valid directory and
+// a symlink whose target does not exist. The scan fails with exit 1 and
+// an error naming the symlink as given, before it walks anything, so no
+// database is created.
+func TestRunScanDanglingSymlinkOperandIsFatal(t *testing.T) {
+	path := testDBPath(t)
+	t.Setenv(databaseEnv, path)
+
+	dir := realTempDir(t)
+	writeFile(t, dir, "f", pattern(1, 10))
+
+	dangling := filepath.Join(realTempDir(t), "dangling")
+	symlink(t, filepath.Join(dir, "missing"), dangling)
+
+	stdout := captureStdout(t)
+
+	var stderr bytes.Buffer
+
+	code := run([]string{cmdScan, dir, dangling}, os.Stdout, &stderr)
+	if code != exitFatal {
+		t.Errorf("run(scan %s %s) = %d, want %d", dir, dangling, code,
+			exitFatal)
+	}
+
+	assertFatalOutput(t, stderr.String(), stdout())
+
+	want := "sfdupes: resolve " + dangling + ": "
+	if !strings.Contains(stderr.String(), want) {
+		t.Errorf("stderr = %q, want %q", stderr.String(), want)
+	}
+
+	_, err := os.Stat(path)
+	if !errors.Is(err, fs.ErrNotExist) {
+		t.Errorf("database: stat error %v, want it missing", err)
+	}
+}
+
+// TestRunScanFromSymlinkedWorkingDirectoryRecordsRealPath runs scan .
+// after a cd through home/proj, a symlink to data/proj. The file is
+// recorded under data/proj, its real path.
+func TestRunScanFromSymlinkedWorkingDirectoryRecordsRealPath(t *testing.T) {
+	path := testDBPath(t)
+	t.Setenv(databaseEnv, path)
+
+	dir := realTempDir(t)
+	f := writeFile(t, dir, "data/proj/f", pattern(1, 10))
+
+	err := os.Mkdir(filepath.Join(dir, "home"), 0o750)
 	if err != nil {
 		t.Fatal(err)
 	}
 
-	// link is dropped as a symlink, but link/sub must still be scanned,
-	// not dropped as lying under link.
-	scanOK(t, link, filepath.Join(link, "sub"))
+	symlink(t, filepath.Join(dir, "data", "proj"),
+		filepath.Join(dir, "home", "proj"))
 
-	db, err := openDB(path, reportParams)
+	// t.Chdir also sets PWD to the path through the symlink, as a
+	// shell does after cd.
+	t.Chdir(filepath.Join(dir, "home", "proj"))
+
+	scanOK(t, ".")
+
+	if got := storedPaths(t, path); !slices.Equal(got, []string{f}) {
+		t.Errorf("records = %q, want %q", got, []string{f})
+	}
+}
+
+// TestRunScanFollowsSymlinkBeforeDotDot scans a path with a ".." after
+// home/proj, a symlink to data/proj: home/proj/.. from dir, and .. after
+// a cd through home/proj. As with realpath, the ".." counts from
+// data/proj, so data is scanned and home is not.
+func TestRunScanFollowsSymlinkBeforeDotDot(t *testing.T) {
+	for _, tc := range []struct{ wd, operand string }{
+		{"", "home/proj/.."},
+		{"home/proj", ".."},
+	} {
+		t.Run(tc.operand, func(t *testing.T) {
+			path := testDBPath(t)
+			t.Setenv(databaseEnv, path)
+
+			dir := realTempDir(t)
+			f := writeFile(t, dir, "data/proj/f", pattern(1, 10))
+			g := writeFile(t, dir, "data/g", pattern(2, 10))
+			writeFile(t, dir, "home/h", pattern(3, 10))
+			symlink(t, filepath.Join(dir, "data", "proj"),
+				filepath.Join(dir, "home", "proj"))
+
+			// t.Chdir also sets PWD to the path given, as a shell does
+			// after cd.
+			t.Chdir(filepath.Join(dir, tc.wd))
+
+			scanOK(t, tc.operand)
+
+			want := []string{f, g}
+			slices.Sort(want)
+
+			if got := storedPaths(t, path); !slices.Equal(got, want) {
+				t.Errorf("records = %q, want %q", got, want)
+			}
+		})
+	}
+}
+
+// TestRunScanSkipsSymlinkToFIFOOperand scans link, a symlink to a FIFO.
+// The scan warns about the FIFO by its real path, counts it as skipped,
+// and exits 0.
+func TestRunScanSkipsSymlinkToFIFOOperand(t *testing.T) {
+	t.Setenv(databaseEnv, testDBPath(t))
+
+	dir := realTempDir(t)
+	fifo := filepath.Join(dir, "fifo")
+
+	err := unix.Mkfifo(fifo, 0o600)
 	if err != nil {
 		t.Fatal(err)
 	}
 
-	t.Cleanup(func() { _ = db.Close() })
+	link := filepath.Join(dir, "link")
+	symlink(t, fifo, link)
 
-	recordByPath(t, dbRecords(t, db), filepath.Join(link, "sub", "f"))
+	stderr := scanOK(t, link)
+
+	warning := "walk " + fifo + ": skipping FIFO operand\n"
+	if !strings.Contains(stderr, warning) {
+		t.Errorf("stderr = %q, want %q", stderr, warning)
+	}
+
+	summary := "scan: 0 files seen (0 added, 0 updated, 0 removed, " +
+		"0 unchanged), 1 skipped\n"
+	if !strings.Contains(stderr, summary) {
+		t.Errorf("stderr = %q, want %q", stderr, summary)
+	}
 }
 
 func TestRunScanSkipsZFSOperand(t *testing.T) {
-	zfs := filepath.Join(t.TempDir(), ".zfs")
+	zfs := filepath.Join(realTempDir(t), ".zfs")
 	f := writeFile(t, zfs, "snapshot/hourly/f", pattern(1, 10))
 
 	// No scan records a file inside a .zfs directory, so the record
@@ -997,7 +1220,7 @@ func TestRunScanSkipsOperandInsideZFS(t *testing.T) {
 	path := testDBPath(t)
 	t.Setenv(databaseEnv, path)
 
-	dir := t.TempDir()
+	dir := realTempDir(t)
 	hourly := filepath.Join(dir, ".zfs", "snapshot", "hourly")
 	writeFile(t, hourly, "f", pattern(1, 10))
 	f := writeFile(t, dir, "f", pattern(2, 10))
@@ -1041,23 +1264,19 @@ func TestRunScanSkipsOperandInsideZFS(t *testing.T) {
 
 // TestRunScanSkipsOperandThroughSymlinkIntoZFS scans snaps/daily, where
 // snaps is a symlink to pool/.zfs/snapshot. The operand is warned about
-// by the path given, counted as skipped, and not walked.
+// by its real path, counted as skipped, and not walked.
 func TestRunScanSkipsOperandThroughSymlinkIntoZFS(t *testing.T) {
 	t.Setenv(databaseEnv, testDBPath(t))
 
-	dir := t.TempDir()
+	dir := realTempDir(t)
 	writeFile(t, dir, "pool/.zfs/snapshot/daily/f", pattern(1, 10))
 
 	snaps := filepath.Join(dir, "snaps")
+	symlink(t, filepath.Join(dir, "pool", ".zfs", "snapshot"), snaps)
 
-	err := os.Symlink(filepath.Join(dir, "pool", ".zfs", "snapshot"), snaps)
-	if err != nil {
-		t.Fatal(err)
-	}
-
-	daily := filepath.Join(snaps, "daily")
-	stderr := scanOK(t, daily)
+	stderr := scanOK(t, filepath.Join(snaps, "daily"))
 
+	daily := filepath.Join(dir, "pool", ".zfs", "snapshot", "daily")
 	warning := "walk " + daily + ": skipping operand inside a .zfs directory\n"
 	summary := "scan: 0 files seen (0 added, 0 updated, 0 removed, " +
 		"0 unchanged), 1 skipped\n"
@@ -1069,24 +1288,19 @@ func TestRunScanSkipsOperandThroughSymlinkIntoZFS(t *testing.T) {
 }
 
 // TestRunScanWalksOperandThroughSymlink scans data/daily, where data is
-// a symlink to a directory outside any .zfs directory. The operand is
-// scanned as usual, and its file is recorded by the path given.
+// a symlink to pool/data. The operand is scanned as usual, and its file
+// is recorded by its real path.
 func TestRunScanWalksOperandThroughSymlink(t *testing.T) {
 	path := testDBPath(t)
 	t.Setenv(databaseEnv, path)
 
-	dir := t.TempDir()
-	writeFile(t, dir, "pool/data/daily/f", pattern(1, 10))
+	dir := realTempDir(t)
+	f := writeFile(t, dir, "pool/data/daily/f", pattern(1, 10))
 
 	data := filepath.Join(dir, "data")
+	symlink(t, filepath.Join(dir, "pool", "data"), data)
 
-	err := os.Symlink(filepath.Join(dir, "pool", "data"), data)
-	if err != nil {
-		t.Fatal(err)
-	}
-
-	daily := filepath.Join(data, "daily")
-	stderr := scanOK(t, daily)
+	stderr := scanOK(t, filepath.Join(data, "daily"))
 
 	summary := "scan: 1 files seen (1 added, 0 updated, 0 removed, " +
 		"0 unchanged), 0 skipped\n"
@@ -1094,14 +1308,9 @@ func TestRunScanWalksOperandThroughSymlink(t *testing.T) {
 		t.Errorf("stderr = %q, want %q", stderr, summary)
 	}
 
-	db, err := openDB(path, reportParams)
-	if err != nil {
-		t.Fatal(err)
+	if got := storedPaths(t, path); !slices.Equal(got, []string{f}) {
+		t.Errorf("records = %q, want %q", got, []string{f})
 	}
-
-	t.Cleanup(func() { _ = db.Close() })
-
-	recordByPath(t, dbRecords(t, db), filepath.Join(daily, "f"))
 }
 
 func TestRunReportSucceeds(t *testing.T) {
@@ -1257,7 +1466,7 @@ func assertRunsUseDatabase(t *testing.T, dir, name string) {
 }
 
 func TestRunDatabasePathUsedAsGiven(t *testing.T) {
-	// README §Database: the path names the database file exactly. In
+	// README §Settings: the path names the database file exactly. In
 	// SQLite's connection string an unescaped ? or # would end the file
 	// name and % would start an escape, and a path starting with //
 	// could be read as a host name. %25 is a valid escape, so unescaped
@@ -1302,9 +1511,8 @@ 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 opening the
-	// database.
+	// README §Database: a second scan that finds the lock held fails
+	// at once, naming the lock file, without opening the database.
 	path := testDBPath(t)
 	t.Setenv(databaseEnv, path)
 
@@ -1363,7 +1571,7 @@ func assertSecondScanFails(t *testing.T, path string) {
 }
 
 func TestRunSecondScanThroughSymlinkFails(t *testing.T) {
-	// README §Database: every path to one database names the same lock
+	// README §Database: a path through a symlink 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.
@@ -1468,8 +1676,8 @@ func TestRunReportsDuringScan(t *testing.T) {
 }
 
 func TestRunStdoutClosedIsFatal(t *testing.T) {
-	// README §Error handling: a stdout write failure exits 1, reported
-	// in one line on stderr.
+	// README §Error handling: a failed write to stdout is a fatal error,
+	// exit 1, reported on stderr starting with "sfdupes:".
 	for _, name := range []string{cmdReport, cmdTrees, cmdInfo} {
 		t.Run(name, func(t *testing.T) {
 			t.Setenv(databaseEnv, testDBPath(t))

internal/sfdupes/db.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes
 
 import (
 	"context"
@@ -146,33 +146,44 @@ var errHashSize = errors.New("hash is not 32 bytes")
 
 // databasePath resolves the database location: SFDUPES_DATABASE when
 // set and non-empty, the compiled-in default otherwise. It returns the
-// path, with the working directory, its symlinks resolved, put in front
-// of it when it is relative, and where the path came from, "default" or
-// "from SFDUPES_DATABASE", for the line each subcommand prints first on
-// stderr.
+// path, made absolute by absolutePath, and where the path came from,
+// "default" or "from SFDUPES_DATABASE", for the line each subcommand
+// prints first on stderr.
 func databasePath() (string, string, error) {
 	path, source := defaultDatabasePath, "default"
 	if p := os.Getenv(databaseEnv); p != "" {
 		path, source = p, "from "+databaseEnv
 	}
 
-	if filepath.IsAbs(path) {
-		return path, source, nil
-	}
-
-	// The working directory as the kernel reports it, with no symlink
-	// in it, as README "Database" says. os.Getwd may return PWD
-	// instead, which can name it through a symlink.
-	wd, err := unix.Getwd()
+	abs, err := absolutePath(path)
 	if err != nil {
 		return "", "", fmt.Errorf("resolve database path %s: %w", path, err)
 	}
 
-	// Not filepath.Abs or filepath.Join: they clean the path, which
-	// drops each ".." together with the directory name before it. When
-	// that directory is a symlink, the cleaned path names another file.
+	return abs, source, nil
+}
+
+// absolutePath returns path unchanged when it is absolute, and
+// otherwise the working directory, a "/" and path. The working
+// directory is the one the kernel reports, with no symlink in it;
+// os.Getwd may return PWD instead, which can name it through a symlink.
+// The result is not cleaned, as filepath.Abs and filepath.Join would
+// clean it. Cleaning drops each ".." together with the directory name
+// before it. When that name is a symlink, the cleaned path names
+// another file than the one the system reaches by following the symlink
+// first.
+func absolutePath(path string) (string, error) {
+	if filepath.IsAbs(path) {
+		return path, nil
+	}
+
+	wd, err := unix.Getwd()
+	if err != nil {
+		return "", err
+	}
+
 	// The working directory ends in "/" only when it is the root.
-	return strings.TrimSuffix(wd, "/") + "/" + path, source, nil
+	return strings.TrimSuffix(wd, "/") + "/" + path, nil
 }
 
 // createDatabaseDirectory creates the directory the database at path

internal/sfdupes/db_test.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes //nolint:testpackage // calls the unexported database openers
 
 import (
 	"context"

internal/sfdupes/dwim.go

@@ -0,0 +1,37 @@
+package sfdupes
+
+import (
+	"context"
+	"fmt"
+	"io"
+	"os"
+	"runtime"
+)
+
+// runDwim implements the dwim subcommand: it runs what "sfdupes scan
+// root" runs with no flags, then what "sfdupes trees" runs, and ends
+// with a line on stderr saying how to print the report again. The dwim
+// command passes "/" as root. It catches SIGINT and SIGTERM as scan
+// does, but only during the scan. An error from the scan, an interrupt
+// included, ends it before the report. During the report, a signal
+// ends it at once, as it ends trees.
+func runDwim(ctx context.Context, root string, stdout io.Writer) error {
+	scanCtx, stop := interruptContext(ctx)
+	err := runScan(scanCtx, []string{root}, runtime.NumCPU(), false, false)
+
+	stop()
+
+	if err != nil {
+		return err
+	}
+
+	err = runTrees(ctx, stdout)
+	if err != nil {
+		return err
+	}
+
+	fmt.Fprintln(os.Stderr,
+		`dwim: run "sfdupes trees" to print this report again`)
+
+	return nil
+}

internal/sfdupes/dwim_test.go

@@ -0,0 +1,83 @@
+package sfdupes //nolint:testpackage // calls the unexported runDwim
+
+import (
+	"bytes"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestRunDwimPrintsLargestTreesFirst(t *testing.T) {
+	// dwim scans its root, then prints the trees report, the larger of
+	// two duplicate-tree pairs first, and ends by saying how to print
+	// the report again.
+	t.Setenv(databaseEnv, testDBPath(t))
+
+	root := realTempDir(t)
+
+	small := []string{
+		filepath.Dir(writeFile(t, root, "a1/f.bin", pattern(1, 300))),
+		filepath.Dir(writeFile(t, root, "a2/f.bin", pattern(1, 300))),
+	}
+	large := []string{
+		filepath.Dir(writeFile(t, root, "b1/f.bin", pattern(2, 5000))),
+		filepath.Dir(writeFile(t, root, "b2/f.bin", pattern(2, 5000))),
+	}
+
+	var stdout bytes.Buffer
+
+	stderr := captureStderr(t)
+
+	err := runDwim(t.Context(), root, &stdout)
+	if err != nil {
+		t.Fatalf("runDwim: %v; stderr: %s", err, stderr())
+	}
+
+	lines := strings.Split(strings.TrimSuffix(stdout.String(), "\n"), "\n")
+	if len(lines) != 3 {
+		t.Fatalf("stdout = %q, want a header and two groups",
+			stdout.String())
+	}
+
+	wantFirst := large[0] + "\t" + large[1] + "\t1\t5000\t"
+	if !strings.HasPrefix(lines[1], wantFirst) {
+		t.Errorf("first group = %q, want it to start %q", lines[1], wantFirst)
+	}
+
+	wantSecond := small[0] + "\t" + small[1] + "\t1\t300\t"
+	if !strings.HasPrefix(lines[2], wantSecond) {
+		t.Errorf("second group = %q, want it to start %q",
+			lines[2], wantSecond)
+	}
+
+	last := "\ndwim: run \"sfdupes trees\" to print this report again\n"
+	if got := stderr(); !strings.HasSuffix(got, last) {
+		t.Errorf("stderr = %q, want it to end %q", got, last)
+	}
+}
+
+func TestRunDwimScanErrorPrintsNoReport(t *testing.T) {
+	// A fatal scan error ends dwim before the report: a root that does
+	// not exist fails the scan as it fails scan itself.
+	t.Setenv(databaseEnv, testDBPath(t))
+
+	missing := filepath.Join(realTempDir(t), "missing")
+
+	var stdout bytes.Buffer
+
+	stderr := captureStderr(t)
+
+	err := runDwim(t.Context(), missing, &stdout)
+	if err == nil {
+		t.Fatal("runDwim on a missing root: error = nil, want it fatal")
+	}
+
+	if got := stdout.String(); got != "" {
+		t.Errorf("stdout = %q, want no report", got)
+	}
+
+	if got := stderr(); strings.Contains(got, "trees:") ||
+		strings.Contains(got, "dwim:") {
+		t.Errorf("stderr = %q, want nothing from trees or dwim", got)
+	}
+}

internal/sfdupes/exclude.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes
 
 // This file holds two rules for the walk (README "Rules for the walk"):
 // the default excludes, the paths a scan's walk does not enter below an

internal/sfdupes/exclude_darwin.go

@@ -1,6 +1,6 @@
 //go:build darwin
 
-package main
+package sfdupes
 
 import (
 	"slices"

internal/sfdupes/exclude_other.go

@@ -1,6 +1,6 @@
 //go:build !darwin
 
-package main
+package sfdupes
 
 import (
 	"fmt"

internal/sfdupes/exclude_test.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes //nolint:testpackage // checks the unexported defaultExcludes
 
 import (
 	"bytes"
@@ -17,7 +17,9 @@ import (
 func TestDefaultExcludes(t *testing.T) {
 	t.Parallel()
 
-	// README "Rules for the walk": each system's list.
+	// README "Rules for the walk": the Linux and macOS lists, and none
+	// on any other system. The Windows list exists in the code only: the
+	// binary does not build for Windows, so the README leaves it out.
 	cases := map[string][]string{
 		goosLinux: {"/proc", "/sys", "/dev", "/run", "/tmp", "/var/tmp"},
 		goosDarwin: {
@@ -284,7 +286,7 @@ func TestRunScanTempDirOperand(t *testing.T) {
 	path := testDBPath(t)
 	t.Setenv(databaseEnv, path)
 
-	dir := t.TempDir()
+	dir := realTempDir(t)
 	if !underAnyRoot(dir, defaultExcludes(runtime.GOOS)) {
 		t.Skip(dir + " is not inside a default exclude")
 	}

internal/sfdupes/info.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes
 
 import (
 	"context"

internal/sfdupes/info_test.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes //nolint:testpackage // seeds the database with unexported scanRec
 
 import (
 	"fmt"

internal/sfdupes/progress.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes
 
 import (
 	"fmt"

internal/sfdupes/progress_test.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes //nolint:testpackage // drives the unexported startProgress
 
 import (
 	"fmt"
@@ -642,9 +642,9 @@ func TestTerminalStalledLines(t *testing.T) {
 		{label: scanPhase("hash"), stalledOn: hashStalledOn},
 		{label: scanPhase("update"), stalledOn: "db"},
 		{label: treesPhase("read"), stalledOn: "db"},
-		{label: treesPhase("group"), stalledOn: "cpu"},
+		{label: treesPhase("group"), stalledOn: "cpu/disk"},
 		{label: treesPhase("write"), stalledOn: "out"},
-		{label: reportPhase("read"), stalledOn: "db/out"},
+		{label: reportPhase("read"), stalledOn: "db/disk/out"},
 	}
 
 	for _, params := range phases {

internal/sfdupes/report.go

@@ -1,14 +1,17 @@
-package main
+package sfdupes
 
 import (
 	"context"
 	"crypto/sha256"
 	"database/sql"
+	"errors"
 	"fmt"
 	"io"
+	"io/fs"
 	"os"
 	"slices"
 	"strings"
+	"syscall"
 	"time"
 )
 
@@ -41,10 +44,10 @@ func reportPhase(name string) string {
 }
 
 // runReport implements the report subcommand: it prints the file-level
-// duplicates report as TSV on stdout. It never touches the scanned
-// filesystem; its only I/O is the database, stdout, and stderr. It
-// names the database on stderr before it opens it. Any database
-// problem, including a missing database, is fatal.
+// duplicates report as TSV on stdout. Of the scanned filesystem it
+// only checks, with pathExists, that each path in a duplicate group is
+// still there. It names the database on stderr before it opens it. Any
+// database problem, including a missing database, is fatal.
 //
 // The work runs in two phases, each under a progress display of its
 // own on stderr: open (open the database) and read (read the number of
@@ -77,13 +80,14 @@ func runReport(ctx context.Context, stdout io.Writer) error {
 
 	defer func() { _ = db.Close() }()
 
-	// The read phase writes the report to stdout while it reads the
-	// records, so it may wait on either.
+	// The read phase checks the paths of each duplicate group on disk
+	// and writes the report to stdout while it reads the records, so it
+	// may wait on any of the three.
 	prog = newProgress(progressParams{
 		label: reportPhase("read"), unit: "records", total: -1,
-		waitingFor: countingRecords, stalledOn: "db/out",
+		waitingFor: countingRecords, stalledOn: "db/disk/out",
 	})
-	report, err := readReport(ctx, db, dbPath, stdout, prog)
+	report, err := readReport(ctx, db, dbPath, stdout, pathExists, prog)
 
 	prog.finish()
 
@@ -104,14 +108,15 @@ func runReport(ctx context.Context, stdout io.Writer) error {
 // dbPath, as its total, then reads every record in signature order,
 // counting each on prog, and writes the report to stdout: the header
 // line, then the rows of each size's duplicate groups once that size is
-// read. stdout may be the terminal prog is drawn on, so the lines go
-// through prog's writer. It returns what it wrote, with the totals for
-// the summary line.
+// read. A path for which exists returns false is left out of its group.
+// stdout may be the terminal prog is drawn on, so the lines go through
+// prog's writer. It returns what it wrote, with the totals for the
+// summary line.
 func readReport(ctx context.Context, db *sql.DB, dbPath string,
-	stdout io.Writer, prog *progress,
+	stdout io.Writer, exists func(path string) bool, prog *progress,
 ) (*reportWriter, error) {
 	out := prog.writer(stdout)
-	report := &reportWriter{out: out}
+	report := &reportWriter{out: out, exists: exists}
 
 	_, err := fmt.Fprintln(out, "first\tdupe\tsize")
 	if err != nil {
@@ -158,6 +163,10 @@ func readReport(ctx context.Context, db *sql.DB, dbPath string,
 type reportWriter struct {
 	out io.Writer
 
+	// exists reports whether a path is still on disk. A path that is
+	// gone is left out of its group.
+	exists func(path string) bool
+
 	sig    scanRec    // the signature being read; its path is not used
 	paths  []string   // the paths read so far with sig
 	groups [][]string // the duplicate groups of sig.size, each sorted
@@ -194,11 +203,20 @@ func (w *reportWriter) add(r scanRec) error {
 	return nil
 }
 
-// endGroup ends the paths read with w.sig: two or more are a duplicate
-// group, held with its paths sorted until writeGroups writes it.
+// endGroup ends the paths read with w.sig: two or more that are still
+// on disk are a duplicate group, held with its paths sorted until
+// writeGroups writes it. Empty files form no group, since removing one
+// frees nothing. Only the paths of a possible group are checked, never
+// a path with no duplicate or an empty file.
 func (w *reportWriter) endGroup() {
-	if len(w.paths) < minGroupSize {
-		// A path with no duplicate is dropped, and its slice reused.
+	if len(w.paths) >= minGroupSize && w.sig.size > 0 {
+		w.paths = slices.DeleteFunc(w.paths, func(p string) bool {
+			return !w.exists(p)
+		})
+	}
+
+	if len(w.paths) < minGroupSize || w.sig.size == 0 {
+		// The paths are dropped, and their slice reused.
 		w.paths = w.paths[:0]
 
 		return
@@ -245,6 +263,16 @@ func (w *reportWriter) finish() error {
 	return w.writeGroups()
 }
 
+// pathExists reports whether path is still on disk, for report and
+// trees. It is false only when lstat finds that the path, or a
+// directory above it, is gone. Any other error counts as present, so
+// a user who may not look inside a directory still sees its copies.
+func pathExists(path string) bool {
+	_, err := os.Lstat(path)
+
+	return !errors.Is(err, fs.ErrNotExist) && !errors.Is(err, syscall.ENOTDIR)
+}
+
 // escapePath returns a path as it is written in a report column (README
 // "Report output format"): a backslash, tab, newline or carriage return
 // becomes \\, \t, \n or \r, and every other byte is kept as it is.

internal/sfdupes/report_test.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes //nolint:testpackage // checks the unexported dupeGroup results
 
 import (
 	"bytes"
@@ -72,15 +72,37 @@ type dupeGroup struct {
 	paths []string
 }
 
+// everyPathExists stands in for pathExists where a test's records name
+// made-up paths that are not on disk.
+func everyPathExists(string) bool { return true }
+
+// recsOnDisk returns a new directory and recs with each path moved
+// under it, after creating an empty file at each moved path: report and
+// trees then find every path still on disk.
+func recsOnDisk(t *testing.T, recs []scanRec) (string, []scanRec) {
+	t.Helper()
+
+	dir := realTempDir(t)
+	moved := make([]scanRec, len(recs))
+
+	for i, r := range recs {
+		r.path = writeFile(t, dir, r.path, nil)
+		moved[i] = r
+	}
+
+	return dir, moved
+}
+
 // dupeGroups returns the duplicate groups report reads from db, in
 // report order, from the rows it writes: a group's rows come together,
-// each naming the group's first path.
+// each naming the group's first path. Every path counts as still on
+// disk.
 func dupeGroups(t *testing.T, db *sql.DB) []dupeGroup {
 	t.Helper()
 
 	var out bytes.Buffer
 
-	_, err := readReport(t.Context(), db, "", &out, nil)
+	_, err := readReport(t.Context(), db, "", &out, everyPathExists, nil)
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -127,7 +149,8 @@ func dupeGroupsOf(t *testing.T, recs []scanRec) []dupeGroup {
 }
 
 func TestRunReportEscapesPaths(t *testing.T) {
-	t.Setenv(databaseEnv, seedDatabase(t, awkwardPairRecs()))
+	dir, recs := recsOnDisk(t, awkwardPairRecs())
+	t.Setenv(databaseEnv, seedDatabase(t, recs))
 
 	var stdout, stderr bytes.Buffer
 
@@ -138,7 +161,7 @@ func TestRunReportEscapesPaths(t *testing.T) {
 	}
 
 	want := "first\tdupe\tsize\n" +
-		`/d/\tone\ntwo\rthree\\four/f` + "\t/d/A/f\t5\n"
+		dir + `/d/\tone\ntwo\rthree\\four/f` + "\t" + dir + "/d/A/f\t5\n"
 	if got := stdout.String(); got != want {
 		t.Errorf("stdout = %q, want %q", got, want)
 	}
@@ -172,7 +195,8 @@ func TestReportStdoutFailsWhileReading(t *testing.T) {
 	// Counts the records read, and draws nothing.
 	prog := &progress{now: time.Now}
 
-	_, err = readReport(t.Context(), db, "", failingWriter{}, prog)
+	_, err = readReport(t.Context(), db, "", failingWriter{},
+		everyPathExists, prog)
 	if !errors.Is(err, errWriteFailed) ||
 		!strings.HasPrefix(err.Error(), "write stdout: ") {
 		t.Errorf("error = %v, want write stdout: %v", err, errWriteFailed)
@@ -203,7 +227,8 @@ const smokeReport = "first\tdupe\tsize\n" +
 // it ends; read counts the 6 records before it reads them. The summary
 // comes last, and stdout holds the report alone.
 func TestRunReportProgressNamesEachPhase(t *testing.T) {
-	path := seedDatabase(t, smokeTreeRecs())
+	dir, recs := recsOnDisk(t, smokeTreeRecs())
+	path := seedDatabase(t, recs)
 	t.Setenv(databaseEnv, path)
 
 	stderr := captureStderr(t)
@@ -216,8 +241,9 @@ func TestRunReportProgressNamesEachPhase(t *testing.T) {
 			code, exitOK, stderr())
 	}
 
-	if got := stdout.String(); got != smokeReport {
-		t.Errorf("stdout = %q, want %q", got, smokeReport)
+	report := strings.ReplaceAll(smokeReport, "/d/", dir+"/d/")
+	if got := stdout.String(); got != report {
+		t.Errorf("stdout = %q, want %q", got, report)
 	}
 
 	// How each line starts; the rate at the end of a phase varies.
@@ -266,7 +292,7 @@ func TestReadReportOnTerminal(t *testing.T) {
 		waitingFor: countingRecords,
 	}, terminalWidth, time.Hour, time.Now)
 
-	_, err = readReport(t.Context(), db, "", os.Stderr, p)
+	_, err = readReport(t.Context(), db, "", os.Stderr, everyPathExists, p)
 
 	p.finish()
 
@@ -301,6 +327,8 @@ func TestRunReportsIgnoreInsertionOrder(t *testing.T) {
 		scanRec{size: 50, head: a, tail: a, content: a, path: "/x/1"},
 	)
 
+	_, recs = recsOnDisk(t, recs)
+
 	reversed := slices.Clone(recs)
 	slices.Reverse(reversed)
 
@@ -434,6 +462,71 @@ func TestDupeGroups(t *testing.T) {
 	}
 }
 
+// TestDupeGroupsLeavesOutEmptyFiles checks that empty files form no
+// duplicate group, while 1-byte files still do.
+func TestDupeGroupsLeavesOutEmptyFiles(t *testing.T) {
+	t.Parallel()
+
+	e, x := sha256.Sum256(nil), testHash("x")
+	recs := []scanRec{
+		{size: 0, head: e, tail: e, content: e, path: "/a/.gitkeep"},
+		{size: 0, head: e, tail: e, content: e, path: "/b/.gitkeep"},
+		{size: 0, head: e, tail: e, content: e, path: "/c/__init__.py"},
+		{size: 1, head: x, tail: x, content: x, path: "/tiny1"},
+		{size: 1, head: x, tail: x, content: x, path: "/tiny2"},
+	}
+
+	groups := dupeGroupsOf(t, recs)
+	if len(groups) != 1 || groups[0].size != 1 ||
+		!slices.Equal(groups[0].paths, []string{"/tiny1", "/tiny2"}) {
+		t.Fatalf("groups = %+v, want only /tiny1 /tiny2 of size 1", groups)
+	}
+}
+
+// TestReadReportChecksOnlyPossibleDuplicates checks that report asks
+// whether a path is on disk only when its signature has two or more
+// records, and never for an empty file.
+func TestReadReportChecksOnlyPossibleDuplicates(t *testing.T) {
+	t.Parallel()
+
+	a, u, e := testHash("a"), testHash("u"), sha256.Sum256(nil)
+	recs := []scanRec{
+		{size: 9, head: a, tail: a, content: a, path: "/x/1"},
+		{size: 9, head: a, tail: a, content: a, path: "/x/2"},
+		{size: 9, head: a, tail: a, content: a, path: "/x/3"},
+		{size: 9, head: u, tail: u, content: u, path: "/lonely"},
+		{size: 0, head: e, tail: e, content: e, path: "/empty1"},
+		{size: 0, head: e, tail: e, content: e, path: "/empty2"},
+	}
+
+	db := openTestDB(t)
+
+	err := applyChanges(t.Context(), db, recs, nil, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	var checked []string
+
+	exists := func(path string) bool {
+		checked = append(checked, path)
+
+		return true
+	}
+
+	_, err = readReport(t.Context(), db, "", io.Discard, exists, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	slices.Sort(checked)
+
+	want := []string{"/x/1", "/x/2", "/x/3"}
+	if !slices.Equal(checked, want) {
+		t.Errorf("paths checked on disk = %q, want %q", checked, want)
+	}
+}
+
 func TestDupeGroupsContentSeparates(t *testing.T) {
 	t.Parallel()
 

internal/sfdupes/scan.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes
 
 import (
 	"cmp"
@@ -209,29 +209,30 @@ func interrupted(walked int) error {
 	return errInterrupted
 }
 
-// resolveRoots converts each PATH operand to an absolute, lexically
-// cleaned path (symlinks are not resolved) and verifies that it
-// exists. Database records are keyed by absolute path, so scan results
-// must not depend on the working directory.
+// resolveRoots converts each PATH operand to its real path: absolute,
+// with every symlink in it followed. Database records are keyed by
+// that path, so scan results depend neither on the working directory
+// nor on the symlinks an operand was given through. An operand that
+// cannot be resolved, because it or a symlink's target does not exist
+// or cannot be read, is a fatal error before any scanning.
 func resolveRoots(roots []string) ([]string, error) {
-	abs := make([]string, 0, len(roots))
+	resolved := make([]string, 0, len(roots))
 
 	for _, root := range roots {
-		a, err := filepath.Abs(root)
+		a, err := absolutePath(root)
 		if err != nil {
 			return nil, fmt.Errorf("resolve %s: %w", root, err)
 		}
 
-		// A nonexistent operand is a fatal error before any scanning.
-		_, err = os.Lstat(a)
+		r, err := filepath.EvalSymlinks(a)
 		if err != nil {
-			return nil, err
+			return nil, fmt.Errorf("resolve %s: %w", root, err)
 		}
 
-		abs = append(abs, a)
+		resolved = append(resolved, r)
 	}
 
-	return abs, nil
+	return resolved, nil
 }
 
 // pruneRoots drops operands already covered by another operand:
@@ -417,14 +418,16 @@ 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, none of them inside a
-// directory 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 are treated as if it had not been given:
-// those under no other root count as outside the roots and are not
-// deleted as unverified. An operand on a filesystem in rules that is not
-// persistent is dropped the same way, with a line saying so that is not
-// a warning, and is not counted as skipped. An operand that fails lstat
-// here is kept, and the walk warns about it unless it no longer exists.
+// directory named .zfs. The operands are real paths from resolveRoots,
+// so these checks apply to what a symlink operand points at. 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
+// are treated as if it had not been given: those under no other root
+// count as outside the roots and are not deleted as unverified. An
+// operand on a filesystem in rules that is not persistent is dropped
+// the same way, with a line saying so that is not a warning, and is not
+// counted as skipped. An operand that fails lstat here is kept, and the
+// walk warns about it unless it no longer exists.
 func (s *scanState) walkableRoots(roots []string, rules walkRules) []string {
 	kept := make([]string, 0, len(roots))
 
@@ -554,7 +557,7 @@ func (s *scanState) walkPhase(events <-chan walkEvent, roots []string) {
 
 		// The space a file takes on disk can change while its size and
 		// mtime stay the same. ZFS, for one, counts a new file's blocks
-		// only seconds after the write.
+		// up to seconds after the write.
 		if old.diskSize != ev.rec.diskSize {
 			s.diskSizes = append(s.diskSizes, ev.rec)
 		}
@@ -894,19 +897,13 @@ func sendEvent(ctx context.Context, events chan<- walkEvent,
 // operandWarning returns the one-line warning for an operand the walk
 // does not start from, naming the path and what it is, or "" for one it
 // does: a regular file, or a directory not named .zfs, that is not
-// inside a directory named .zfs, neither as given nor with its symlinks
-// resolved. Symlinks are never followed, including as operands.
+// inside a directory named .zfs. resolveRoots has already followed the
+// operand's symlinks, so a symlink here is an operand replaced by one
+// after it was resolved, and is not followed.
 func operandWarning(root string, fi fs.FileInfo) string {
 	// The walk never enters a .zfs directory, so it starts from nothing
-	// inside one either, not even through a symlink. An operand whose
-	// symlinks cannot be resolved is checked as given.
-	resolved, err := filepath.EvalSymlinks(root)
-	if err != nil {
-		resolved = root
-	}
-
-	if slices.Contains(strings.Split(filepath.Dir(root), "/"), ".zfs") ||
-		slices.Contains(strings.Split(filepath.Dir(resolved), "/"), ".zfs") {
+	// inside one either.
+	if slices.Contains(strings.Split(filepath.Dir(root), "/"), ".zfs") {
 		return fmt.Sprintf("walk %s: skipping operand inside a .zfs directory",
 			root)
 	}

internal/sfdupes/scan_dev_darwin.go

@@ -1,6 +1,6 @@
 //go:build darwin
 
-package main
+package sfdupes
 
 import "syscall"
 

internal/sfdupes/scan_dev_other.go

@@ -1,6 +1,6 @@
 //go:build !darwin
 
-package main
+package sfdupes
 
 import "syscall"
 

internal/sfdupes/scan_test.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes //nolint:testpackage // drives the unexported syncTree
 
 import (
 	"bytes"
@@ -43,10 +43,16 @@ func writeFile(t *testing.T, dir, name string, data []byte) string {
 }
 
 // diskSizeOf returns the bytes the file at path takes on disk, from its
-// own lstat: st_blocks counts 512-byte units. ZFS counts a new file's
-// blocks only seconds after the write, and fsync does not hasten that.
-// A test therefore calls unix.Sync, which waits for it, before the scan
-// whose disk_size it compares with this.
+// own lstat: st_blocks counts 512-byte units. ZFS counts a write's
+// blocks only when it commits the write, up to seconds later, and one
+// commit can take the file through several growing sizes. So this value
+// can change at any moment. Neither fsync nor unix.Sync hastens that,
+// but a unix.Sync call often takes long enough that the blocks are
+// counted when it returns. A test that needs the value to change waits
+// for the change. A test that compares it with a scan's disk_size reads
+// it before and after the scan. The rewrite test rescans until the two
+// reads match, then compares exactly. The other two tests fail only on
+// a disk_size outside the two reads.
 func diskSizeOf(t *testing.T, path string) int64 {
 	t.Helper()
 
@@ -1082,12 +1088,13 @@ func TestScanOneFilesystemWalksNestedFileOperand(t *testing.T) {
 	}
 }
 
-// buildSmokeTree recreates the README smoke-test filesystem layout
-// with deterministic content and returns the tree root.
+// buildSmokeTree recreates the tree of the test under README
+// "Definition of done" with deterministic content and returns the tree
+// root.
 func buildSmokeTree(t *testing.T) string {
 	t.Helper()
 
-	dir := t.TempDir()
+	dir := realTempDir(t)
 	one := pattern(10, 2000)
 	f1 := pattern(30, 3000)
 	f2 := pattern(40, 100)
@@ -1178,11 +1185,12 @@ func assertSmokeDupeGroups(t *testing.T, dir string, db *sql.DB) {
 	t.Helper()
 
 	groups := dupeGroups(t, db)
-	if len(groups) != 5 {
-		t.Fatalf("len(groups) = %d, want 5", len(groups))
+	if len(groups) != 4 {
+		t.Fatalf("len(groups) = %d, want 4", len(groups))
 	}
 
-	wantSizes := []int64{3000, 2000, 100, 1, 0}
+	// The empty files empty1 and empty2 form no group.
+	wantSizes := []int64{3000, 2000, 100, 1}
 	for i, g := range groups {
 		if g.size != wantSizes[i] {
 			t.Errorf("groups[%d].size = %d, want %d",
@@ -1207,7 +1215,7 @@ func assertSmokeTreeGroups(t *testing.T, dir string, db *sql.DB) {
 
 	super, dirs := dbTree(t, db)
 
-	tg := collectTreeGroups(dirs, super, nil)
+	tg := collectTreeGroups(dirs, super, everyPathExists, nil)
 	if len(tg) != 1 {
 		t.Fatalf("len(tree groups) = %d, want 1", len(tg))
 	}
@@ -1447,20 +1455,26 @@ func TestScanStoresDiskSize(t *testing.T) {
 
 	unix.Sync() // see diskSizeOf
 
-	want := diskSizeOf(t, p)
-	if want == 0 || want >= length {
+	size := diskSizeOf(t, p)
+	if size == 0 || size >= length {
 		t.Fatalf("the file takes %d bytes on disk, want more than none "+
-			"and fewer than its length %d", want, length)
+			"and fewer than its length %d", size, length)
 	}
 
 	for _, operand := range []string{filepath.Dir(p), p} {
 		db := openTestDB(t)
+
+		// ZFS may count the blocks during the scan; see diskSizeOf.
+		before := diskSizeOf(t, p)
+
 		syncTree(t, db, operand)
 
+		after := diskSizeOf(t, p)
+
 		got := recordByPath(t, dbRecords(t, db), p).diskSize
-		if got != want {
-			t.Errorf("scan of %s: disk_size = %d, want %d",
-				operand, got, want)
+		if got < before || got > after {
+			t.Errorf("scan of %s: disk_size = %d, want %d to %d",
+				operand, got, before, after)
 		}
 	}
 }
@@ -1478,7 +1492,7 @@ func TestSyncScanRewriteUpdatesDiskSize(t *testing.T) {
 
 	syncTree(t, db, dir)
 
-	before := recordByPath(t, dbRecords(t, db), p).diskSize
+	recorded := recordByPath(t, dbRecords(t, db), p).diskSize
 
 	pokeAt(t, p, 512*1024, pattern(7, 64*1024))
 
@@ -1491,22 +1505,53 @@ func TestSyncScanRewriteUpdatesDiskSize(t *testing.T) {
 		t.Fatal(err)
 	}
 
-	unix.Sync() // see diskSizeOf
+	// Wait for ZFS to count the write; see diskSizeOf.
+	deadline := time.Now().Add(30 * time.Second)
+	for diskSizeOf(t, p) == recorded {
+		if time.Now().After(deadline) {
+			t.Fatalf("the file still takes %d bytes on disk 30 seconds "+
+				"after the write into its hole", recorded)
+		}
 
-	want := diskSizeOf(t, p)
-	if want == before {
-		t.Fatalf("the file still takes %d bytes on disk after the write "+
-			"into its hole", want)
+		unix.Sync()
 	}
 
-	st := syncTree(t, db, dir)
-	if st != (scanStats{walked: 1, updated: 1}) {
-		t.Fatalf("rescan stats = %+v, want 1 updated", st)
-	}
+	// ZFS may still be counting, so the size may change during a rescan.
+	// Only a rescan with the same size on both sides of it can be compared
+	// exactly. A rescan that keeps the old size still fails, because the
+	// wait made before differ from it.
+	for {
+		before := diskSizeOf(t, p)
 
-	got := recordByPath(t, dbRecords(t, db), p).diskSize
-	if got != want {
-		t.Errorf("disk_size = %d, want %d", got, want)
+		st := syncTree(t, db, dir)
+
+		after := diskSizeOf(t, p)
+
+		if st != (scanStats{walked: 1, updated: 1}) {
+			t.Fatalf("rescan stats = %+v, want 1 updated", st)
+		}
+
+		if before == after {
+			got := recordByPath(t, dbRecords(t, db), p).diskSize
+			if got != after {
+				t.Errorf("disk_size = %d, want %d", got, after)
+			}
+
+			return
+		}
+
+		if time.Now().After(deadline) {
+			t.Fatalf("the size on disk was still changing 30 seconds after "+
+				"the write into its hole: %d, then %d", before, after)
+		}
+
+		// A later mtime makes the next rescan read the file again.
+		later = later.Add(time.Second)
+
+		err = os.Chtimes(p, later, later)
+		if err != nil {
+			t.Fatal(err)
+		}
 	}
 }
 
@@ -1532,15 +1577,21 @@ func TestSyncScanUnchangedUpdatesDiskSize(t *testing.T) {
 
 	unix.Sync() // see diskSizeOf
 
+	// ZFS may count the blocks during the rescan; see diskSizeOf.
+	before := diskSizeOf(t, p)
+
 	// A file read again would count as updated.
 	st := syncTree(t, db, dir)
+
+	after := diskSizeOf(t, p)
+
 	if st != (scanStats{walked: 1, unchanged: 1}) {
 		t.Fatalf("rescan stats = %+v, want 1 unchanged", st)
 	}
 
 	got := recordByPath(t, dbRecords(t, db), p).diskSize
-	if want := diskSizeOf(t, p); got != want {
-		t.Errorf("disk_size = %d, want %d", got, want)
+	if got < before || got > after {
+		t.Errorf("disk_size = %d, want %d to %d", got, before, after)
 	}
 }
 
@@ -2215,23 +2266,86 @@ func TestPruneRoots(t *testing.T) {
 	}
 }
 
-func TestReportsNeverTouchFilesystem(t *testing.T) {
-	t.Parallel()
+// TestRunReportsLeaveOutRemovedCopies scans the smoke tree, then
+// removes copies the reports name. report leaves out each removed file,
+// and a group left with one path. trees checks only the root of each
+// duplicate tree: with a file under t2 removed it still names t2, and
+// with t2 removed it names nothing.
+func TestRunReportsLeaveOutRemovedCopies(t *testing.T) {
+	t.Setenv(databaseEnv, testDBPath(t))
 
 	dir := buildSmokeTree(t)
-	db := openTestDB(t)
+	p := func(name string) string { return filepath.Join(dir, name) }
 
-	syncTree(t, db, dir)
+	scanOK(t, dir)
 
-	// Remove the scanned tree entirely; the analysis must be
-	// unaffected because it reads the database alone.
-	err := os.RemoveAll(dir)
+	for _, name := range []string{"b/copy2.bin", "tiny2", "t2/sub/f2"} {
+		err := os.Remove(p(name))
+		if err != nil {
+			t.Fatal(err)
+		}
+	}
+
+	want := "first\tdupe\tsize\n" +
+		p("t1/f1") + "\t" + p("t2/f1") + "\t3000\n" +
+		p("t1/f1") + "\t" + p("t3/f1") + "\t3000\n" +
+		p("a/one.bin") + "\t" + p("b/copy.bin") + "\t2000\n" +
+		p("t1/sub/f2") + "\t" + p("t3/sub/f2renamed") + "\t100\n"
+	if got := runStdout(t, cmdReport); got != want {
+		t.Errorf("report stdout = %q, want %q", got, want)
+	}
+
+	// disk_size, the last column, depends on the filesystem.
+	header := "first\tdupe\tfiles\tsize\tdisk_size\n"
+
+	want = header + p("t1") + "\t" + p("t2") + "\t2\t3100\t"
+	if got := runStdout(t, cmdTrees); !strings.HasPrefix(got, want) ||
+		strings.Count(got, "\n") != 2 {
+		t.Errorf("trees stdout = %q, want one row starting %q", got, want)
+	}
+
+	err := os.RemoveAll(p("t2"))
 	if err != nil {
 		t.Fatal(err)
 	}
 
-	assertSmokeDupeGroups(t, dir, db)
-	assertSmokeTreeGroups(t, dir, db)
+	if got := runStdout(t, cmdTrees); got != header {
+		t.Errorf("trees stdout after removing t2 = %q, want %q", got, header)
+	}
+}
+
+func TestPathExists(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	file := writeFile(t, dir, "file", nil)
+	locked := writeFile(t, dir, "locked/file", nil)
+
+	// Without search permission on its directory, a file cannot be
+	// looked at by anyone but root.
+	err := os.Chmod(filepath.Dir(locked), 0)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	// Runs before t.TempDir's own cleanup, which must delete the files.
+	t.Cleanup(func() {
+		//nolint:gosec // removing the directory needs its search bit back
+		_ = os.Chmod(filepath.Dir(locked), 0o700)
+	})
+
+	cases := map[string]bool{
+		dir:                                 true,
+		file:                                true,
+		locked:                              true,
+		filepath.Join(dir, "gone"):          false,
+		filepath.Join(file, "under-a-file"): false,
+	}
+	for path, want := range cases {
+		if got := pathExists(path); got != want {
+			t.Errorf("pathExists(%q) = %v, want %v", path, got, want)
+		}
+	}
 }
 
 func TestUnderRoot(t *testing.T) {
@@ -2260,33 +2374,24 @@ func TestUnderRoot(t *testing.T) {
 }
 
 // TestRunScanPassesOverDatabase scans a tree that holds the scan's own
-// database, reached directly and through a symlinked directory. The
-// walk passes over the database file, its -wal and -shm files and its
-// .lock file with no line and no count, and the record an earlier scan
-// left for the .lock file is deleted. A rescan of the unchanged tree
-// updates nothing, and report lists none of the database's files.
+// database, and in one case also a hard link to the database file. The
+// walk knows the database's files by device ID and inode number, so it
+// passes over the database file, its -wal and -shm files, its .lock
+// file and the hard link with no line and no count. The record an
+// earlier scan left for the .lock file is deleted. A rescan of the
+// unchanged tree updates nothing, and report lists none of the
+// database's files.
 func TestRunScanPassesOverDatabase(t *testing.T) {
-	for _, viaSymlink := range []bool{false, true} {
-		t.Run(fmt.Sprintf("via symlink %v", viaSymlink), func(t *testing.T) {
-			base := t.TempDir()
-			tree := filepath.Join(base, "real", "tree")
-			operand := tree
+	for _, viaHardLink := range []bool{false, true} {
+		t.Run(fmt.Sprintf("via hard link %v", viaHardLink), func(t *testing.T) {
+			tree := realTempDir(t)
+			hardLink := filepath.Join(tree, "hardlink")
 
 			writeFile(t, tree, "a", pattern(1, 100))
 			writeFile(t, tree, "b", pattern(1, 100))
 			writeFile(t, tree, "empty1", nil)
 			writeFile(t, tree, "empty2", nil)
 
-			if viaSymlink {
-				err := os.Symlink(filepath.Join(base, "real"),
-					filepath.Join(base, "link"))
-				if err != nil {
-					t.Fatal(err)
-				}
-
-				operand = filepath.Join(base, "link", "tree")
-			}
-
 			dbPath := filepath.Join(tree, "db.sqlite")
 			t.Setenv(databaseEnv, dbPath)
 
@@ -2296,7 +2401,7 @@ func TestRunScanPassesOverDatabase(t *testing.T) {
 			}
 
 			err = applyChanges(t.Context(), db, []scanRec{
-				{path: filepath.Join(operand, "db.sqlite.lock")},
+				{path: filepath.Join(tree, "db.sqlite.lock")},
 			}, nil, nil)
 			if err != nil {
 				t.Fatal(err)
@@ -2304,17 +2409,30 @@ func TestRunScanPassesOverDatabase(t *testing.T) {
 
 			closeScanDatabase(t.Context(), db, dbPath)
 
-			assertScanSummary(t,
+			if viaHardLink {
+				err = os.Link(dbPath, hardLink)
+				if err != nil {
+					t.Fatal(err)
+				}
+			}
+
+			stderr := assertScanSummary(t,
 				"4 files seen (4 added, 0 updated, 1 removed, 0 unchanged)",
-				operand)
-			assertScanSummary(t,
+				tree)
+			stderr += assertScanSummary(t,
 				"4 files seen (0 added, 0 updated, 0 removed, 4 unchanged)",
-				operand)
+				tree)
+
+			if strings.Contains(stderr, hardLink) {
+				t.Errorf("scan stderr = %q, want no line naming %s",
+					stderr, hardLink)
+			}
 
 			report := runStdout(t, cmdReport)
 			if strings.Contains(report, "db.sqlite") ||
-				!strings.Contains(report, filepath.Join(operand, "empty2")) {
-				t.Errorf("report = %q, want the empty files and none of "+
+				strings.Contains(report, hardLink) ||
+				!strings.Contains(report, filepath.Join(tree, "b")) {
+				t.Errorf("report = %q, want a and b and none of "+
 					"the database's files", report)
 			}
 		})
@@ -2338,8 +2456,9 @@ func TestRunScanPassesOverDatabaseOperands(t *testing.T) {
 
 // assertScanSummary scans operands and fails the test unless the
 // summary line gives counts with nothing skipped, and the line naming
-// the database is the only one that names one of its files.
-func assertScanSummary(t *testing.T, counts string, operands ...string) {
+// the database is the only one that names one of its files. It returns
+// everything the scan printed to stderr.
+func assertScanSummary(t *testing.T, counts string, operands ...string) string {
 	t.Helper()
 
 	stderr := scanOK(t, operands...)
@@ -2353,4 +2472,6 @@ func assertScanSummary(t *testing.T, counts string, operands ...string) {
 		t.Errorf("scan %q: stderr = %q, want only the line naming the "+
 			"database to name one of its files", operands, stderr)
 	}
+
+	return stderr
 }

internal/sfdupes/trees.go

@@ -1,4 +1,4 @@
-package main
+package sfdupes
 
 import (
 	"context"
@@ -38,10 +38,11 @@ func treesPhase(name string) string {
 // runTrees implements the trees subcommand: it reads every record from
 // the database in path order, reconstructs the directory hierarchy from
 // the record paths, computes a Merkle-style digest per directory, and
-// prints maximal duplicate-tree groups as TSV on stdout. It never
-// touches the scanned filesystem; its only I/O is the database, stdout,
-// and stderr. It names the database on stderr before it opens it. Any
-// database problem, including a missing database, is fatal.
+// prints maximal duplicate-tree groups as TSV on stdout. Of the scanned
+// filesystem it only checks, with pathExists, that the root of each
+// duplicate tree is still there, never the files below it. It names the
+// database on stderr before it opens it. Any database problem,
+// including a missing database, is fatal.
 //
 // The work runs in four phases, each under a progress display of its
 // own on stderr: open (open the database), read (read the number of
@@ -86,13 +87,13 @@ func runTrees(ctx context.Context, stdout io.Writer) error {
 		return fmt.Errorf("database %s: %w", dbPath, err)
 	}
 
-	// Grouping works in memory, so it waits on nothing but the
-	// processor.
+	// Grouping works in memory, then checks the root of each duplicate
+	// tree on disk, so it waits on the processor or the disk.
 	prog = newProgress(progressParams{
 		label: treesPhase("group"), unit: "directories",
-		total: int64(len(allDirs)), stalledOn: "cpu",
+		total: int64(len(allDirs)), stalledOn: "cpu/disk",
 	})
-	dupes := collectTreeGroups(allDirs, super, prog)
+	dupes := collectTreeGroups(allDirs, super, pathExists, prog)
 
 	prog.finish()
 
@@ -300,10 +301,14 @@ func fileEntry(name string, r scanRec) string {
 
 // collectTreeGroups groups directories by digest, counting each one on
 // prog as it is grouped, and returns every maximal group with two or
-// more members, each group's members sorted by path, groups ordered by
-// tree size descending then by first path ascending.
+// more members for which exists returns true, each group's members
+// sorted by path, groups ordered by tree size descending then by first
+// path ascending. A group whose trees hold 0 bytes is left out, since
+// removing one frees nothing. The groups it implies hold 0 bytes too,
+// so leaving it out hides nothing. exists is called only on the members
+// of maximal groups.
 func collectTreeGroups(allDirs []*treeNode, super *treeNode,
-	prog *progress,
+	exists func(path string) bool, prog *progress,
 ) [][]*treeNode {
 	groups := make(map[[sha256.Size]byte][]*treeNode)
 	for _, d := range allDirs {
@@ -315,7 +320,19 @@ func collectTreeGroups(allDirs []*treeNode, super *treeNode,
 	var dupes [][]*treeNode
 
 	for _, g := range groups {
-		if len(g) < minGroupSize || suppressed(g, super) {
+		// The members share a digest, so they share a total size.
+		if len(g) < minGroupSize || g[0].totalSize == 0 ||
+			suppressed(g, super) {
+			continue
+		}
+
+		// A member that is gone leaves the group. A suppressed group is
+		// still implied: its members still on disk have parents still
+		// on disk, and those parents' group is checked the same way.
+		g = slices.DeleteFunc(g, func(n *treeNode) bool {
+			return !exists(n.path)
+		})
+		if len(g) < minGroupSize {
 			continue
 		}
 

internal/sfdupes/trees_test.go

@@ -1,10 +1,12 @@
-package main
+package sfdupes //nolint:testpackage // checks the unexported treeNode results
 
 import (
 	"bytes"
+	"crypto/sha256"
 	"database/sql"
 	"os"
 	"slices"
+	"strconv"
 	"strings"
 	"testing"
 	"time"
@@ -15,9 +17,9 @@ import (
 const treesOpenLine = "[1/4] open: opening the database, elapsed 0s, " +
 	"remain unknown"
 
-// smokeTreeRecs mirrors the README smoke-test tree layout: /d/t1 and
-// /d/t2 are identical, /d/t3 differs from them only by one filename.
-// Each file takes one 4 KiB block on disk.
+// smokeTreeRecs mirrors the tree of the test under README "Definition
+// of done": /d/t1 and /d/t2 are identical, /d/t3 differs from them only
+// by one filename. Each file takes one 4 KiB block on disk.
 func smokeTreeRecs() []scanRec {
 	f1Head, f1Tail, f1Content := testHash("f1h"), testHash("f1t"), testHash("f1c")
 	f2Head, f2Tail, f2Content := testHash("f2h"), testHash("f2t"), testHash("f2c")
@@ -178,7 +180,7 @@ func TestTreeNamesSortingBeforeSlash(t *testing.T) {
 		t.Fatalf("directory paths = %q, want %q", got, want)
 	}
 
-	groups := collectTreeGroups(dirs, super, nil)
+	groups := collectTreeGroups(dirs, super, everyPathExists, nil)
 
 	gotGroups := groupPaths(groups)
 	wantGroups := [][]string{{"/a", "/c"}}
@@ -194,7 +196,8 @@ func TestTreeNamesSortingBeforeSlash(t *testing.T) {
 }
 
 func TestRunTreesEscapesPaths(t *testing.T) {
-	t.Setenv(databaseEnv, seedDatabase(t, awkwardPairRecs()))
+	dir, recs := recsOnDisk(t, awkwardPairRecs())
+	t.Setenv(databaseEnv, seedDatabase(t, recs))
 
 	var stdout, stderr bytes.Buffer
 
@@ -205,7 +208,7 @@ func TestRunTreesEscapesPaths(t *testing.T) {
 	}
 
 	want := "first\tdupe\tfiles\tsize\tdisk_size\n" +
-		`/d/\tone\ntwo\rthree\\four` + "\t/d/A\t1\t5\t4096\n"
+		dir + `/d/\tone\ntwo\rthree\\four` + "\t" + dir + "/d/A\t1\t5\t4096\n"
 	if got := stdout.String(); got != want {
 		t.Errorf("stdout = %q, want %q", got, want)
 	}
@@ -223,9 +226,11 @@ func TestRunTreesDiskSize(t *testing.T) {
 		{size: 20, diskSize: 1024, head: g, tail: g, content: g, path: "/b/sub/g"},
 	}
 
+	dir, recs := recsOnDisk(t, recs)
 	t.Setenv(databaseEnv, seedDatabase(t, recs))
 
-	want := "first\tdupe\tfiles\tsize\tdisk_size\n/a\t/b\t2\t30\t1536\n"
+	want := "first\tdupe\tfiles\tsize\tdisk_size\n" +
+		dir + "/a\t" + dir + "/b\t2\t30\t1536\n"
 	if got := runStdout(t, cmdTrees); got != want {
 		t.Errorf("stdout = %q, want %q", got, want)
 	}
@@ -236,10 +241,11 @@ func TestRunTreesDiskSize(t *testing.T) {
 // there. After the line naming the database, each phase prints a line
 // naming it with its place among the four as it starts and another as
 // it ends. read counts the 6 records before it reads them, group counts
-// the 8 directories, and write the 1 group. The summary comes last, and
+// the directories, and write the 1 group. The summary comes last, and
 // stdout holds the report alone.
 func TestRunTreesProgressNamesEachPhase(t *testing.T) {
-	path := seedDatabase(t, smokeTreeRecs())
+	dir, recs := recsOnDisk(t, smokeTreeRecs())
+	path := seedDatabase(t, recs)
 	t.Setenv(databaseEnv, path)
 
 	stderr := captureStderr(t)
@@ -253,11 +259,15 @@ func TestRunTreesProgressNamesEachPhase(t *testing.T) {
 	}
 
 	report := "first\tdupe\tfiles\tsize\tdisk_size\n" +
-		"/d/t1\t/d/t2\t2\t3100\t8192\n"
+		dir + "/d/t1\t" + dir + "/d/t2\t2\t3100\t8192\n"
 	if got := stdout.String(); got != report {
 		t.Errorf("stdout = %q, want %q", got, report)
 	}
 
+	// The smoke-test records name 8 directories, / included. Moved under
+	// dir, they name one more for each slash in dir.
+	dirs := strconv.Itoa(8 + strings.Count(dir, "/"))
+
 	// How each line starts; the rate at the end of a phase varies.
 	want := []string{
 		"trees: database " + path + " (from " + databaseEnv + ")",
@@ -265,8 +275,9 @@ func TestRunTreesProgressNamesEachPhase(t *testing.T) {
 		treesOpenLine,
 		"[2/4] read: counting the records, elapsed 0s, remain unknown",
 		"[2/4] read: [6/6] 100%, ",
-		"[3/4] group: [0/8] 0%, 0 directories/s, elapsed 0s, remain unknown",
-		"[3/4] group: [8/8] 100%, ",
+		"[3/4] group: [0/" + dirs + "] 0%, 0 directories/s, elapsed 0s, " +
+			"remain unknown",
+		"[3/4] group: [" + dirs + "/" + dirs + "] 100%, ",
 		"[4/4] write: [0/1] 0%, 0 groups/s, elapsed 0s, remain unknown",
 		"[4/4] write: [1/1] 100%, ",
 		"trees: 6 records read, 1 duplicate tree groups, 1 dupe trees, ",
@@ -295,7 +306,7 @@ func TestRunTreesProgressNamesEachPhase(t *testing.T) {
 func TestWriteTreeGroupsOnTerminal(t *testing.T) {
 	stderr := captureStderr(t)
 	super, dirs := treeOf(t, smokeTreeRecs())
-	dupes := collectTreeGroups(dirs, super, nil)
+	dupes := collectTreeGroups(dirs, super, everyPathExists, nil)
 
 	// No timed draws: the display is drawn as it starts and as it ends.
 	p := startProgress(progressParams{
@@ -376,7 +387,7 @@ func TestCollectTreeGroupsMaximal(t *testing.T) {
 
 	super, dirs := treeOf(t, smokeTreeRecs())
 
-	groups := collectTreeGroups(dirs, super, nil)
+	groups := collectTreeGroups(dirs, super, everyPathExists, nil)
 
 	want := [][]string{{"/d/t1", "/d/t2"}}
 	if got := groupPaths(groups); !slices.EqualFunc(got, want,
@@ -400,14 +411,16 @@ func TestCollectTreeGroupsDeterministic(t *testing.T) {
 
 	super, dirs := treeOf(t, recs)
 
-	forward := groupPaths(collectTreeGroups(dirs, super, nil))
+	forward := groupPaths(collectTreeGroups(dirs, super, everyPathExists,
+		nil))
 
 	reversed := slices.Clone(recs)
 	slices.Reverse(reversed)
 
 	superR, dirsR := treeOf(t, reversed)
 
-	backward := groupPaths(collectTreeGroups(dirsR, superR, nil))
+	backward := groupPaths(collectTreeGroups(dirsR, superR, everyPathExists,
+		nil))
 	if !slices.EqualFunc(forward, backward, slices.Equal) {
 		t.Fatalf("output depends on record order: %v vs %v",
 			forward, backward)
@@ -427,7 +440,36 @@ func TestCollectTreeGroupsSiblings(t *testing.T) {
 
 	super, dirs := treeOf(t, recs)
 
-	got := groupPaths(collectTreeGroups(dirs, super, nil))
+	got := groupPaths(collectTreeGroups(dirs, super, everyPathExists, nil))
+
+	want := [][]string{{"/p/x1", "/p/x2"}}
+	if !slices.EqualFunc(got, want, slices.Equal) {
+		t.Fatalf("groups = %v, want %v", got, want)
+	}
+}
+
+// TestCollectTreeGroupsLeavesOutEmptyTrees checks that directories
+// holding only empty files form no group, and that an empty file still
+// counts toward the digest of a tree that holds other files.
+func TestCollectTreeGroupsLeavesOutEmptyTrees(t *testing.T) {
+	t.Parallel()
+
+	h, tl, c, e := testHash("h"), testHash("t"), testHash("c"),
+		sha256.Sum256(nil)
+	recs := []scanRec{
+		{size: 0, head: e, tail: e, content: e, path: "/e/a/.gitkeep"},
+		{size: 0, head: e, tail: e, content: e, path: "/e/b/.gitkeep"},
+		{size: 10, head: h, tail: tl, content: c, path: "/p/x1/f"},
+		{size: 0, head: e, tail: e, content: e, path: "/p/x1/.gitkeep"},
+		{size: 10, head: h, tail: tl, content: c, path: "/p/x2/f"},
+		{size: 0, head: e, tail: e, content: e, path: "/p/x2/.gitkeep"},
+		// Without the empty file, /p/x3 is no copy of /p/x1.
+		{size: 10, head: h, tail: tl, content: c, path: "/p/x3/f"},
+	}
+
+	super, dirs := treeOf(t, recs)
+
+	got := groupPaths(collectTreeGroups(dirs, super, everyPathExists, nil))
 
 	want := [][]string{{"/p/x1", "/p/x2"}}
 	if !slices.EqualFunc(got, want, slices.Equal) {
@@ -450,10 +492,56 @@ func TestCollectTreeGroupsDifferingParents(t *testing.T) {
 
 	super, dirs := treeOf(t, recs)
 
-	got := groupPaths(collectTreeGroups(dirs, super, nil))
+	got := groupPaths(collectTreeGroups(dirs, super, everyPathExists, nil))
 
 	want := [][]string{{"/p/a/x", "/q/b/x"}}
 	if !slices.EqualFunc(got, want, slices.Equal) {
 		t.Fatalf("groups = %v, want %v", got, want)
 	}
 }
+
+// TestCollectTreeGroupsChecksOnlyReportedCopies checks that trees asks
+// whether a directory is on disk only for the members of the groups it
+// returns. It never asks about /a/proj/sub, which lies inside a copy
+// and whose group the group of /a/proj implies, nor about /a/empty,
+// which holds 0 bytes.
+func TestCollectTreeGroupsChecksOnlyReportedCopies(t *testing.T) {
+	t.Parallel()
+
+	f, g, u, e := testHash("f"), testHash("g"), testHash("u"),
+		sha256.Sum256(nil)
+	recs := []scanRec{
+		{size: 10, head: f, tail: f, content: f, path: "/a/proj/f"},
+		{size: 20, head: g, tail: g, content: g, path: "/a/proj/sub/g"},
+		{size: 0, head: e, tail: e, content: e, path: "/a/empty/.gitkeep"},
+		{size: 10, head: f, tail: f, content: f, path: "/b/proj/f"},
+		{size: 20, head: g, tail: g, content: g, path: "/b/proj/sub/g"},
+		{size: 0, head: e, tail: e, content: e, path: "/b/empty/.gitkeep"},
+		// /a lacks this file, so /a and /b are no copies of each other.
+		{size: 30, head: u, tail: u, content: u, path: "/b/lonely"},
+	}
+
+	super, dirs := treeOf(t, recs)
+
+	var checked []string
+
+	exists := func(path string) bool {
+		checked = append(checked, path)
+
+		return true
+	}
+
+	got := groupPaths(collectTreeGroups(dirs, super, exists, nil))
+
+	want := [][]string{{"/a/proj", "/b/proj"}}
+	if !slices.EqualFunc(got, want, slices.Equal) {
+		t.Fatalf("groups = %v, want %v", got, want)
+	}
+
+	slices.Sort(checked)
+
+	if !slices.Equal(checked, want[0]) {
+		t.Errorf("directories checked on disk = %q, want %q",
+			checked, want[0])
+	}
+}