scan: drop the stray [flags] from the usage line (closes #169)

The scan Use string already names every flag, so cobra no longer appends
its generic [flags]. A test checks the usage line in the help and in the
usage error against the one README.md shows.

Model: opus-5-5

README.md

@@ -252,7 +252,7 @@ In order:
   report.
 
 ```
-sfdupes scan [--workers N] [-x] [--no-default-excludes] [--exclude PATH]... PATH...
+sfdupes scan [--workers N] [-x] [--no-default-excludes] PATH...
 sfdupes report > dupes.tsv
 sfdupes trees > dupetrees.tsv
 sfdupes info
@@ -297,10 +297,6 @@ The reference below is also the program's specification.
 - `--no-default-excludes` (`scan`) lets the walk enter the default excludes.
   Those are the system and temporary directories the walk otherwise leaves out,
   such as `/var/tmp` on Linux (see "Rules for the walk").
-- `--exclude PATH` (`scan`) keeps the walk out of `PATH` and everything below
-  it. `PATH` may be a directory or a file. The flag may be given more than once.
-  `PATH` is resolved to its real path, as an operand is. A `PATH` that does not
-  exist is a fatal error, and so is an operand at or below one (see "Operands").
 - `--version`, `-v` prints `sfdupes VERSION` (see "Install") to stdout and
   exits 0. It writes nothing to stderr.
 - `--help`, `-h`, alone or after a subcommand, prints the help text to stderr
@@ -359,8 +355,6 @@ default. An operand may be a directory or a regular file.
 - An operand that does not exist is a fatal error, and so is a symlink whose
   target does not exist. `scan` then stops before it walks anything, and exits
   with code 1.
-- An operand at or below an `--exclude` path is a fatal error too. The message
-  names the operand and the `--exclude` path. Both are compared as real paths.
 - Each operand is resolved to its real path before the walk, as `realpath`
   prints it. A relative operand is joined to the working directory as `pwd -P`
   prints it. Every symlink in the path is then followed. A `..` after a symlink
@@ -437,16 +431,15 @@ operands:
   scanned on different schedules into one database.
 - The scan keeps every record at or below a path that the walk leaves out for
   one of these reasons:
-    - it is an `--exclude` path;
     - it is a default exclude;
     - it is not on a persistent filesystem;
     - with `-x`, it is a directory on another filesystem than its operand.
 
     Such records count as outside the scanned operands. So with `-x`, a
     filesystem mounted under an operand can be scanned on its own schedule into
-    the same database. An operand may itself lie at or inside such a path, other
-    than an `--exclude` path (see "Operands"). Its walk verifies the records
-    below it, so they are deleted when their files are gone.
+    the same database. An operand may itself lie at or inside such a path, as
+    "Operands" describes. Its walk verifies the records below it, so they are
+    deleted when their files are gone.
 
 #### Phases
 
@@ -545,17 +538,6 @@ walk practical on large or busy storage pools.
     The path is not counted as skipped. The records below it are kept, as
     described under "What a scan does to the database".
 
-- The walk never enters or records an `--exclude` path, nor anything below it.
-  For each one it reaches, `scan` prints a line on stderr naming it:
-
-    ```
-    scan: skipped /srv/cache (--exclude)
-    ```
-
-    The path is not counted as skipped. The scan keeps the records at and below
-    it, as described under "What a scan does to the database".
-    `--no-default-excludes` does not change this rule.
-
 - Below an operand, the walk does not enter a default exclude. On Linux, the
   default excludes hold temporary files and the kernel's view of the running
   system. They depend on the system, and `sfdupes scan --help` lists those of
@@ -630,8 +612,7 @@ from a thread of its own and never blocks the workers.
   it repeats another or lies under another;
 - the progress display of each phase (see "Progress"). `scan` prints each
   warning for a skipped path as it happens. It prints a line the same way for
-  each path left out as an `--exclude` path, as a default exclude or as not on a
-  persistent filesystem;
+  each path left out as a default exclude or as not on a persistent filesystem;
 - the summary line;
 - a warning when a report still has the database open as the scan ends (see
   "Concurrent reads").
@@ -684,6 +665,7 @@ Processing:
 - Records are grouped by signature, the four values
   `(size, head, tail, content)`.
 - Every group with two or more paths is a duplicate group.
+- Empty files form no group, because removing one frees nothing.
 - Within a group, paths are sorted in byte order. The first is `first`, and
   every other path is a `dupe`.
 - Groups are ordered by size, largest first, then by `first` path. The output is
@@ -732,7 +714,7 @@ The summary line on stderr gives:
 - the reclaimable bytes, the sum of `size` over all rows.
 
 ```
-report: 14 records read, 5 duplicate groups, 8 dupe files, 10.0 KiB reclaimable
+report: 14 records read, 4 duplicate groups, 7 dupe files, 10.0 KiB reclaimable
 ```
 
 ### `trees` mode
@@ -760,6 +742,9 @@ Processing:
 - `trees` builds the directory tree and computes every directory's digest. It
   then groups the directories by digest. Every group with two or more
   directories is a duplicate-tree group.
+- `trees` leaves out a group whose trees hold 0 bytes, because removing one
+  frees nothing. An empty file still counts toward the digest of a tree that
+  holds other files.
 - `trees` leaves out a group that a group of its members' parents already
   implies. A group is left out when its members' parents are distinct
   directories that all have the same digest. The parents' group, or an
@@ -1194,7 +1179,6 @@ showing the count it stopped at.
 - `1`: a fatal error, a `scan` stopped by `SIGINT` or `SIGTERM`, or a `dwim`
   stopped by either during its scan. A fatal error is one of these:
     - an operand that does not exist, or whose real path `scan` cannot find;
-    - an `--exclude` path that does not exist, or an operand at or below one;
     - a list of mounted filesystems that `scan` cannot read;
     - another `scan` holding the lock (see "The scan lock");
     - a database, its directory or its lock file that cannot be created or
@@ -1402,7 +1386,7 @@ All of the following, run in this directory, must pass:
     head -c 2000 /dev/urandom > "$d/a/unique.bin"     # same size, different content
     printf 'x' > "$d/tiny1"; printf 'x' > "$d/tiny2"  # 1-byte duplicates
     printf 'y' > "$d/tiny3"                           # 1-byte non-duplicate
-    : > "$d/empty1"; : > "$d/empty2"                  # empty duplicates
+    : > "$d/empty1"; : > "$d/empty2"                  # empty files
     # duplicate trees: t1 and t2 are identical; t3 differs by one filename
     mkdir -p "$d/t1/sub" "$d/t2/sub" "$d/t3/sub"
     head -c 3000 /dev/urandom > "$d/t1/f1"
@@ -1427,8 +1411,8 @@ All of the following, run in this directory, must pass:
       is the path that sorts first.
     - `t1/f1`, `t2/f1` and `t3/f1` form one group.
     - `t1/sub/f2`, `t2/sub/f2` and `t3/sub/f2renamed` form one group.
-    - `tiny1` and `tiny2` form a pair, and so do `empty1` and `empty2`.
-    - `unique.bin` and `tiny3` appear nowhere.
+    - `tiny1` and `tiny2` form a pair.
+    - `unique.bin`, `tiny3`, `empty1` and `empty2` appear nowhere.
     - The groups come in order of size, largest first.
 
     `trees` prints exactly one row, `$d/t1` as `first` and `$d/t2` as `dupe`.

TODO.md

@@ -29,11 +29,13 @@
 Newest first. An entry ends with its date and its issue or branch, where those
 are known.
 
-- New `scan` flag `--exclude PATH`, which may be repeated. The walk neither
-  enters nor records an excluded path, and keeps the records below it. An
-  operand at or below one is a fatal error (2026-11-10,
-  https://git.eeqj.de/sneak/sfdupes/issues/163)
-
+- The usage line of `scan` no longer ends in `[flags]`. It is the line
+  `README.md` shows under "Subcommands" (2026-11-11,
+  https://git.eeqj.de/sneak/sfdupes/issues/169)
+- `report` and `trees` leave out empty files. `report` writes no group of size
+  0, and `trees` writes no group whose trees hold 0 bytes. An empty file still
+  counts toward a tree's digest (2026-11-11,
+  https://git.eeqj.de/sneak/sfdupes/issues/178)
 - The Go code moved out of the repository root. `cmd/sfdupes/main.go` is the
   command, and it calls `Main` in the package `internal/sfdupes`. `main.go`
   became `internal/sfdupes/cli.go`. Every other file kept its name. The install

internal/sfdupes/cancel_test.go

@@ -359,7 +359,7 @@ func TestRunScanInterrupted(t *testing.T) {
 	dir := buildSmokeTree(t)
 
 	err := runScan(t.Context(), []string{dir}, walkCancelWorkers, false,
-		false, nil)
+		false)
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -383,7 +383,7 @@ func TestRunScanInterrupted(t *testing.T) {
 		defer close(done)
 
 		err = runScan(cancelledContext(t), []string{dir}, walkCancelWorkers,
-			false, false, nil)
+			false, false)
 	}()
 
 	awaitReturn(t, done, "runScan")
@@ -411,7 +411,7 @@ func TestRunScanInterrupted(t *testing.T) {
 	}
 
 	err = runScan(t.Context(), []string{dir}, walkCancelWorkers, false,
-		false, nil)
+		false)
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -437,7 +437,7 @@ func TestRunScanInterruptedMidHash(t *testing.T) {
 	dir := buildWalkCancelTree(t)
 
 	err := runScan(newWalkClock(hashCancelAtDone), []string{dir},
-		walkCancelWorkers, false, false, nil)
+		walkCancelWorkers, false, false)
 	if !errors.Is(err, errInterrupted) {
 		t.Fatalf("runScan interrupted mid-hash = %v, want %v",
 			err, errInterrupted)

internal/sfdupes/cli.go

@@ -201,26 +201,27 @@ func newRootCommand(stdout, stderr io.Writer) *cobra.Command {
 	return root
 }
 
-// newScanCommand builds the scan subcommand, with its --workers, -x,
-// --no-default-excludes and --exclude flags. Its help lists the default
-// excludes of the system it runs on, and the filesystem types it never
-// records anything on.
+// newScanCommand builds the scan subcommand, with its --workers, -x and
+// --no-default-excludes flags. Its help lists the default excludes of
+// the system it runs on, and the filesystem types it never records
+// anything on.
 func newScanCommand() *cobra.Command {
 	var (
 		scanWorkers           int
 		scanOneFS             bool
 		scanNoDefaultExcludes bool
-		scanExclude           []string
 	)
 
 	short := "Walk trees and synchronize the scan database"
 
 	scanCmd := &cobra.Command{
-		Use: cmdScan + " [--workers N] [-x] [--no-default-excludes] " +
-			"[--exclude PATH]... PATH...",
-		Short: short,
-		Long:  short + ".\n\n" + defaultExcludesHelp(runtime.GOOS),
-		Args:  cobra.MinimumNArgs(1),
+		Use: cmdScan + " [--workers N] [-x] [--no-default-excludes] PATH...",
+		// The Use line already names every flag, so cobra must not
+		// append its generic "[flags]" to it.
+		DisableFlagsInUseLine: true,
+		Short:                 short,
+		Long:                  short + ".\n\n" + defaultExcludesHelp(runtime.GOOS),
+		Args:                  cobra.MinimumNArgs(1),
 		PreRunE: func(cmd *cobra.Command, _ []string) error {
 			return checkScanWorkers(cmd, scanWorkers)
 		},
@@ -229,7 +230,7 @@ func newScanCommand() *cobra.Command {
 			defer stop()
 
 			return runScan(ctx, args, scanWorkers, scanOneFS,
-				scanNoDefaultExcludes, scanExclude)
+				scanNoDefaultExcludes)
 		}),
 	}
 	scanCmd.Flags().IntVar(&scanWorkers, "workers", runtime.NumCPU(),
@@ -238,10 +239,6 @@ func newScanCommand() *cobra.Command {
 		"do not cross filesystem boundaries")
 	scanCmd.Flags().BoolVar(&scanNoDefaultExcludes, "no-default-excludes",
 		false, "enter the default excludes, the paths listed above")
-	// A string array, not a slice, so a comma in a path is not a
-	// separator.
-	scanCmd.Flags().StringArrayVar(&scanExclude, "exclude", nil,
-		"never enter or record `PATH` or anything below it; repeatable")
 
 	return scanCmd
 }

internal/sfdupes/cli_test.go

@@ -570,8 +570,7 @@ func TestRunNamesDefaultDatabase(t *testing.T) {
 	}{
 		cmdScan: {
 			run: func() error {
-				return runScan(t.Context(), []string{missing}, 1, false, false,
-					nil)
+				return runScan(t.Context(), []string{missing}, 1, false, false)
 			},
 			want: scanWant,
 		},
@@ -713,15 +712,33 @@ func TestRunHelp(t *testing.T) {
 				args, got)
 		}
 	}
+}
 
-	// The scan help lists --exclude with its argument.
-	var stdout, stderr bytes.Buffer
+func TestRunScanUsageLine(t *testing.T) {
+	t.Parallel()
 
-	run([]string{cmdScan, "-h"}, &stdout, &stderr)
+	// README §Subcommands shows this usage line for scan, and the help
+	// and the usage error both print it.
+	const want = "\n  sfdupes scan [--workers N] [-x] [--no-default-excludes] PATH...\n"
 
-	if !strings.Contains(stderr.String(), excludeFlag+" PATH") {
-		t.Errorf("scan -h stderr = %q, want %s PATH", stderr.String(),
-			excludeFlag)
+	cases := map[string][]string{
+		"help":          {cmdScan, "-h"},
+		"missing paths": {cmdScan},
+	}
+
+	for name, args := range cases {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			var stdout, stderr bytes.Buffer
+
+			run(args, &stdout, &stderr)
+
+			if !strings.Contains(stderr.String(), want) {
+				t.Errorf("run(%v) stderr = %q, want the usage line %q",
+					args, stderr.String(), want)
+			}
+		})
 	}
 }
 

internal/sfdupes/dwim.go

@@ -17,8 +17,7 @@ import (
 // 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,
-		nil)
+	err := runScan(scanCtx, []string{root}, runtime.NumCPU(), false, false)
 
 	stop()
 

internal/sfdupes/exclude.go

@@ -1,9 +1,8 @@
 package sfdupes
 
-// This file holds three rules for the walk (README "Rules for the
-// walk"): the paths given with --exclude, which the scan never enters;
+// 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
-// operand unless scan is given --no-default-excludes; and the
+// operand unless scan is given --no-default-excludes, and the
 // filesystems that are not persistent, on which the scan never records
 // or reads anything.
 
@@ -44,20 +43,14 @@ const typesPerHelpLine = 6
 // readMountInfo reads.
 var errMountInfoLine = errors.New("unexpected line")
 
-// errExcludedOperand reports an operand at or below a path given with
-// --exclude.
-var errExcludedOperand = errors.New("operand excluded by --exclude")
-
 // walkRules holds the rules for the walk that a scan sets up as it
-// starts. excluded are the real paths given with --exclude, which the
-// walk neither enters nor records. excludes are the default excludes,
-// or none with --no-default-excludes. nonPersistent maps the device ID
-// of every mounted filesystem that is not persistent to its type; the
-// scan records and reads nothing on one of those, whatever the flags.
+// starts. excludes are the default excludes, or none with
+// --no-default-excludes. nonPersistent maps the device ID of every
+// mounted filesystem that is not persistent to its type; the scan
+// records and reads nothing on one of those, whatever the flags.
 // databaseFiles are the scan's own database files, which the walk
 // passes over (see databaseFiles in db.go).
 type walkRules struct {
-	excluded      []string
 	excludes      []string
 	nonPersistent map[uint64]string
 	databaseFiles []fileRec
@@ -104,36 +97,6 @@ func isDefaultExclude(path string, excludes []string) bool {
 	return false
 }
 
-// resolveExcluded returns the real paths of excluded, the --exclude
-// values. One that cannot be resolved is a fatal error, and so is one
-// of roots at or below one of them. roots are real paths already.
-func resolveExcluded(roots, excluded []string) ([]string, error) {
-	excluded, err := resolveRoots(excluded)
-	if err != nil {
-		return nil, fmt.Errorf("--exclude: %w", err)
-	}
-
-	for _, root := range roots {
-		exclude := deepestRoot(root, excluded)
-		if exclude != "" {
-			return nil, fmt.Errorf("scan %s: %w %s", root,
-				errExcludedOperand, exclude)
-		}
-	}
-
-	return excluded, nil
-}
-
-// excludedLine returns the line the scan prints for path when it is one
-// of rules.excluded, and "" when it is not.
-func (rules walkRules) excludedLine(path string) string {
-	if !slices.Contains(rules.excluded, path) {
-		return ""
-	}
-
-	return fmt.Sprintf("scan: skipped %s (--exclude)", path)
-}
-
 // nonPersistentFilesystemTypes returns the filesystem types that are
 // not persistent: filesystems that the kernel makes up or that are kept
 // in memory. devfs is the macOS filesystem of /dev; the others are

internal/sfdupes/exclude_test.go

@@ -14,9 +14,6 @@ import (
 	"golang.org/x/sys/unix"
 )
 
-// excludeFlag is the scan flag that names a path the walk never enters.
-const excludeFlag = "--exclude"
-
 func TestDefaultExcludes(t *testing.T) {
 	t.Parallel()
 
@@ -359,121 +356,6 @@ func TestRunScanNoDefaultExcludes(t *testing.T) {
 	assertRecorded(t, path, f, true)
 }
 
-// TestRunScanExcludeNested scans a tree through the command with an
-// --exclude path two levels below the operand. The walk records nothing
-// at or below it and says so. The record an earlier scan left there is
-// kept although its file is gone.
-func TestRunScanExcludeNested(t *testing.T) {
-	path := testDBPath(t)
-	t.Setenv(databaseEnv, path)
-
-	dir := realTempDir(t)
-	excluded := filepath.Join(dir, "a", "b")
-	kept := writeFile(t, dir, "a/f", pattern(1, 10))
-	gone := writeFile(t, excluded, "gone", pattern(2, 10))
-
-	scanOK(t, dir)
-
-	err := os.Remove(gone)
-	if err != nil {
-		t.Fatal(err)
-	}
-
-	unseen := writeFile(t, excluded, "c/new", pattern(3, 10))
-
-	stderr := scanOK(t, excludeFlag, excluded, dir)
-
-	line := "scan: skipped " + excluded + " (--exclude)\n"
-	if !strings.Contains(stderr, line) {
-		t.Errorf("stderr = %q, want %q", stderr, line)
-	}
-
-	assertRecorded(t, path, kept, true)
-	assertRecorded(t, path, gone, true)
-	assertRecorded(t, path, unseen, false)
-}
-
-// TestRunScanExcludeRepeated gives --exclude twice, once for a
-// directory and once for a file, the file through a symlink to it. The
-// walk records neither, and records the file beside them.
-func TestRunScanExcludeRepeated(t *testing.T) {
-	path := testDBPath(t)
-	t.Setenv(databaseEnv, path)
-
-	dir := realTempDir(t)
-	inDir := writeFile(t, dir, "skip/f", pattern(1, 10))
-	file := writeFile(t, dir, "skip-file", pattern(2, 10))
-	kept := writeFile(t, dir, "keep", pattern(3, 10))
-
-	link := filepath.Join(t.TempDir(), "link")
-	symlink(t, file, link)
-
-	scanOK(t, excludeFlag, filepath.Dir(inDir), excludeFlag, link, dir)
-
-	assertRecorded(t, path, inDir, false)
-	assertRecorded(t, path, file, false)
-	assertRecorded(t, path, kept, true)
-}
-
-// TestRunScanExcludedOperand checks that an operand at or below an
-// --exclude path is a fatal error that names both, and so is an
-// --exclude path that does not exist. Neither scan writes a database.
-func TestRunScanExcludedOperand(t *testing.T) {
-	dir := realTempDir(t)
-	sub := filepath.Join(dir, "sub")
-	writeFile(t, sub, "f", pattern(1, 10))
-
-	cases := map[string]struct {
-		args []string
-		want string
-	}{
-		"at it": {
-			[]string{excludeFlag, sub, sub},
-			"scan " + sub + ": operand excluded by --exclude " + sub + "\n",
-		},
-		"below it": {
-			[]string{excludeFlag, dir, sub},
-			"scan " + sub + ": operand excluded by --exclude " + dir + "\n",
-		},
-		"after an operand it does not exclude": {
-			[]string{dir, excludeFlag, sub, sub},
-			"scan " + sub + ": operand excluded by --exclude " + sub + "\n",
-		},
-		"exclude missing": {
-			[]string{excludeFlag, filepath.Join(dir, "nope"), dir},
-			"--exclude: resolve " + filepath.Join(dir, "nope") + ": ",
-		},
-	}
-
-	for name, tc := range cases {
-		t.Run(name, func(t *testing.T) {
-			path := testDBPath(t)
-			t.Setenv(databaseEnv, path)
-
-			stdout := captureStdout(t)
-			stderr := captureStderr(t)
-
-			code := run(append([]string{cmdScan}, tc.args...), os.Stdout,
-				os.Stderr)
-			if code != exitFatal {
-				t.Errorf("run(scan %q) = %d, want %d", tc.args, code,
-					exitFatal)
-			}
-
-			assertFatalOutput(t, stderr(), stdout())
-
-			if !strings.Contains(stderr(), "sfdupes: "+tc.want) {
-				t.Errorf("stderr = %q, want %q", stderr(), tc.want)
-			}
-
-			_, err := os.Lstat(path)
-			if !errors.Is(err, os.ErrNotExist) {
-				t.Errorf("lstat %s: %v, want no database", path, err)
-			}
-		})
-	}
-}
-
 // TestRunScanSkipsNonPersistentOperand scans, through the command, a
 // directory on a filesystem that is not persistent, with and without
 // --no-default-excludes: either way it is skipped, with a line saying

internal/sfdupes/report.go

@@ -195,10 +195,11 @@ func (w *reportWriter) add(r scanRec) error {
 }
 
 // endGroup ends the paths read with w.sig: two or more are a duplicate
-// group, held with its paths sorted until writeGroups writes it.
+// group, held with its paths sorted until writeGroups writes it. Empty
+// files form no group, since removing one frees nothing.
 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 {
+		// The paths are dropped, and their slice reused.
 		w.paths = w.paths[:0]
 
 		return

internal/sfdupes/report_test.go

@@ -434,6 +434,27 @@ 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)
+	}
+}
+
 func TestDupeGroupsContentSeparates(t *testing.T) {
 	t.Parallel()
 

internal/sfdupes/scan.go

@@ -102,12 +102,10 @@ func scanPhase(name string) string {
 // scan command rejects anything less. Before the lock is taken, the
 // scan lists the filesystems that are not persistent, on which the walk
 // records nothing; unless noDefaultExcludes is set, the walk does not
-// enter the default excludes either. The walk neither enters nor
-// records the paths in excluded, the --exclude values; an operand at or
-// below one is a fatal error. Once the database is open, the scan notes
-// its files, which the walk passes over.
+// enter the default excludes either. Once the database is open, the
+// scan notes its files, which the walk passes over.
 func runScan(ctx context.Context, roots []string, workers int,
-	oneFS, noDefaultExcludes bool, excluded []string,
+	oneFS, noDefaultExcludes bool,
 ) error {
 	dbPath, source, err := databasePath()
 	if err != nil {
@@ -130,17 +128,12 @@ func runScan(ctx context.Context, roots []string, workers int,
 		return err
 	}
 
-	excluded, err = resolveExcluded(roots, excluded)
-	if err != nil {
-		return err
-	}
-
 	nonPersistent, err := nonPersistentFilesystems()
 	if err != nil {
 		return fmt.Errorf("list the mounted filesystems: %w", err)
 	}
 
-	rules := walkRules{excluded: excluded, nonPersistent: nonPersistent}
+	rules := walkRules{nonPersistent: nonPersistent}
 	if !noDefaultExcludes {
 		rules.excludes = defaultExcludes(runtime.GOOS)
 	}
@@ -216,12 +209,12 @@ func interrupted(walked int) error {
 	return errInterrupted
 }
 
-// resolveRoots converts each PATH operand, or each --exclude value, 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.
-// A path 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.
+// 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) {
 	resolved := make([]string, 0, len(roots))
 
@@ -500,11 +493,10 @@ func (s *scanState) loadIndex(ctx context.Context, roots []string) error {
 // as verified. When its disk_size differs from the record's, it is
 // queued for the update phase, which writes the new disk_size. A record
 // at or below a path the walk left out, because -x stopped at it, it is
-// an --exclude path or a default exclude, or it is not on a persistent
-// filesystem, counts as outside the roots: it is not deleted. That does
-// not hold below a root at or inside that path, since that root's own
-// walk verifies the records below it; nor is a line printed for such a
-// root.
+// a default exclude, or it is not on a persistent filesystem, counts as
+// outside the roots: it is not deleted. That does not hold below a root
+// at or inside that path, since that root's own walk verifies the
+// records below it; nor is a line printed for such a root.
 func (s *scanState) walkPhase(events <-chan walkEvent, roots []string) {
 	// The records the last scan left under the roots estimate how many
 	// files the walk will find. A first scan has none, and no estimate.
@@ -852,9 +844,9 @@ type dirJob struct {
 // file's statted record, a warning when fail is set, or a path the walk
 // left out: when otherFSDir is set, a directory -x did not enter
 // because it is on another filesystem than its operand, and when
-// leftOut is set, an --exclude path, a default exclude or a directory or
-// file on a filesystem that is not persistent, with warn holding the
-// line that says so.
+// leftOut is set, a default exclude or a directory or file on a
+// filesystem that is not persistent, with warn holding the line that
+// says so.
 type walkEvent struct {
 	rec        fileRec
 	warn       string
@@ -1136,8 +1128,8 @@ func walkOneDir(ctx context.Context, job dirJob, oneFS bool,
 // no longer exists, and one that has stopped being a regular file is
 // skipped. A file on a filesystem in rules that is not persistent, as
 // through a bind mount of one file, is not recorded: it gets an event
-// naming it instead, and so does a file given with --exclude. One of
-// the scan's own database files in rules gets no event at all.
+// naming it instead. One of the scan's own database files in rules gets
+// no event at all.
 func emitFile(ctx context.Context, p string, e fs.DirEntry,
 	rules walkRules, events chan<- walkEvent,
 ) {
@@ -1161,10 +1153,6 @@ func emitFile(ctx context.Context, p string, e fs.DirEntry,
 	}
 
 	line := rules.nonPersistentLine(p, info)
-	if line == "" {
-		line = rules.excludedLine(p)
-	}
-
 	if line != "" {
 		sendEvent(ctx, events, walkEvent{leftOut: p, warn: line})
 
@@ -1189,11 +1177,11 @@ 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), never enter a directory on a filesystem in rules that is
-// not persistent, nor an --exclude path or a default exclude in rules,
-// and with -x never enter a directory on a different filesystem than
-// its operand. For all but .zfs it sends an event that names the
-// directory, so the scan keeps the records below it, except those below
-// an operand at or inside it.
+// not persistent, nor a default exclude in rules, and with -x never
+// enter a directory on a different filesystem than its operand. For the
+// last three it sends an event that names the directory, 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, rules walkRules,
 	events chan<- walkEvent,
@@ -1218,10 +1206,6 @@ func subdirJob(ctx context.Context, p string, e fs.DirEntry,
 	}
 
 	line := rules.nonPersistentLine(p, info)
-	if line == "" {
-		line = rules.excludedLine(p)
-	}
-
 	if line != "" {
 		sendEvent(ctx, events, walkEvent{leftOut: p, warn: line})
 

internal/sfdupes/scan_test.go

@@ -1185,11 +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",
@@ -2367,8 +2368,8 @@ func TestRunScanPassesOverDatabase(t *testing.T) {
 			report := runStdout(t, cmdReport)
 			if strings.Contains(report, "db.sqlite") ||
 				strings.Contains(report, hardLink) ||
-				!strings.Contains(report, filepath.Join(tree, "empty2")) {
-				t.Errorf("report = %q, want the empty files and none of "+
+				!strings.Contains(report, filepath.Join(tree, "b")) {
+				t.Errorf("report = %q, want a and b and none of "+
 					"the database's files", report)
 			}
 		})

internal/sfdupes/trees.go

@@ -301,7 +301,9 @@ 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.
+// 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.
 func collectTreeGroups(allDirs []*treeNode, super *treeNode,
 	prog *progress,
 ) [][]*treeNode {
@@ -315,7 +317,9 @@ 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
 		}
 

internal/sfdupes/trees_test.go

@@ -2,6 +2,7 @@ package sfdupes //nolint:testpackage // checks the unexported treeNode results
 
 import (
 	"bytes"
+	"crypto/sha256"
 	"database/sql"
 	"os"
 	"slices"
@@ -435,6 +436,35 @@ func TestCollectTreeGroupsSiblings(t *testing.T) {
 	}
 }
 
+// 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, nil))
+
+	want := [][]string{{"/p/x1", "/p/x2"}}
+	if !slices.EqualFunc(got, want, slices.Equal) {
+		t.Fatalf("groups = %v, want %v", got, want)
+	}
+}
+
 func TestCollectTreeGroupsDifferingParents(t *testing.T) {
 	t.Parallel()