Limit report and trees to given paths (closes #174)

report and trees take optional PATH operands and use only the records
at or below them. Operands are made absolute and cleaned as text, never
looked up on the filesystem; each reported copy is still checked on
disk. With operands, trees reports only directories at or below an
operand: any other directory lies above an operand and can hold unused
files, so its digest neither gets reported nor suppresses its
children's group. The summary still counts every record read.

Model: opus-5-5

README.md

@@ -21,9 +21,10 @@ file takes too long. It has five subcommands. `scan` walks the filesystem and
 records the files it finds in an SQLite database. SQLite keeps a whole database
 in one file. The database is kept between runs. A rescan reads only new and
 changed files. That makes `scan` cheap enough to run every day from `cron`, the
-system's job scheduler. `report`, `trees` and `info` read the database alone and
-can run at any time. `dwim` scans `/` and then prints the `trees` report, for a
-first look at a new machine with one command.
+system's job scheduler. `report`, `trees` and `info` work from the database and
+can run at any time. `report` and `trees` leave out a copy that was deleted
+after the scan. `dwim` scans `/` and then prints the `trees` report, for a first
+look at a new machine with one command.
 
 ## Getting Started
 
@@ -100,13 +101,15 @@ Each `-v` flag below makes a bind mount, which shows a host directory at a path
 inside the container. Bind-mount `/var/lib/sfdupes` to keep the database between
 runs. Mount the tree to scan at the same path inside the container as on the
 host. Read-only access is enough. The database then records the host's paths,
-and so do the reports.
+and so do the reports. `report` and `trees` need that mount too. Without it,
+every recorded path counts as gone, and each report holds only its header line.
 
 ```sh
 make docker
 docker run --rm -v /srv:/srv:ro -v /var/lib/sfdupes:/var/lib/sfdupes \
     sfdupes scan /srv
-docker run --rm -v /var/lib/sfdupes:/var/lib/sfdupes sfdupes report > dupes.tsv
+docker run --rm -v /srv:/srv:ro -v /var/lib/sfdupes:/var/lib/sfdupes \
+    sfdupes report > dupes.tsv
 ```
 
 ### Daily scan from `cron`
@@ -161,8 +164,10 @@ to keep is your choice.
 
 A row is a candidate, not proof:
 
-- The reports show each file as it was when a scan last recorded it. A file may
-  have changed or gone since.
+- The reports show each file as it was when a scan last recorded it. They check
+  only that each copy still exists: the file, or the directory at the top of a
+  tree. A file may have changed since, and a file inside a tree may be gone. Run
+  `scan` again to bring the reports up to date.
 - A file of 100 MiB or more is compared only on samples of its content (see
   "Duplicate detection").
 - Two paths that are hard links, two names for one file, are listed as
@@ -210,8 +215,9 @@ makes the comparison exact. Reading samples cuts a 150 GiB file to about 150 MiB
 of reads, at the price of a comparison that is not exact.
 
 The hashes live in a database that is kept between runs. A rescan reads only new
-files, and files whose size changed or whose modification time (mtime) is newer
-than recorded. All analysis then works from the database alone.
+files, and files whose size or modification time (mtime) differs from their
+record. All analysis then works from the database. The reports only check that
+each copy they name still exists.
 
 The goal is whole duplicated trees, not only single files. A download extracted
 twice, or a project copied once too often, is such a tree. It can be removed as
@@ -237,9 +243,10 @@ In order:
    the files of the directories it is reading.
 3. **Rescan cheaply, analyze from the database.** The scan keeps its database
    between runs, and an unchanged file is never read again. `report`, `trees`
-   and `info` work from the database alone and never touch the scanned
-   filesystem. `scan` is built to run from `cron`. The reports run at any time,
-   against what the database holds.
+   and `info` work from the database and never read a scanned file. `report` and
+   `trees` check only that each copy they name still exists, and leave out a
+   copy that is gone. `scan` is built to run from `cron`. The reports run at any
+   time, against what the database holds.
 4. **Keep the streams apart.** Everything on stdout is machine-readable data.
    Everything for a human reader, such as progress and warnings, goes to stderr.
 
@@ -254,7 +261,7 @@ In order:
   report.
 
 ```
-sfdupes scan [--workers N] [-x] [--no-default-excludes] PATH...
+sfdupes scan [--workers N] [-x] [--no-default-excludes] [--exclude PATH]... PATH...
 sfdupes report [PATH...] > dupes.tsv
 sfdupes trees [PATH...] > dupetrees.tsv
 sfdupes info
@@ -299,6 +306,16 @@ 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.
+  The walk knows `PATH` by its device ID and inode number, as it knows the
+  database files (see "Rules for the walk"). So the walk leaves `PATH` out
+  whatever path leads to it. That includes a hard link to a file given as
+  `PATH`. A symlink given as `PATH` excludes its target. An empty `PATH`, as in
+  `--exclude ""`, is a usage error, reported in one line on stderr with exit 2
+  before anything is scanned. A `PATH` that does not exist, or whose real path
+  `scan` cannot find, is a fatal error. 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
@@ -357,6 +374,10 @@ 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. `scan` compares the operand and
+  each directory above it with the `--exclude` paths by device ID and inode
+  number, not by name.
 - 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
@@ -412,17 +433,16 @@ operands:
 
 - A file not yet in the database is hashed and inserted.
 - A file already in the database is not read again when its size and mtime match
-  its record. The mtime matches when it is not newer than the recorded one. This
-  is what makes a daily rescan cheap.
+  its record. This is what makes a daily rescan cheap.
 - When such a file's size on disk differs from its recorded `disk_size`, `scan`
   updates `disk_size` alone. It still does not read the file, and counts it as
   unchanged. ZFS, for example, counts a new file's blocks up to seconds after
   the write. A block is the unit in which a filesystem allocates disk space. A
   file scanned within those seconds gets its real `disk_size` at the next scan.
-- `scan` hashes a file again when its size differs or its mtime is newer. The
-  mtime is compared to the nanosecond, as finely as the filesystem records it. A
-  same-size rewrite counts as a change whenever the filesystem gives it a later
-  mtime, even within the same second.
+- `scan` hashes a file again when its size or its mtime differs from its record.
+  An older mtime counts as much as a newer one. A file put back by `cp -p`,
+  `rsync -a` or a restore from backup often has an older mtime. The mtime is
+  compared to the nanosecond, as finely as the filesystem records it.
 - The scan deletes each record under a scanned operand whose file it could not
   verify. That covers deleted files, and paths the scan could not stat or read
   this run. To stat a file is to read its details, such as its size, without
@@ -433,15 +453,16 @@ 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, as
-    "Operands" describes. 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, other
+    than an `--exclude` path (see "Operands"). Its walk verifies the records
+    below it, so they are deleted when their files are gone.
 
 #### Phases
 
@@ -540,6 +561,17 @@ 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
@@ -614,7 +646,8 @@ 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 a default exclude or as not on a persistent filesystem;
+  each path left out as an `--exclude` path, 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").
@@ -657,21 +690,30 @@ and `scan` leaves it ignored.
 
 `report` reads every record from the database. It takes optional `PATH`
 operands. With none, it uses every record. With one or more, it uses only the
-records at or below them (see "Report paths"). `report` never touches the
-scanned filesystem. It neither stats nor opens any path in the records. It reads
-the database and writes to stdout and stderr, and nothing else. Its output is
-the same whether or not the scanned filesystem is still mounted.
+records at or below them (see "Operands of `report` and `trees`"). `report`
+never opens a scanned file. It checks that each path in a group still exists,
+and looks at no other path. It never looks up an operand. The check is `lstat`,
+the system call that looks up a path without following a symlink:
+
+- A path is gone when `lstat` finds that it, or a directory above it, does not
+  exist.
+- Any other error, such as a permission error, counts as present. So a user who
+  may not look inside a directory still sees its copies.
+
+The check does not notice a file that changed after the scan. Run `scan` again
+to bring the report up to date.
 
 Processing:
 
 - Records are grouped by signature, the four values
   `(size, head, tail, content)`.
-- Every group with two or more paths is a duplicate group.
+- In a group with two or more paths, a path that is gone is left out. A group
+  that still has 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
-  the same for the same database contents.
+  the same for the same database contents and the same paths on disk.
 
 `report` has two phases, each with its own progress display on stderr (see
 "Progress"). `open` opens the database. `read` gets the number of records from
@@ -683,7 +725,7 @@ with one signature come together, and so do the records of one size. So `report`
 holds only the duplicate groups of the size it is reading. Once it reaches a
 smaller size, it writes them, ordered by `first` path.
 
-#### Report paths
+#### Operands of `report` and `trees`
 
 `report` and `trees` take the same `PATH` operands:
 
@@ -699,7 +741,8 @@ smaller size, it writes them, ordered by `first` path.
   element before it.
 - No operand is looked up on the filesystem. A symlink in an operand is not
   followed, and an operand need not exist. The records hold real paths (see
-  "Operands"), so an operand that passes through a symlink matches no record.
+  "Operands" under "`scan` mode"), so an operand that passes through a symlink
+  matches no record.
 - An operand that matches no record is not an error. The report then has no
   rows.
 
@@ -743,11 +786,12 @@ report: 14 records read, 4 duplicate groups, 7 dupe files, 10.0 KiB reclaimable
 ### `trees` mode
 
 `trees` reads the same database as `report` and takes the same `PATH` operands
-(see "Report paths"). It reports whole duplicate directory trees. Two
-directories are duplicate trees when they hold the same relative paths, and each
-path holds a file with the same signature in both. Like `report`, it never
-touches the scanned filesystem. It rebuilds the directory tree from the paths in
-the records, split on `/`.
+(see "Operands of `report` and `trees`"). It reports whole duplicate directory
+trees. Two directories are duplicate trees when they hold the same relative
+paths, and each path holds a file with the same signature in both. It rebuilds
+the directory tree from the paths in the records, split on `/`. Like `report`,
+it never opens a scanned file and never looks up an operand. It checks only that
+the directory at the top of each copy still exists, as `report` checks a path.
 
 Definitions:
 
@@ -775,13 +819,17 @@ Processing:
   ancestor's, already implies it. A group is always reported when it holds
   sibling directories, or when its members' parents have different digests.
 - With operands, `trees` builds the tree from the records it uses. It reports
-  only directories at or below an operand. A directory above every operand holds
-  files that are not used, so its digest does not describe it. Such a directory
-  is never reported and never implies a group of its children.
+  only directories at or below an operand. Any other directory lies above an
+  operand and can hold files that are not used, so its digest does not describe
+  it. Such a directory is never reported and never implies a group of its
+  children.
+- A directory that is gone is dropped from its group. A group left with fewer
+  than two directories is not reported.
 - Within a group, paths are sorted in byte order. The first is `first`, and
   every other path is a `dupe`.
 - Groups are ordered by total tree size, largest first, then by `first` path.
-  The output is the same for the same database contents.
+  The output is the same for the same database contents and the same paths on
+  disk.
 
 Two limitations are accepted:
 
@@ -795,8 +843,9 @@ Two limitations are accepted:
 `trees` has four phases, each with its own progress display on stderr (see
 "Progress"). `open` opens the database. `read` gets the number of records from
 the `totals` table, then reads them in path order. It builds the directory tree
-and computes the digests as it goes. `group` groups the directories by digest
-and picks the groups to report. `write` writes them to stdout.
+and computes the digests as it goes. `group` groups the directories by digest,
+picks the groups to report and checks that their directories still exist.
+`write` writes the groups to stdout.
 
 #### Trees output format
 
@@ -857,8 +906,8 @@ The report goes to stdout, exactly as `trees` prints it. On stderr comes what
 dwim: run "sfdupes trees" to print this report again
 ```
 
-The database keeps the scan, so `sfdupes trees` prints the same report later,
-even after the terminal is gone.
+The database keeps the scan, so `sfdupes trees` prints the report again later,
+even after the terminal is gone. It then leaves out a copy deleted in between.
 
 `SIGINT` or `SIGTERM` stops the scan as it stops `scan` (see "Stopping a scan").
 `dwim` then prints no report and exits 1. A fatal scan error also ends it before
@@ -1150,9 +1199,10 @@ in, and a phase that may wait in two places names both, as `disk/db`:
 - `hash` says `disk/db`, because it reads files and writes their records to the
   database between them.
 - `load`, `update` and the `read` phase of `trees` say `db`.
-- The `read` phase of `report` says `db/out`, because it writes the report to
-  stdout while it reads.
-- `group` of `trees` says `cpu`, for work in memory, and its `write` says `out`.
+- The `read` phase of `report` says `db/disk/out`. It checks that the paths of
+  each group still exist, and writes the report to stdout, while it reads.
+- `group` of `trees` says `cpu/disk`, for work in memory and the check that each
+  copy still exists. Its `write` says `out`.
 - A phase still waiting for its total says what it waits for, and nothing more.
 
 On a terminal:
@@ -1210,6 +1260,9 @@ 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 whose real path `scan` cannot
+      find;
+    - an operand at or below an `--exclude` path;
     - 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
@@ -1229,6 +1282,7 @@ showing the count it stopped at.
       `--workers abc`;
     - `scan` with no operand;
     - `--workers` below 1;
+    - an empty `--exclude` value, as in `--exclude ""`;
     - `info` or `dwim` with a positional argument.
 
 A fatal error is reported on stderr, starting with `sfdupes:`. A failed write to
@@ -1392,8 +1446,8 @@ commands of their own:
   not a goal. `modernc.org/sqlite` is pure Go too, so the binary builds without
   cgo. The `Makefile` exports `CGO_ENABLED=0`. The test build is the one
   exception, because the race detector needs cgo (see `script/test`).
-- `report` and `trees` give the same output for the same database contents,
-  whatever order the records were inserted in.
+- `report` and `trees` give the same output for the same database contents and
+  the same paths on disk, whatever order the records were inserted in.
 
 ### Definition of done
 
@@ -1458,7 +1512,7 @@ All of the following, run in this directory, must pass:
 
     The test suite automates this scenario (see
     `internal/sfdupes/scan_test.go`). It also checks that `report` and `trees`
-    never touch the scanned filesystem.
+    leave out a copy removed after the scan.
 
 ## TODO
 

TODO.md

@@ -34,6 +34,19 @@ are known.
   below an operand. Operands are made absolute and cleaned as text, never looked
   up on the filesystem (2026-11-11,
   https://git.eeqj.de/sneak/sfdupes/issues/174)
+- 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 (2026-11-11,
+  https://git.eeqj.de/sneak/sfdupes/issues/163)
+
+- `report` and `trees` leave out a copy that was deleted after the scan. Each
+  checks only the copy itself with `lstat`: the file, or the directory at the
+  top of a tree. A group left with one copy is not reported. A missing `scan`
+  operand is still a fatal error (2026-11-11,
+  https://git.eeqj.de/sneak/sfdupes/issues/173)
+- 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,

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)
+		false, nil)
 	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)
+			false, false, nil)
 	}()
 
 	awaitReturn(t, done, "runScan")
@@ -411,7 +411,7 @@ func TestRunScanInterrupted(t *testing.T) {
 	}
 
 	err = runScan(t.Context(), []string{dir}, walkCancelWorkers, false,
-		false)
+		false, nil)
 	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)
+		walkCancelWorkers, false, false, nil)
 	if !errors.Is(err, errInterrupted) {
 		t.Fatalf("runScan interrupted mid-hash = %v, want %v",
 			err, errInterrupted)

internal/sfdupes/cli.go

@@ -10,6 +10,7 @@ import (
 	"os"
 	"runtime"
 	"runtime/debug"
+	"slices"
 
 	"github.com/spf13/cobra"
 )
@@ -31,9 +32,9 @@ const (
 	cmdDwim   = "dwim"
 )
 
-// reportPathsHelp explains the PATH operands of report and trees in
-// their help.
-const reportPathsHelp = "With PATH operands, only the records at or " +
+// operandsHelp explains the PATH operands of report and trees in their
+// help.
+const operandsHelp = "With PATH operands, only the records at or " +
 	"below them are used. A relative PATH is joined to the working " +
 	"directory. No PATH is looked up on the filesystem, so a symlink in " +
 	"one is not followed."
@@ -47,6 +48,11 @@ var errNoSubcommand = errors.New("no subcommand")
 // below 1.
 var errWorkersBelowOne = errors.New("--workers must be at least 1")
 
+// errEmptyExcludeValue is the usage error for an empty scan --exclude
+// value, as from --exclude "$DIR" with DIR unset. Taken as a path, it
+// would name the working directory.
+var errEmptyExcludeValue = errors.New("--exclude must not be empty")
+
 // Version is the build version, injected at link time via -ldflags
 // (see the Makefile); empty when the linker set none, as for a binary
 // built by go install. buildVersion turns it into what --version prints.
@@ -171,7 +177,7 @@ func newRootCommand(stdout, stderr io.Writer) *cobra.Command {
 		Use:   cmdReport + " [PATH...]",
 		Short: "Read the scan database and print the file-level duplicates report",
 		Long: "Read the scan database and print the file-level duplicates " +
-			"report.\n\n" + reportPathsHelp,
+			"report.\n\n" + operandsHelp,
 		Args: cobra.ArbitraryArgs,
 		RunE: runE(func(ctx context.Context, args []string) error {
 			return runReport(ctx, args, stdout)
@@ -182,7 +188,7 @@ func newRootCommand(stdout, stderr io.Writer) *cobra.Command {
 		Use:   cmdTrees + " [PATH...]",
 		Short: "Read the scan database and print the duplicate-tree report",
 		Long: "Read the scan database and print the duplicate-tree " +
-			"report.\n\n" + reportPathsHelp,
+			"report.\n\n" + operandsHelp,
 		Args: cobra.ArbitraryArgs,
 		RunE: runE(func(ctx context.Context, args []string) error {
 			return runTrees(ctx, args, stdout)
@@ -212,33 +218,43 @@ func newRootCommand(stdout, stderr io.Writer) *cobra.Command {
 	return root
 }
 
-// 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.
+// 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.
 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] PATH...",
-		Short: short,
-		Long:  short + ".\n\n" + defaultExcludesHelp(runtime.GOOS),
-		Args:  cobra.MinimumNArgs(1),
+		Use: cmdScan + " [--workers N] [-x] [--no-default-excludes] " +
+			"[--exclude PATH]... 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)
+			err := checkScanWorkers(cmd, scanWorkers)
+			if err != nil {
+				return err
+			}
+
+			return rejectEmptyExcludeValue(cmd, scanExclude)
 		},
 		RunE: runE(func(ctx context.Context, args []string) error {
 			ctx, stop := interruptContext(ctx)
 			defer stop()
 
 			return runScan(ctx, args, scanWorkers, scanOneFS,
-				scanNoDefaultExcludes)
+				scanNoDefaultExcludes, scanExclude)
 		}),
 	}
 	scanCmd.Flags().IntVar(&scanWorkers, "workers", runtime.NumCPU(),
@@ -247,6 +263,10 @@ 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
 }
@@ -264,6 +284,18 @@ func checkScanWorkers(cmd *cobra.Command, workers int) error {
 	return fmt.Errorf("%w, got %d", errWorkersBelowOne, workers)
 }
 
+// rejectEmptyExcludeValue rejects an empty scan --exclude value. That
+// is a usage error reported in one line, as for --workers below 1.
+func rejectEmptyExcludeValue(cmd *cobra.Command, excludePaths []string) error {
+	if !slices.Contains(excludePaths, "") {
+		return nil
+	}
+
+	cmd.SilenceUsage = true
+
+	return errEmptyExcludeValue
+}
+
 // runE adapts a subcommand implementation, or the version print, to
 // cobra's RunE. Cobra prints the error and the command's usage text for
 // every error RunE returns, but a subcommand that ran and failed has no

internal/sfdupes/cli_test.go

@@ -570,7 +570,8 @@ func TestRunNamesDefaultDatabase(t *testing.T) {
 	}{
 		cmdScan: {
 			run: func() error {
-				return runScan(t.Context(), []string{missing}, 1, false, false)
+				return runScan(t.Context(), []string{missing}, 1, false, false,
+					nil)
 			},
 			want: scanWant,
 		},
@@ -710,6 +711,45 @@ func TestRunHelp(t *testing.T) {
 				args, got)
 		}
 	}
+
+	// The scan help lists --exclude with its argument.
+	var stdout, stderr bytes.Buffer
+
+	run([]string{cmdScan, "-h"}, &stdout, &stderr)
+
+	if !strings.Contains(stderr.String(), excludeFlag+" PATH") {
+		t.Errorf("scan -h stderr = %q, want %s PATH", stderr.String(),
+			excludeFlag)
+	}
+}
+
+func TestRunScanUsageLine(t *testing.T) {
+	t.Parallel()
+
+	// 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] " +
+		"[--exclude PATH]... PATH...\n"
+
+	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)
+			}
+		})
+	}
 }
 
 func TestRunVersion(t *testing.T) {

internal/sfdupes/dwim.go

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

internal/sfdupes/exclude.go

@@ -1,8 +1,9 @@
 package sfdupes
 
-// This file holds two rules for the walk (README "Rules for the walk"):
+// This file holds three rules for the walk (README "Rules for the
+// walk"): the paths given with --exclude, which the scan never enters;
 // 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.
 
@@ -12,6 +13,7 @@ import (
 	"fmt"
 	"io"
 	"io/fs"
+	"os"
 	"path/filepath"
 	"slices"
 	"strings"
@@ -43,17 +45,25 @@ 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. 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).
+// starts. excludePaths are the paths given with --exclude, each with
+// the device ID and inode number of the file it names (see
+// excludePathInodes), which the walk neither enters nor records,
+// whatever path leads to them. defaultExcludes 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 {
-	excludes      []string
-	nonPersistent map[uint64]string
-	databaseFiles []fileRec
+	excludePaths    []fileRec
+	defaultExcludes []string
+	nonPersistent   map[uint64]string
+	databaseFiles   []fileRec
 }
 
 // defaultExcludes returns the default excludes of the system goos
@@ -97,6 +107,88 @@ func isDefaultExclude(path string, excludes []string) bool {
 	return false
 }
 
+// excludePathInodes returns each of paths, the --exclude values, as its
+// real path (see realPaths) with the device ID and inode number of the
+// file there. The walk compares what it reaches with those, as it does
+// with the database files, so it also leaves out an --exclude path
+// spelled another way, such as in another letter case on macOS.
+func excludePathInodes(paths []string) ([]fileRec, error) {
+	resolved, err := realPaths(paths)
+	if err != nil {
+		return nil, err
+	}
+
+	files := make([]fileRec, 0, len(resolved))
+
+	for _, path := range resolved {
+		fi, err := os.Lstat(path)
+		if err != nil {
+			return nil, err
+		}
+
+		dev, ino := inodeOfInfo(fi)
+		files = append(files, fileRec{path: path, dev: dev, ino: ino})
+	}
+
+	return files, nil
+}
+
+// matchingExcludePath returns the path of the one of excludePaths with
+// the device ID and inode number of fi, an lstat result, or "" when
+// there is none.
+func matchingExcludePath(fi fs.FileInfo, excludePaths []fileRec) string {
+	dev, ino := inodeOfInfo(fi)
+	f := fileRec{dev: dev, ino: ino}
+
+	for _, exclude := range excludePaths {
+		if sameInode(exclude, f) {
+			return exclude.path
+		}
+	}
+
+	return ""
+}
+
+// checkOperandsNotExcluded returns an error when one of roots, the
+// operands, or a directory above it is one of excludePaths, the
+// --exclude paths, by device ID and inode number. The error names the
+// operand and the --exclude path. The roots are absolute, so the
+// directories above each one end at /. A path here that lstat cannot
+// read is an error too.
+func checkOperandsNotExcluded(roots []string, excludePaths []fileRec) error {
+	for _, root := range roots {
+		for path := root; ; path = filepath.Dir(path) {
+			fi, err := os.Lstat(path)
+			if err != nil {
+				return fmt.Errorf("scan %s: %w", root, err)
+			}
+
+			exclude := matchingExcludePath(fi, excludePaths)
+			if exclude != "" {
+				return fmt.Errorf("scan %s: %w %s", root, errExcludedOperand,
+					exclude)
+			}
+
+			if path == "/" {
+				break
+			}
+		}
+	}
+
+	return nil
+}
+
+// excludePathLine returns the line the scan prints for path when fi,
+// its lstat, makes it one of rules.excludePaths, and "" when it does
+// not.
+func (rules walkRules) excludePathLine(path string, fi fs.FileInfo) string {
+	if matchingExcludePath(fi, rules.excludePaths) == "" {
+		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

@@ -14,6 +14,9 @@ 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()
 
@@ -188,7 +191,7 @@ func TestScanDoesNotEnterDefaultExclude(t *testing.T) {
 	unseen := writeFile(t, excluded, "new", pattern(2, 10))
 
 	st, err := syncScan(t.Context(), db, []string{dir}, 1, false,
-		walkRules{excludes: []string{excluded}})
+		walkRules{defaultExcludes: []string{excluded}})
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -234,7 +237,7 @@ func TestScanWalksOperandInDefaultExclude(t *testing.T) {
 			db := openTestDB(t)
 
 			st, err := syncScan(t.Context(), db, roots, 1, false,
-				walkRules{excludes: []string{excluded}})
+				walkRules{defaultExcludes: []string{excluded}})
 			if err != nil {
 				t.Fatal(err)
 			}
@@ -262,7 +265,7 @@ func TestScanNamesNoDefaultExcludeThatIsAnOperand(t *testing.T) {
 	f := writeFile(t, excluded, "f", pattern(1, 10))
 
 	st, err := syncScan(t.Context(), db, []string{dir, excluded}, 1, false,
-		walkRules{excludes: []string{excluded}})
+		walkRules{defaultExcludes: []string{excluded}})
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -356,6 +359,217 @@ 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)
+}
+
+// TestRunScanExcludeReachedByAnotherPath gives --exclude a directory
+// through a symlink and a file through "..", so the walk reaches
+// neither by the path given. The walk also reaches the file through a
+// hard link. It records none of these, prints a line naming each, and
+// records the file beside them.
+func TestRunScanExcludeReachedByAnotherPath(t *testing.T) {
+	path := testDBPath(t)
+	t.Setenv(databaseEnv, path)
+
+	dir := realTempDir(t)
+	inDir := writeFile(t, dir, "a/cache/f", pattern(1, 10))
+	file := writeFile(t, dir, "a/big", pattern(2, 10))
+	kept := writeFile(t, dir, "keep", pattern(3, 10))
+
+	hardLink := filepath.Join(dir, "big-link")
+
+	err := os.Link(file, hardLink)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	link := filepath.Join(t.TempDir(), "link")
+	symlink(t, filepath.Join(dir, "a"), link)
+
+	// Joined as text, since filepath.Join would drop the "..".
+	dotDot := dir + "/a/cache/../big"
+
+	stderr := scanOK(t, excludeFlag, filepath.Join(link, "cache"),
+		excludeFlag, dotDot, dir)
+
+	for _, skipped := range []string{filepath.Dir(inDir), file, hardLink} {
+		line := "scan: skipped " + skipped + " (--exclude)\n"
+		if !strings.Contains(stderr, line) {
+			t.Errorf("stderr = %q, want %q", stderr, line)
+		}
+	}
+
+	assertRecorded(t, path, inDir, false)
+	assertRecorded(t, path, file, false)
+	assertRecorded(t, path, hardLink, 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. An operand that is a hard link to
+// an --exclude file is at it. Neither scan writes a database.
+func TestRunScanExcludedOperand(t *testing.T) {
+	dir := realTempDir(t)
+	sub := filepath.Join(dir, "sub")
+	f := writeFile(t, sub, "f", pattern(1, 10))
+
+	hardLink := filepath.Join(dir, "f-link")
+
+	err := os.Link(f, hardLink)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	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",
+		},
+		"a hard link to it": {
+			[]string{excludeFlag, f, hardLink},
+			"scan " + hardLink + ": operand excluded by --exclude " + f + "\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)
+			}
+		})
+	}
+}
+
+// TestRunScanRejectsEmptyExclude checks that an empty --exclude value,
+// given as its own argument, after "=" or after another --exclude, is
+// a usage error reported in one line before anything is scanned
+// (README "Settings").
+func TestRunScanRejectsEmptyExclude(t *testing.T) {
+	dir := t.TempDir()
+
+	cases := map[string][]string{
+		"separate":     {excludeFlag, "", dir},
+		"joined by =":  {excludeFlag + "=", dir},
+		"after a path": {excludeFlag, t.TempDir(), excludeFlag, "", dir},
+	}
+
+	for name, args := range cases {
+		t.Run(name, func(t *testing.T) {
+			path := testDBPath(t)
+			t.Setenv(databaseEnv, path)
+
+			var stdout, stderr bytes.Buffer
+
+			code := run(append([]string{cmdScan}, args...), &stdout,
+				&stderr)
+			if code != exitUsage {
+				t.Errorf("run(scan %q) = %d, want %d", args, code,
+					exitUsage)
+			}
+
+			want := "Error: --exclude must not be empty\n"
+			if stdout.String() != "" || stderr.String() != want {
+				t.Errorf("stdout, stderr = %q, %q, want \"\", %q",
+					stdout.String(), stderr.String(), 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/progress_test.go

@@ -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

@@ -4,12 +4,15 @@ import (
 	"context"
 	"crypto/sha256"
 	"database/sql"
+	"errors"
 	"fmt"
 	"io"
+	"io/fs"
 	"os"
 	"path/filepath"
 	"slices"
 	"strings"
+	"syscall"
 	"time"
 )
 
@@ -43,10 +46,11 @@ func reportPhase(name string) string {
 
 // runReport implements the report subcommand: it prints the file-level
 // duplicates report as TSV on stdout, from the records at or below the
-// given paths, or from every record when none is given. 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.
+// operands in args, or from every record when args is empty. Of the
+// scanned filesystem it only checks, with pathExists, that each path in
+// a duplicate group is still there; it never looks up an operand. 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
@@ -55,7 +59,7 @@ func reportPhase(name string) string {
 // is read; see readReport). Each display ends before the next phase
 // starts, and before an error is returned to be printed.
 func runReport(ctx context.Context, args []string, stdout io.Writer) error {
-	paths, err := reportPaths(args)
+	operands, err := cleanOperands(args)
 	if err != nil {
 		return err
 	}
@@ -84,13 +88,15 @@ func runReport(ctx context.Context, args []string, 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, paths, stdout, prog)
+	report, err := readReport(ctx, db, dbPath, operands, stdout, pathExists,
+		prog)
 
 	prog.finish()
 
@@ -111,15 +117,17 @@ func runReport(ctx context.Context, args []string, 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. Only the records that inReportPaths selects from paths join a
+// read. Only the records that underOperand finds under operands join a
+// group, and 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,
-	paths []string, stdout io.Writer, prog *progress,
+	operands []string, 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 {
@@ -133,7 +141,7 @@ func readReport(ctx context.Context, db *sql.DB, dbPath string,
 
 		report.records++
 
-		if !inReportPaths(r.path, paths) {
+		if !underOperand(r.path, operands) {
 			return nil
 		}
 
@@ -172,6 +180,10 @@ 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
@@ -206,10 +218,18 @@ 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. Empty
-// files form no group, since removing one frees nothing.
+// 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 && 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]
@@ -258,13 +278,23 @@ func (w *reportWriter) finish() error {
 	return w.writeGroups()
 }
 
-// reportPaths returns the paths given to report or trees, each made
+// 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)
+}
+
+// cleanOperands returns the operands of report or trees, each made
 // absolute by absolutePath and then cleaned. The records hold real
 // paths, with no "." or ".." element and no repeated or trailing
-// slash, so a given path is cleaned to match them. No path is looked up
-// on the filesystem.
-func reportPaths(args []string) ([]string, error) {
-	paths := make([]string, 0, len(args))
+// slash, so an operand is cleaned to match them. No operand is looked
+// up on the filesystem.
+func cleanOperands(args []string) ([]string, error) {
+	operands := make([]string, 0, len(args))
 
 	for _, a := range args {
 		abs, err := absolutePath(a)
@@ -272,25 +302,25 @@ func reportPaths(args []string) ([]string, error) {
 			return nil, fmt.Errorf("resolve path %s: %w", escapePath(a), err)
 		}
 
-		paths = append(paths, filepath.Clean(abs))
+		operands = append(operands, filepath.Clean(abs))
 	}
 
-	return paths, nil
+	return operands, nil
 }
 
-// inReportPaths reports whether path is one of paths or lies below one
-// of them. Each of paths is clean and absolute, as reportPaths returns
-// it. With no paths, a report covers the whole database, so every path
-// is in it.
-func inReportPaths(path string, paths []string) bool {
-	if len(paths) == 0 {
+// underOperand reports whether path is one of operands or lies below
+// one of them. Each operand is clean and absolute, as cleanOperands
+// returns it. With no operands, a report covers the whole database, so
+// underOperand is true for every path.
+func underOperand(path string, operands []string) bool {
+	if len(operands) == 0 {
 		return true
 	}
 
-	for _, p := range paths {
+	for _, o := range operands {
 		// Only the root directory's clean path ends in "/".
-		dir := strings.TrimSuffix(p, "/") + "/"
-		if path == p || strings.HasPrefix(path, dir) {
+		dir := strings.TrimSuffix(o, "/") + "/"
+		if path == o || strings.HasPrefix(path, dir) {
 			return true
 		}
 	}

internal/sfdupes/report_test.go

@@ -72,15 +72,38 @@ 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, "", nil, &out, nil)
+	_, err := readReport(t.Context(), db, "", nil, &out, everyPathExists,
+		nil)
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -126,22 +149,27 @@ func dupeGroupsOf(t *testing.T, recs []scanRec) []dupeGroup {
 	return dupeGroups(t, db)
 }
 
-// TestRunReportPaths runs report with paths on three copies of one
-// file, two of them under /srv/photos, and a fourth copy in
-// /srv/photos2. Only the records at or below the given paths form the
-// groups and the totals, however each path is written.
+// TestRunReportOperands runs report with operands on three copies of
+// one file, two of them under srv/photos, and a fourth copy in
+// srv/photos2, all in a new directory. Only the records at or below the
+// operands form the groups and the totals, however each operand is
+// written.
 //
 //nolint:paralleltest // captureStderr replaces the process-wide os.Stderr
-func TestRunReportPaths(t *testing.T) {
+func TestRunReportOperands(t *testing.T) {
 	h := testHash("h")
-	a, x, y, z := "/a/copy", "/srv/photos/x", "/srv/photos/y", "/srv/photos2/z"
 
 	recs := make([]scanRec, 0, 4)
-	for _, p := range []string{a, x, y, z} {
+	for _, p := range []string{
+		"/a/copy", "/srv/photos/x", "/srv/photos/y", "/srv/photos2/z",
+	} {
 		recs = append(recs,
 			scanRec{size: 7, head: h, tail: h, content: h, path: p})
 	}
 
+	dir, recs := recsOnDisk(t, recs)
+	a, x, y, z := recs[0].path, recs[1].path, recs[2].path, recs[3].path
+
 	t.Setenv(databaseEnv, seedDatabase(t, recs))
 
 	header := "first\tdupe\tsize\n"
@@ -151,20 +179,20 @@ func TestRunReportPaths(t *testing.T) {
 	photos := header + row(x, y)
 
 	cases := map[string]struct {
-		paths   []string
-		want    string
-		summary string
+		operands []string
+		want     string
+		summary  string
 	}{
-		"directory": {[]string{"/srv/photos"}, photos,
+		"directory": {[]string{dir + "/srv/photos"}, photos,
 			"1 duplicate groups, 1 dupe files, 7 B reclaimable"},
-		"trailing slash":  {[]string{"/srv/photos/"}, photos, ""},
-		"dot and dot-dot": {[]string{"/srv/./a/../photos"}, photos, ""},
+		"trailing slash":  {[]string{dir + "/srv/photos/"}, photos, ""},
+		"dot and dot-dot": {[]string{dir + "/srv/./a/../photos"}, photos, ""},
 		"files":           {[]string{a, z}, header + row(a, z), ""},
-		"overlapping": {[]string{"/srv", "/srv/photos"},
+		"overlapping": {[]string{dir + "/srv", dir + "/srv/photos"},
 			header + row(x, y) + row(x, z), ""},
 		"root": {[]string{"/"},
 			header + row(a, x) + row(a, y) + row(a, z), ""},
-		"no record": {[]string{"/srv/photo"}, header,
+		"no record": {[]string{dir + "/srv/photo"}, header,
 			"0 duplicate groups, 0 dupe files, 0 B reclaimable"},
 	}
 
@@ -174,18 +202,18 @@ func TestRunReportPaths(t *testing.T) {
 
 			stderr := captureStderr(t)
 
-			code := run(append([]string{cmdReport}, tc.paths...),
+			code := run(append([]string{cmdReport}, tc.operands...),
 				&stdout, os.Stderr)
 			if code != exitOK {
 				t.Fatalf("run(report %q) = %d, want %d; stderr: %s",
-					tc.paths, code, exitOK, stderr())
+					tc.operands, code, exitOK, stderr())
 			}
 
 			if got := stdout.String(); got != tc.want {
 				t.Errorf("stdout = %q, want %q", got, tc.want)
 			}
 
-			// The records read are all four, whatever the paths.
+			// The records read are all four, whatever the operands.
 			summary := "report: 4 records read, " + tc.summary + "\n"
 			if got := stderr(); tc.summary != "" &&
 				!strings.HasSuffix(got, summary) {
@@ -196,7 +224,7 @@ func TestRunReportPaths(t *testing.T) {
 }
 
 //nolint:paralleltest // t.Chdir changes the process-wide working directory
-func TestReportPathsMakesRelativePathsAbsolute(t *testing.T) {
+func TestCleanOperandsMakesRelativePathsAbsolute(t *testing.T) {
 	dir := t.TempDir()
 	t.Chdir(dir)
 
@@ -205,7 +233,7 @@ func TestReportPathsMakesRelativePathsAbsolute(t *testing.T) {
 		t.Fatal(err)
 	}
 
-	got, err := reportPaths([]string{"photos/", "a/../b", "/c//d"})
+	got, err := cleanOperands([]string{"photos/", "a/../b", "/c//d"})
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -214,12 +242,13 @@ func TestReportPathsMakesRelativePathsAbsolute(t *testing.T) {
 		filepath.Join(wd, "photos"), filepath.Join(wd, "b"), "/c/d",
 	}
 	if !slices.Equal(got, want) {
-		t.Errorf("reportPaths = %q, want %q", got, want)
+		t.Errorf("cleanOperands = %q, want %q", got, want)
 	}
 }
 
 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
 
@@ -230,7 +259,7 @@ 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)
 	}
@@ -264,7 +293,8 @@ func TestReportStdoutFailsWhileReading(t *testing.T) {
 	// Counts the records read, and draws nothing.
 	prog := &progress{now: time.Now}
 
-	_, err = readReport(t.Context(), db, "", nil, failingWriter{}, prog)
+	_, err = readReport(t.Context(), db, "", nil, failingWriter{},
+		everyPathExists, prog)
 	if !errors.Is(err, errWriteFailed) ||
 		!strings.HasPrefix(err.Error(), "write stdout: ") {
 		t.Errorf("error = %v, want write stdout: %v", err, errWriteFailed)
@@ -295,7 +325,8 @@ 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)
@@ -308,8 +339,9 @@ 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.
@@ -358,7 +390,8 @@ func TestReadReportOnTerminal(t *testing.T) {
 		waitingFor: countingRecords,
 	}, terminalWidth, time.Hour, time.Now)
 
-	_, err = readReport(t.Context(), db, "", nil, os.Stderr, p)
+	_, err = readReport(t.Context(), db, "", nil, os.Stderr,
+		everyPathExists, p)
 
 	p.finish()
 
@@ -393,6 +426,8 @@ 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)
 
@@ -547,6 +582,120 @@ func TestDupeGroupsLeavesOutEmptyFiles(t *testing.T) {
 	}
 }
 
+// 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: "/copy/1"},
+		{size: 9, head: a, tail: a, content: a, path: "/copy/2"},
+		{size: 9, head: a, tail: a, content: a, path: "/copy/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, "", nil, io.Discard, exists, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	slices.Sort(checked)
+
+	want := []string{"/copy/1", "/copy/2", "/copy/3"}
+	if !slices.Equal(checked, want) {
+		t.Errorf("paths checked on disk = %q, want %q", checked, want)
+	}
+}
+
+// TestReadReportDropsGroupLeftWithOnePath checks that a group of two
+// paths, one of them gone, is no duplicate group. If kept, it would
+// write no row, but the summary line would count it.
+func TestReadReportDropsGroupLeftWithOnePath(t *testing.T) {
+	t.Parallel()
+
+	a := testHash("a")
+	recs := []scanRec{
+		{size: 9, head: a, tail: a, content: a, path: "/a/kept"},
+		{size: 9, head: a, tail: a, content: a, path: "/a/gone"},
+	}
+
+	db := openTestDB(t)
+
+	err := applyChanges(t.Context(), db, recs, nil, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	exists := func(path string) bool { return path != "/a/gone" }
+
+	report, err := readReport(t.Context(), db, "", nil, io.Discard, exists,
+		nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	if report.dupeGroups != 0 {
+		t.Errorf("duplicate groups = %d, want 0", report.dupeGroups)
+	}
+}
+
+// TestReadReportKeepsGroupLeftWithTwoPaths checks that a group of three
+// paths, one of them gone, is a duplicate group of the other two.
+func TestReadReportKeepsGroupLeftWithTwoPaths(t *testing.T) {
+	t.Parallel()
+
+	a := testHash("a")
+	recs := []scanRec{
+		{size: 9, head: a, tail: a, content: a, path: "/b/kept1"},
+		{size: 9, head: a, tail: a, content: a, path: "/b/gone"},
+		{size: 9, head: a, tail: a, content: a, path: "/b/kept2"},
+	}
+
+	db := openTestDB(t)
+
+	err := applyChanges(t.Context(), db, recs, nil, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	exists := func(path string) bool { return path != "/b/gone" }
+
+	var out bytes.Buffer
+
+	report, err := readReport(t.Context(), db, "", nil, &out, exists, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	if report.dupeGroups != 1 {
+		t.Errorf("duplicate groups = %d, want 1", report.dupeGroups)
+	}
+
+	want := "first\tdupe\tsize\n/b/kept1\t/b/kept2\t9\n"
+	if got := out.String(); got != want {
+		t.Errorf("stdout = %q, want %q", got, want)
+	}
+}
+
 func TestDupeGroupsContentSeparates(t *testing.T) {
 	t.Parallel()
 

internal/sfdupes/scan.go

@@ -102,40 +102,44 @@ 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. Once the database is open, the
-// scan notes its files, which the walk passes over.
+// enter the default excludes either. The walk neither enters nor
+// records the paths in excludePaths, 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.
 func runScan(ctx context.Context, roots []string, workers int,
-	oneFS, noDefaultExcludes bool,
+	oneFS, noDefaultExcludes bool, excludePaths []string,
 ) error {
 	dbPath, source, err := databasePath()
 	if err != nil {
 		return err
 	}
 
-	// A database file missing now is created by lockScanDatabase below.
-	what := "database"
+	printDatabasePath(dbPath, source)
 
-	_, err = os.Stat(dbPath)
-	if errors.Is(err, fs.ErrNotExist) {
-		what = "new database"
-	}
-
-	fmt.Fprintf(os.Stderr, "scan: %s %s (%s)\n", what, escapePath(dbPath),
-		source)
-
-	roots, err = resolveRoots(roots)
+	roots, err = realPaths(roots)
 	if err != nil {
 		return err
 	}
 
-	nonPersistent, err := nonPersistentFilesystems()
+	var rules walkRules
+
+	rules.excludePaths, err = excludePathInodes(excludePaths)
+	if err != nil {
+		return fmt.Errorf("--exclude: %w", err)
+	}
+
+	err = checkOperandsNotExcluded(roots, rules.excludePaths)
+	if err != nil {
+		return err
+	}
+
+	rules.nonPersistent, err = nonPersistentFilesystems()
 	if err != nil {
 		return fmt.Errorf("list the mounted filesystems: %w", err)
 	}
 
-	rules := walkRules{nonPersistent: nonPersistent}
 	if !noDefaultExcludes {
-		rules.excludes = defaultExcludes(runtime.GOOS)
+		rules.defaultExcludes = defaultExcludes(runtime.GOOS)
 	}
 
 	lock, err := lockScanDatabase(dbPath)
@@ -181,6 +185,21 @@ func runScan(ctx context.Context, roots []string, workers int,
 	return nil
 }
 
+// printDatabasePath prints on stderr the line that names the database
+// at dbPath, with source, saying whether it is new. A database file
+// missing now is new: lockScanDatabase creates it.
+func printDatabasePath(dbPath, source string) {
+	what := "database"
+
+	_, err := os.Stat(dbPath)
+	if errors.Is(err, fs.ErrNotExist) {
+		what = "new database"
+	}
+
+	fmt.Fprintf(os.Stderr, "scan: %s %s (%s)\n", what, escapePath(dbPath),
+		source)
+}
+
 // interruptContext returns a copy of ctx that the first SIGINT or
 // SIGTERM cancels; the scan command runs the scan under it. stop
 // releases the signals.
@@ -209,24 +228,25 @@ func interrupted(walked int) error {
 	return errInterrupted
 }
 
-// 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))
+// realPaths returns the real path of each of paths, the PATH operands
+// or the --exclude values: 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.
+func realPaths(paths []string) ([]string, error) {
+	resolved := make([]string, 0, len(paths))
 
-	for _, root := range roots {
-		a, err := absolutePath(root)
+	for _, path := range paths {
+		a, err := absolutePath(path)
 		if err != nil {
-			return nil, fmt.Errorf("resolve %s: %w", root, err)
+			return nil, fmt.Errorf("resolve %s: %w", path, err)
 		}
 
 		r, err := filepath.EvalSymlinks(a)
 		if err != nil {
-			return nil, fmt.Errorf("resolve %s: %w", root, err)
+			return nil, fmt.Errorf("resolve %s: %w", path, err)
 		}
 
 		resolved = append(resolved, r)
@@ -295,7 +315,7 @@ func walkReaches(above, r string, oneFS bool, rules walkRules,
 	}
 
 	for ; dir != above; dir = filepath.Dir(dir) {
-		if isDefaultExclude(dir, rules.excludes) {
+		if isDefaultExclude(dir, rules.defaultExcludes) {
 			return false
 		}
 
@@ -418,7 +438,7 @@ 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. The operands are real paths from resolveRoots,
+// directory named .zfs. The operands are real paths from realPaths,
 // 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
@@ -493,10 +513,11 @@ 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
-// 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.
+// 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.
 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.
@@ -545,7 +566,7 @@ func (s *scanState) walkPhase(events <-chan walkEvent, roots []string) {
 		prog.increment()
 
 		old, ok := s.existing[ev.rec.path]
-		if !ok || old.size != ev.rec.size || mtimeAfter(ev.rec.mtime, old.mtime) {
+		if !ok || old.size != ev.rec.size || !ev.rec.mtime.Equal(old.mtime) {
 			s.toHash = append(s.toHash, ev.rec)
 
 			continue
@@ -780,16 +801,6 @@ func (s *scanState) updatePhase(ctx context.Context) error {
 	return applyChanges(ctx, s.db, nil, deletes, prog)
 }
 
-// mtimeAfter reports whether mtime a is later than mtime b.
-// Not a.After(b): time.Time wraps an mtime past year 292 billion; Unix() undoes it.
-func mtimeAfter(a, b time.Time) bool {
-	if a.Unix() != b.Unix() {
-		return a.Unix() > b.Unix()
-	}
-
-	return a.Nanosecond() > b.Nanosecond()
-}
-
 // underAnyRoot reports whether path is any of the roots or lies under
 // one of them.
 func underAnyRoot(path string, roots []string) bool {
@@ -844,9 +855,9 @@ 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, 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, 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.
 type walkEvent struct {
 	rec        fileRec
 	warn       string
@@ -897,7 +908,7 @@ 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. resolveRoots has already followed the
+// inside a directory named .zfs. realPaths 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 {
@@ -1128,8 +1139,9 @@ 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. One of the scan's own database files in rules gets
-// no event at all.
+// naming it instead, and so does a file given with --exclude, reached
+// by any path, a hard link to it included. 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,
 ) {
@@ -1153,6 +1165,10 @@ func emitFile(ctx context.Context, p string, e fs.DirEntry,
 	}
 
 	line := rules.nonPersistentLine(p, info)
+	if line == "" {
+		line = rules.excludePathLine(p, info)
+	}
+
 	if line != "" {
 		sendEvent(ctx, events, walkEvent{leftOut: p, warn: line})
 
@@ -1177,11 +1193,11 @@ 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 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.
+// 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.
 func subdirJob(ctx context.Context, p string, e fs.DirEntry,
 	parent dirJob, oneFS bool, rules walkRules,
 	events chan<- walkEvent,
@@ -1206,13 +1222,17 @@ func subdirJob(ctx context.Context, p string, e fs.DirEntry,
 	}
 
 	line := rules.nonPersistentLine(p, info)
+	if line == "" {
+		line = rules.excludePathLine(p, info)
+	}
+
 	if line != "" {
 		sendEvent(ctx, events, walkEvent{leftOut: p, warn: line})
 
 		return dirJob{}, false
 	}
 
-	if isDefaultExclude(p, rules.excludes) {
+	if isDefaultExclude(p, rules.defaultExcludes) {
 		sendEvent(ctx, events, walkEvent{
 			leftOut: p,
 			warn:    fmt.Sprintf("scan: skipped %s (default exclude)", p),

internal/sfdupes/scan_test.go

@@ -1215,7 +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))
 	}
@@ -1384,6 +1384,47 @@ func TestSyncScanMtimeBump(t *testing.T) {
 	}
 }
 
+// TestSyncScanMtimeMovedBack replaces a file with other content of the
+// same size and an older mtime, as cp -p or a restore from backup does.
+// The next scan must hash the file again.
+func TestSyncScanMtimeMovedBack(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	a := writeFile(t, dir, "a.bin", pattern(1, 500))
+
+	recorded := time.Date(2026, 1, 2, 3, 4, 5, 0, time.UTC)
+
+	err := os.Chtimes(a, recorded, recorded)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	syncTree(t, db, dir)
+
+	replaced := pattern(3, 500)
+	writeFile(t, dir, "a.bin", replaced)
+
+	older := recorded.Add(-time.Hour)
+
+	err = os.Chtimes(a, older, older)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	st := syncTree(t, db, dir)
+	if st != (scanStats{walked: 1, updated: 1}) {
+		t.Fatalf("rescan stats = %+v, want 1 updated", st)
+	}
+
+	assertWholeFileHashed(t, db, a, replaced)
+
+	if r := recordByPath(t, dbRecords(t, db), a); !r.mtime.Equal(older) {
+		t.Fatalf("mtime = %v, want %v", r.mtime, older)
+	}
+}
+
 // assertWholeFileHashed fails unless the record for path holds the
 // whole-file hash of data as its head, tail, and content.
 func assertWholeFileHashed(t *testing.T, db *sql.DB, path string,
@@ -2248,7 +2289,7 @@ func TestPruneRoots(t *testing.T) {
 
 	// The walk of /p does not enter /p/q when it is a default exclude, so
 	// /p/q is kept, without -x too; /p/q/r lies under it and is dropped.
-	got = pruneRoots(nested, false, walkRules{excludes: []string{pqRoot}},
+	got = pruneRoots(nested, false, walkRules{defaultExcludes: []string{pqRoot}},
 		device)
 	if !slices.Equal(got, want) {
 		t.Fatalf("pruneRoots excluding %s = %q, want %q", pqRoot, got, want)
@@ -2266,23 +2307,86 @@ 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) {

internal/sfdupes/trees.go

@@ -37,12 +37,14 @@ 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 paths of the records at or below the given paths (of every record
-// when none is given), 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.
+// the paths of the records at or below the operands in args (of every
+// record when args is empty), computes a Merkle-style digest per
+// directory, and 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 never looks up an operand. 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
@@ -51,7 +53,7 @@ func treesPhase(name string) string {
 // the groups to stdout). Each display ends before the next phase
 // starts, and before an error is returned to be printed.
 func runTrees(ctx context.Context, args []string, stdout io.Writer) error {
-	paths, err := reportPaths(args)
+	operands, err := cleanOperands(args)
 	if err != nil {
 		return err
 	}
@@ -84,7 +86,7 @@ func runTrees(ctx context.Context, args []string, stdout io.Writer) error {
 		label: treesPhase("read"), unit: "records", total: -1,
 		waitingFor: countingRecords, stalledOn: "db",
 	})
-	records, super, allDirs, err := readTree(ctx, db, paths, prog)
+	records, super, allDirs, err := readTree(ctx, db, operands, prog)
 
 	prog.finish()
 
@@ -92,13 +94,13 @@ func runTrees(ctx context.Context, args []string, 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()
 
@@ -124,16 +126,16 @@ func runTrees(ctx context.Context, args []string, stdout io.Writer) error {
 
 // readTree gives prog the number of records in db as its total, then
 // reads every record in path order, counting each on prog. It adds the
-// records that inReportPaths selects from paths to the directory
+// records that underOperand finds under operands to the directory
 // hierarchy. It returns the number of records read, the super-root and
-// every directory at or below one of paths.
+// every directory at or below one of operands.
 //
-// A directory above every one of paths holds only the selected records
-// under it, so its digest does not describe it. It is left out of the
+// Any other directory lies above an operand and can hold files that are
+// not used, so its digest does not describe it. It is left out of the
 // directories returned. A directory whose parent is left out gets the
 // super-root as its parent, so suppressed never judges its group by
 // that parent's digest.
-func readTree(ctx context.Context, db *sql.DB, paths []string,
+func readTree(ctx context.Context, db *sql.DB, operands []string,
 	prog *progress,
 ) (int, *treeNode, []*treeNode, error) {
 	records := 0
@@ -144,7 +146,7 @@ func readTree(ctx context.Context, db *sql.DB, paths []string,
 
 		prog.increment()
 
-		if inReportPaths(r.path, paths) {
+		if underOperand(r.path, operands) {
 			tree.add(r)
 		}
 	})
@@ -157,11 +159,11 @@ func readTree(ctx context.Context, db *sql.DB, paths []string,
 	dirs := allDirs[:0]
 
 	for _, d := range allDirs {
-		if !inReportPaths(d.path, paths) {
+		if !underOperand(d.path, operands) {
 			continue
 		}
 
-		if !inReportPaths(d.parent.path, paths) {
+		if !underOperand(d.parent.path, operands) {
 			d.parent = super
 		}
 
@@ -330,12 +332,14 @@ 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. 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.
+// 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 {
@@ -353,6 +357,16 @@ func collectTreeGroups(allDirs []*treeNode, super *treeNode,
 			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
+		}
+
 		slices.SortFunc(g, func(a, b *treeNode) int {
 			return strings.Compare(a.path, b.path)
 		})

internal/sfdupes/trees_test.go

@@ -6,6 +6,7 @@ import (
 	"database/sql"
 	"os"
 	"slices"
+	"strconv"
 	"strings"
 	"testing"
 	"time"
@@ -179,7 +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"}}
@@ -195,7 +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
 
@@ -206,39 +208,41 @@ 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)
 	}
 }
 
-// TestRunTreesPaths runs trees with paths. /x/a and /y/a are copies,
-// and so are /y/a and /srv/b. /x and /y also hold files that differ.
-// Given /x/a and /y/a, trees reads /x and /y as holding one copy each
-// of a, yet neither is reported: only the directories at or below a
-// given path are.
-func TestRunTreesPaths(t *testing.T) {
+// TestRunTreesOperands runs trees with operands on records in a new
+// directory. x/a and y/a are copies, and so are y/a and srv/b. x and y
+// also hold files that differ. Given x/a and y/a, trees reads x and y
+// as holding one copy each of a, yet neither is reported: only the
+// directories at or below an operand are.
+func TestRunTreesOperands(t *testing.T) {
 	f, g, k := testHash("f"), testHash("g"), testHash("k")
-	recs := []scanRec{
+	dir, recs := recsOnDisk(t, []scanRec{
 		{size: 10, head: f, tail: f, content: f, path: "/srv/b/f"},
 		{size: 10, head: f, tail: f, content: f, path: "/x/a/f"},
 		{size: 20, head: g, tail: g, content: g, path: "/x/g"},
 		{size: 10, head: f, tail: f, content: f, path: "/y/a/f"},
 		{size: 30, head: k, tail: k, content: k, path: "/y/k"},
-	}
+	})
+	b, xa, ya := dir+"/srv/b", dir+"/x/a", dir+"/y/a"
 
 	header := "first\tdupe\tfiles\tsize\tdisk_size\n"
+	row := func(first, dupe string) string {
+		return first + "\t" + dupe + "\t1\t10\t0\n"
+	}
 
 	cases := map[string]struct {
-		paths []string
-		want  string
+		operands []string
+		want     string
 	}{
-		"none": {nil, header + "/srv/b\t/x/a\t1\t10\t0\n" +
-			"/srv/b\t/y/a\t1\t10\t0\n"},
-		"two copies": {[]string{"/x/a", "/y/a"},
-			header + "/x/a\t/y/a\t1\t10\t0\n"},
-		"parents":  {[]string{"/x", "/y"}, header + "/x/a\t/y/a\t1\t10\t0\n"},
-		"one copy": {[]string{"/srv/b"}, header},
+		"none":       {nil, header + row(b, xa) + row(b, ya)},
+		"two copies": {[]string{xa, ya}, header + row(xa, ya)},
+		"parents":    {[]string{dir + "/x", dir + "/y"}, header + row(xa, ya)},
+		"one copy":   {[]string{b}, header},
 	}
 
 	for name, tc := range cases {
@@ -247,11 +251,11 @@ func TestRunTreesPaths(t *testing.T) {
 
 			var stdout, stderr bytes.Buffer
 
-			code := run(append([]string{cmdTrees}, tc.paths...),
+			code := run(append([]string{cmdTrees}, tc.operands...),
 				&stdout, &stderr)
 			if code != exitOK {
 				t.Fatalf("run(trees %q) = %d, want %d; stderr: %s",
-					tc.paths, code, exitOK, stderr.String())
+					tc.operands, code, exitOK, stderr.String())
 			}
 
 			if got := stdout.String(); got != tc.want {
@@ -273,9 +277,11 @@ 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)
 	}
@@ -286,10 +292,11 @@ 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)
@@ -303,11 +310,15 @@ 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 + ")",
@@ -315,8 +326,9 @@ 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, ",
@@ -345,7 +357,7 @@ 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{
@@ -426,7 +438,7 @@ 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,
@@ -450,14 +462,16 @@ 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)
@@ -477,7 +491,7 @@ 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) {
@@ -506,7 +520,7 @@ func TestCollectTreeGroupsLeavesOutEmptyTrees(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) {
@@ -529,10 +543,98 @@ 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.
+func TestCollectTreeGroupsChecksOnlyReportedCopies(t *testing.T) {
+	t.Parallel()
+
+	f, g, u := testHash("f"), testHash("g"), testHash("u")
+	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: 10, head: f, tail: f, content: f, path: "/b/proj/f"},
+		{size: 20, head: g, tail: g, content: g, path: "/b/proj/sub/g"},
+		// /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])
+	}
+}
+
+// TestCollectTreeGroupsDropsGroupLeftWithOneCopy checks that a group of
+// two copies, one of them gone, is not returned. If kept, it would
+// write no row, but the summary line would count it.
+func TestCollectTreeGroupsDropsGroupLeftWithOneCopy(t *testing.T) {
+	t.Parallel()
+
+	f := testHash("f")
+	recs := []scanRec{
+		{size: 10, head: f, tail: f, content: f, path: "/c/kept/f"},
+		{size: 10, head: f, tail: f, content: f, path: "/c/gone/f"},
+	}
+
+	super, dirs := treeOf(t, recs)
+
+	exists := func(path string) bool { return path != "/c/gone" }
+
+	got := groupPaths(collectTreeGroups(dirs, super, exists, nil))
+	if len(got) != 0 {
+		t.Errorf("groups = %v, want none", got)
+	}
+}
+
+// TestCollectTreeGroupsKeepsGroupLeftWithTwoCopies checks that a group
+// of three copies, one of them gone, is returned with the other two.
+func TestCollectTreeGroupsKeepsGroupLeftWithTwoCopies(t *testing.T) {
+	t.Parallel()
+
+	f := testHash("f")
+	recs := []scanRec{
+		{size: 10, head: f, tail: f, content: f, path: "/d/kept1/f"},
+		{size: 10, head: f, tail: f, content: f, path: "/d/gone/f"},
+		{size: 10, head: f, tail: f, content: f, path: "/d/kept2/f"},
+	}
+
+	super, dirs := treeOf(t, recs)
+
+	exists := func(path string) bool { return path != "/d/gone" }
+
+	got := groupPaths(collectTreeGroups(dirs, super, exists, nil))
+
+	want := [][]string{{"/d/kept1", "/d/kept2"}}
+	if !slices.EqualFunc(got, want, slices.Equal) {
+		t.Errorf("groups = %v, want %v", got, want)
+	}
+}