Add 64 KiB head/tail and content-hash duplicate ladder (closes #61) (#62)

files.dat was the scan format before the SQLite database; nothing has
produced it since. Drop the stale references from the Makefile clean
target, .gitignore and .dockerignore. make clean still removes the
binary and .gitignore still covers the database files. The only
remaining mention is the historical entry in TODO.md.

Model: opus-4-8 (implementation); fable-5-1 (merge)

.dockerignore

@@ -2,7 +2,6 @@
 .claude
 .DS_Store
 sfdupes
-files.dat
 *.log
 *.out
 *.test

.gitignore

@@ -27,7 +27,6 @@ node_modules/
 *.log
 
 # Local scan data
-files.dat
 *.sqlite
 *.sqlite-shm
 *.sqlite-wal

Makefile

@@ -46,4 +46,4 @@ hooks:
 	@script/install-precommit
 
 clean:
-	rm -f $(BINARY) files.dat
+	rm -f $(BINARY)

README.md

@@ -5,14 +5,19 @@
 `sfdupes` is an MIT-licensed Go CLI tool by
 [@sneak](https://sneak.berlin) that quickly identifies *candidate*
 duplicate files — and, ultimately, entire duplicate directory trees —
-across very large filesystems without reading full file contents. Files
+across very large filesystems without reading every byte of every file.
-are considered duplicates when they have identical size, identical
+Files are considered duplicates when their sizes are equal and they
-SHA-256 of their first 1024 bytes, and identical SHA-256 of their last
+agree on a short ladder of hashes. A file under 10 MiB is hashed in full
-1024 bytes. This is a strong candidate signal, not proof of identical
+and compared directly. A larger file is gated first on the SHA-256 of
-content (the middle of the file is never read); the intended use is
+its first 64 KiB and of its last 64 KiB, and then compared on a content
+hash — the SHA-256 of the whole file when it is under 50 MiB, or of
+gigabyte-spaced 1 MiB samples when it is 50 MiB or larger. Below 50 MiB
+the content hash is proof of identical content; at or above 50 MiB it is
+a strong candidate signal rather than proof, because the gaps between
+samples are never read. The intended use is
 finding duplicate downloads and duplicated directory trees on
-multi-terabyte ZFS servers where reading every byte is prohibitively
+multi-terabyte ZFS servers where reading every byte of every file is
-expensive. `scan` maintains a persistent SQLite database of file
+prohibitively expensive. `scan` maintains a persistent SQLite database of file
 signatures that survives between runs, so it can be run from cron and
 the reports can be generated at any time from the most recent scan.
 
@@ -29,7 +34,8 @@ export SFDUPES_DATABASE="$HOME/.local/share/sfdupes/db.sqlite"
 ```
 
 `scan` walks one or more filesystem trees and maintains one database
-record per regular file (path, size, mtime, head hash, tail hash). The
+record per regular file (path, size, mtime, head hash, tail hash,
+content hash). The
 database persists between runs; a rescan only hashes files that are new
 or changed, and removes records for files that no longer exist.
 `report` reads the database and prints the file-level duplicates
@@ -47,10 +53,13 @@ completed scan.
 
 Duplicate finders that hash entire files do not scale to the target
 environment: ~10 million files and ~150 TB on possibly slow or busy
-disks (a ZFS pool under resilver). Reading at most 2 KiB per file — and
+disks (a ZFS pool under resilver). sfdupes spends disk I/O only on files
-only from files whose size at least one other file shares, since a
+whose size at least one other file shares, since a size-unique file
-size-unique file cannot be a duplicate — makes a full-filesystem sweep
+cannot be a duplicate; for those it reads the cheap end windows first
-tractable, and the signatures are kept in a persistent database, so
+and a content hash second — the whole file below 50 MiB, but only
+gigabyte-spaced samples at or above 50 MiB, so the largest files are
+never read in full. This keeps a full-filesystem sweep tractable, and
+the signatures are kept in a persistent database, so
 the expensive filesystem pass is incremental: a rescan re-hashes only
 files whose recorded mtime or size changed, and all analysis happens
 offline from the database alone. The end goal is
@@ -68,14 +77,18 @@ Goals, in order:
     downloads, copied project trees), so the operator can consider
     removing an entire subtree at once. File-level duplicate detection is
     the foundation; tree-level detection is built on top of it.
-2.  **Never read full file contents.** At most 2 KiB is read per file
+2.  **Spend I/O in proportion to duplicate likelihood.** Only files
-    (first and last 1024 bytes), and only files whose size at least
+    whose size at least one other file shares are read at all — a
-    one other file shares are read at all — a size-unique file cannot
+    size-unique file cannot be a duplicate. Those are compared by the
-    be a duplicate. Scale target: tens of millions of files, ~150 TB
+    ladder in "Duplicate detection" below: a file under 10 MiB is hashed
-    filesystem, possibly slow or busy disks (ZFS pool under resilver).
+    in full, while a larger file is gated on cheap 64 KiB end windows
-    Holding one small record (path, size, mtime) per file in memory
+    first, then a content hash that reads the whole file below 50 MiB
-    during a scan is acceptable; holding every file's hashes is not
+    but only gigabyte-spaced 1 MiB samples at or above it, so the very
-    (they stay in the database).
+    largest files are still never read in full. Scale target: tens of
+    millions of files, ~150 TB filesystem, possibly slow or busy disks
+    (ZFS pool under resilver). Holding one small record (path, size,
+    mtime) per file in memory during a scan is acceptable; holding
+    every file's hashes is not (they stay in the database).
 3.  **Scan incrementally, analyze offline.** The expensive filesystem
     scan maintains a persistent database; an unchanged file is never
     read again on a rescan. All analysis (`report`, `trees`) works from
@@ -141,26 +154,72 @@ All three subcommands operate on a single SQLite database file:
     that dies partway leaves a valid database holding everything
     hashed so far; the next scan skips those records and converges
     toward the filesystem.
--   Schema (`PRAGMA user_version` is the schema version, currently 1; a
+-   Schema (`PRAGMA user_version` is the schema version, currently 2; a
-    database with any other version is a fatal error):
+    database with any other version is a fatal error). Version 2 added
+    the `content` column and the 64 KiB head/tail signature (replacing
+    the version 1 1 KiB end windows), so a version 1 database cannot be
+    reused: it is rejected and the tree must be rescanned from scratch.
 
     ```sql
     CREATE TABLE files (
-        path  BLOB PRIMARY KEY,  -- absolute path, raw bytes
+        path    BLOB PRIMARY KEY,  -- absolute path, raw bytes
-        size  INTEGER NOT NULL,  -- bytes, from lstat
+        size    INTEGER NOT NULL,  -- bytes, from lstat
-        mtime INTEGER NOT NULL,  -- Unix seconds, from lstat
+        mtime   INTEGER NOT NULL,  -- Unix seconds, from lstat
-        head  TEXT NOT NULL,     -- lowercase-hex SHA-256, first 1 KiB
+        head    TEXT NOT NULL,     -- lowercase-hex SHA-256; first 64 KiB, or whole file under 10 MiB
-        tail  TEXT NOT NULL      -- lowercase-hex SHA-256, last 1 KiB
+        tail    TEXT NOT NULL,     -- lowercase-hex SHA-256; last 64 KiB, or whole file under 10 MiB
+        content TEXT NOT NULL      -- lowercase-hex SHA-256, whole file or samples
     ) WITHOUT ROWID;
     ```
 
     Paths are stored as BLOBs because Unix paths are raw bytes, not
     guaranteed UTF-8. `mtime` is used only for change detection; it is
-    not part of the duplicate key. `head` and `tail` are empty strings
+    not part of the duplicate key. For a file under 10 MiB `head`, `tail`,
-    when the file has never been hashed because its size was unique as
+    and `content` all hold the whole-file hash (that range is hashed in
-    of the last scan that covered it; such records still define the
+    full, with no end windows); for a larger file `head` and `tail` hold
-    file for tree reconstruction but never participate in duplicate
+    the first- and last-64 KiB hashes and `content` the whole-file or
-    groups.
+    sampled hash. All three are empty strings when the file has never
+    been hashed because its size was unique as of the last scan that
+    covered it; such records still define the file for tree
+    reconstruction but never participate in duplicate groups.
+
+### Duplicate detection
+
+Two files are duplicates only when they agree on every rung of this
+ladder; a mismatch at any rung means they are not duplicates. `scan`
+stores each file's hashes once, and `report` and `trees` group files by
+the whole signature — size, `head`, `tail`, and `content` — so the
+grouping is exactly this ladder applied across everything scanned into
+the database, even across separate scans.
+
+1.  **Size.** Files of different sizes are never compared. Only files
+    whose size at least one other file shares are hashed at all.
+2.  **Under 10 MiB: whole file.** A file smaller than 10 MiB is hashed
+    in full and compared directly, with no separate end-window step —
+    small files are cheap to read to the last byte, and doing so makes
+    the comparison exact. `head`, `tail`, and `content` all hold this
+    whole-file SHA-256, so such a file's signature is decided entirely
+    by its size and its content.
+3.  **10 MiB and above: head and tail.** For a larger file, the SHA-256
+    of the first 64 KiB (`head`) and of the last 64 KiB (`tail`) are a
+    cheap gate that eliminates most same-size pairs before any bulk
+    reading. At 10 MiB and above the two windows never overlap.
+4.  **10 MiB and above, content below 50 MiB.** The SHA-256 of the
+    entire file. Agreement here is proof of identical content (barring a
+    SHA-256 collision).
+5.  **10 MiB and above, content 50 MiB and above.** A sampled SHA-256:
+    the 1 MiB window at each gigabyte-aligned offset (0, 1 GiB, 2 GiB, …
+    while inside the file, the final window truncated at end of file) is
+    fed, in order, into one hash. This is **deliberately probabilistic**
+    — the gaps between samples are never read, so two large files that
+    agree on every sample are reported as duplicates without being read
+    in full. It is the price of never reading a 150 GB file end to end.
+    Because size is already part of the signature, only equal-size files
+    reach this rung, so their sample boundaries always align.
+
+`head`, `tail`, and `content` are one column each. A file below 10 MiB
+and one at or above it never share a size, and neither do a file below
+50 MiB and one at or above it, so a stored value is never ambiguous
+between the whole-file, end-window, and sampled forms.
 
 ### `scan` mode
 
@@ -229,10 +288,9 @@ during the hash phase:
     decides its fate. Size-unique files are never read: new or
     changed ones are recorded without hashes in the update phase,
     unchanged unhashed ones simply keep their records. Every file
-    with a shared size is hashed by the worker pool: read the first
+    with a shared size is hashed by the worker pool, computing the
-    `min(1024, size)` bytes and the last `min(1024, size)` bytes
+    full signature — head, tail, and content — described in "Duplicate
-    (one read when `size <= 1024`, since the two windows coincide)
+    detection" below. Zero-length files have constant
-    and compute the SHA-256 of each. Zero-length files have constant
     hashes and are never opened. Files are hashed in **inode order**
     (minimizing seeks on spinning disks), and paths that are hard
     links to the same inode are **read once**, all sharing the one

TODO.md

@@ -29,6 +29,24 @@
 
 # Completed Steps
 
+- replace the 1 KiB end-window sampling with the head/tail plus
+  content-hash ladder (2026-09-22, branch `next`, closes
+  https://git.eeqj.de/sneak/sfdupes/issues/61): a file under 10 MiB is
+  hashed in full and compared directly, with no end-window step — its
+  `head`, `tail`, and `content` all hold the whole-file hash. A file at
+  10 MiB or above is gated on the 64 KiB `head` and `tail`, then
+  compared on a `content` hash — the whole file below 50 MiB,
+  gigabyte-spaced 1 MiB samples at or above. Schema bumps to version 2
+  (new `content` column); a version 1 database is rejected and must be
+  rescanned, which is required anyway since every stored hash changed.
+  `report` and `trees` group by the extended signature, so the ladder is
+  applied across the whole database. README "Duplicate detection"
+  documents every rung including the probabilistic large-file path.
+
+- remove the dead `files.dat` references from `Makefile`, `.gitignore`
+  and `.dockerignore` (2026-09-21, branch `next`, closes
+  https://git.eeqj.de/sneak/sfdupes/issues/22)
+
 - fix the lint-image pin comments and `FROM` form in `Dockerfile` and
   `Dockerfile.lint` (2026-08-10, branch `next`, closes
   https://git.eeqj.de/sneak/sfdupes/issues/25): dropped the false

db.go

@@ -25,8 +25,11 @@ const defaultDatabasePath = "/var/lib/sfdupes/db.sqlite"
 const databaseEnv = "SFDUPES_DATABASE"
 
 // schemaVersion is the database schema version this build reads and
-// writes, stored in PRAGMA user_version.
+// writes, stored in PRAGMA user_version. Version 2 adds the content
-const schemaVersion = 1
+// column and the head/tail/content signature (replacing the version 1
+// 1 KiB end windows), so a version 1 database is rejected and must be
+// rescanned.
+const schemaVersion = 2
 
 // dbDirPerm is the mode for a database parent directory created by
 // scan.
@@ -36,22 +39,24 @@ const dbDirPerm = 0o755
 // BLOBs because Unix paths are raw bytes, not guaranteed UTF-8.
 const createTableSQL = `
 CREATE TABLE files (
-    path  BLOB PRIMARY KEY,
+    path    BLOB PRIMARY KEY,
-    size  INTEGER NOT NULL,
+    size    INTEGER NOT NULL,
-    mtime INTEGER NOT NULL,
+    mtime   INTEGER NOT NULL,
-    head  TEXT NOT NULL,
+    head    TEXT NOT NULL,
-    tail  TEXT NOT NULL
+    tail    TEXT NOT NULL,
+    content TEXT NOT NULL
 ) WITHOUT ROWID
 `
 
 // upsertSQL inserts one file record, replacing any existing record for
 // the same path.
 const upsertSQL = `
-INSERT INTO files (path, size, mtime, head, tail)
+INSERT INTO files (path, size, mtime, head, tail, content)
-VALUES (?, ?, ?, ?, ?)
+VALUES (?, ?, ?, ?, ?, ?)
 ON CONFLICT (path) DO UPDATE SET
     size = excluded.size, mtime = excluded.mtime,
-    head = excluded.head, tail = excluded.tail
+    head = excluded.head, tail = excluded.tail,
+    content = excluded.content
 `
 
 // errNoDatabase reports a missing database file for report/trees.
@@ -205,7 +210,7 @@ func userVersion(ctx context.Context, db *sql.DB) (int, error) {
 // loadFileRows reads every record from the files table.
 func loadFileRows(ctx context.Context, db *sql.DB) ([]scanRec, error) {
 	rows, err := db.QueryContext(ctx,
-		"SELECT path, size, mtime, head, tail FROM files")
+		"SELECT path, size, mtime, head, tail, content FROM files")
 	if err != nil {
 		return nil, fmt.Errorf("read records: %w", err)
 	}
@@ -220,7 +225,8 @@ func loadFileRows(ctx context.Context, db *sql.DB) ([]scanRec, error) {
 			r    scanRec
 		)
 
-		err = rows.Scan(&path, &r.size, &r.mtime, &r.head, &r.tail)
+		err = rows.Scan(&path, &r.size, &r.mtime, &r.head, &r.tail,
+			&r.content)
 		if err != nil {
 			return nil, fmt.Errorf("read record: %w", err)
 		}
@@ -348,7 +354,7 @@ func execUpserts(ctx context.Context, tx *sql.Tx, upserts []scanRec,
 
 	for _, r := range upserts {
 		_, err = st.ExecContext(ctx,
-			[]byte(r.path), r.size, r.mtime, r.head, r.tail)
+			[]byte(r.path), r.size, r.mtime, r.head, r.tail, r.content)
 		if err != nil {
 			return fmt.Errorf("upsert %s: %w", r.path, err)
 		}

report.go

@@ -17,14 +17,15 @@ const ioBufSize = 1 << 20
 const minGroupSize = 2
 
 // scanRec is one file record from the database. The signature (size,
-// head, tail) is the duplicate key; mtime is informational only and
+// head, tail, content) is the duplicate key; mtime is informational
-// used by scan for change detection.
+// only and used by scan for change detection.
 type scanRec struct {
-	size  int64
+	size    int64
-	mtime int64
+	mtime   int64
-	head  string
+	head    string
-	tail  string
+	tail    string
-	path  string
+	content string
+	path    string
 }
 
 // loadRecords opens the database and reads every file record for the
@@ -52,8 +53,9 @@ func loadRecords(ctx context.Context) ([]scanRec, error) {
 }
 
 // dupeGroup is one set of candidate-duplicate files: identical size,
-// head hash, and tail hash. paths is sorted lexicographically; the
+// head hash, tail hash, and content hash. paths is sorted
-// first entry is the group's "first", the rest are dupes.
+// lexicographically; the first entry is the group's "first", the rest
+// are dupes.
 type dupeGroup struct {
 	size  int64
 	paths []string
@@ -122,7 +124,9 @@ func collectDupeGroups(recs []scanRec) []dupeGroup {
 			continue
 		}
 
-		k := fileSig{size: r.size, head: r.head, tail: r.tail}
+		k := fileSig{
+			size: r.size, head: r.head, tail: r.tail, content: r.content,
+		}
 		groups[k] = append(groups[k], r.path)
 	}
 

report_test.go

@@ -38,6 +38,28 @@ func TestCollectDupeGroups(t *testing.T) {
 	}
 }
 
+func TestCollectDupeGroupsContentSeparates(t *testing.T) {
+	t.Parallel()
+
+	// Same size, head, and tail, but different content hashes: the final
+	// rung keeps them apart, so no group forms. Matching content groups.
+	recs := []scanRec{
+		{size: 100, head: "h", tail: "t", content: "c1", path: "/a"},
+		{size: 100, head: "h", tail: "t", content: "c2", path: "/b"},
+		{size: 100, head: "h", tail: "t", content: "c1", path: "/c"},
+	}
+
+	groups := collectDupeGroups(recs)
+	if len(groups) != 1 {
+		t.Fatalf("len(groups) = %d, want 1 (only the matching content)",
+			len(groups))
+	}
+
+	if !slices.Equal(groups[0].paths, []string{"/a", "/c"}) {
+		t.Errorf("group paths = %q, want /a /c", groups[0].paths)
+	}
+}
+
 func TestCollectDupeGroupsMtimeExcluded(t *testing.T) {
 	t.Parallel()
 

scan.go

@@ -7,6 +7,7 @@ import (
 	"database/sql"
 	"encoding/hex"
 	"fmt"
+	"io"
 	"io/fs"
 	"os"
 	"path/filepath"
@@ -16,8 +17,37 @@ import (
 	"syscall"
 )
 
-// chunk is the number of bytes hashed from each end of a file.
+// The duplicate ladder (see hashSignature and README "Duplicate
-const chunk = 1024
+// detection"). A same-size candidate below headTailMin is hashed in
+// full and compared directly; a larger one is separated first by the
+// hashes of its end windows, then by a content hash that is exact below
+// wholeFileMax and deliberately sampled at or above it.
+
+// headTailMin is the size threshold for the end-window gate. A file
+// smaller than this is hashed in full directly, with no separate head
+// and tail step: its head, tail, and content all carry the whole-file
+// hash. A file this size or larger is separated first by its end
+// windows.
+const headTailMin = 10 * 1024 * 1024
+
+// headTailWindow is the number of bytes hashed from each end of a file
+// at or above headTailMin (the head and tail rungs). Because
+// headTailMin is far larger than two windows, the head and tail windows
+// never overlap.
+const headTailWindow = 64 * 1024
+
+// wholeFileMax is the size boundary between the two content rungs: a
+// file strictly smaller than this is content-hashed in full; a file
+// this size or larger is content-hashed by sampling.
+const wholeFileMax = 50 * 1024 * 1024
+
+// sampleStride is the spacing between content samples for large files:
+// one window is read at each gigabyte-aligned offset (0, 1 GiB, ...).
+const sampleStride = 1024 * 1024 * 1024
+
+// sampleWindow is the number of bytes read at each large-file sample
+// offset, truncated at end of file.
+const sampleWindow = 1024 * 1024
 
 // workQueueDepth bounds the job and result channels feeding the walk
 // and hash worker pools.
@@ -439,11 +469,12 @@ func (s *scanState) recordRun(ctx context.Context, r hashResult) error {
 		s.resolve(rec.path)
 
 		s.batch = append(s.batch, scanRec{
-			size:  rec.size,
+			size:    rec.size,
-			mtime: rec.mtime,
+			mtime:   rec.mtime,
-			head:  r.head,
+			head:    r.head,
-			tail:  r.tail,
+			tail:    r.tail,
-			path:  rec.path,
+			content: r.content,
+			path:    rec.path,
 		})
 	}
 
@@ -834,13 +865,15 @@ func inodeOfInfo(fi fs.FileInfo) (uint64, uint64) {
 	return statDev(st), st.Ino
 }
 
-// hashResult carries one inode run's head/tail hashes (or the error
+// hashResult carries one inode run's signature hashes — head, tail, and
-// that prevented hashing it) from the hash workers to the hash phase.
+// content — (or the error that prevented hashing it) from the hash
+// workers to the hash phase.
 type hashResult struct {
-	run  []fileRec
+	run     []fileRec
-	head string
+	head    string
-	tail string
+	tail    string
-	err  error
+	content string
+	err     error
 }
 
 // hashPool owns every goroutine of the hash worker pool: the feeder
@@ -930,11 +963,11 @@ func hashWorker(ctx context.Context, jobs <-chan []fileRec,
 			continue
 		}
 
-		head, tail, err := hashHeadTail(run[0].path, run[0].size)
+		head, tail, content, err := hashSignature(run[0].path, run[0].size)
 
 		select {
 		case results <- hashResult{
-			run: run, head: head, tail: tail, err: err,
+			run: run, head: head, tail: tail, content: content, err: err,
 		}:
 		case <-ctx.Done():
 			return
@@ -942,55 +975,138 @@ func hashWorker(ctx context.Context, jobs <-chan []fileRec,
 	}
 }
 
-// emptyHash is the lowercase-hex SHA-256 of the empty input: the head
+// emptyHash is the lowercase-hex SHA-256 of the empty input: the head,
-// and tail hash of every zero-length file.
+// tail, and content hash of every zero-length file.
 const emptyHash = "e3b0c44298fc1c149afbf4c8996fb924" +
 	"27ae41e4649b934ca495991b7852b855"
 
-// hashHeadTail returns the lowercase-hex SHA-256 of the first
+// hashSignature computes the three content hashes that, with the file
-// min(chunk, size) bytes and of the last min(chunk, size) bytes of the
+// size, form its duplicate signature. A file below headTailMin is
-// file at path. The two reads overlap when size < 2*chunk. size is the
+// hashed in full and its whole-file SHA-256 is returned as head, tail,
-// value recorded when the file was statted; a zero-length file's
+// and content alike — that range takes no separate end-window step. For
-// hashes are constant, so it is never even opened.
+// a file at or above headTailMin the head and tail are the SHA-256 of
-func hashHeadTail(path string, size int64) (string, string, error) {
+// its first and last headTailWindow bytes, and content is the SHA-256
+// of the whole file below wholeFileMax (the exact rung) or of
+// gigabyte-spaced samples at or above it (the sampled, deliberately
+// probabilistic rung). Two files are duplicates only when all four
+// agree; any mismatch means not a duplicate. size is the value recorded
+// when the file was statted; a zero-length file has constant hashes and
+// is never opened.
+func hashSignature(path string, size int64) (string, string, string, error) {
 	if size == 0 {
-		return emptyHash, emptyHash, nil
+		return emptyHash, emptyHash, emptyHash, nil
 	}
 
 	//nolint:gosec // hashing operator-supplied paths is the tool's purpose
 	f, err := os.Open(path)
 	if err != nil {
-		return "", "", err
+		return "", "", "", err
 	}
 
 	defer func() { _ = f.Close() }()
 
-	n := min(int64(chunk), size)
+	// Below the threshold the whole file is hashed directly, with no
+	// end-window step: head and tail both carry the whole-file hash.
+	if size < int64(headTailMin) {
+		content, err := hashWhole(f, size)
+		if err != nil {
+			return "", "", "", err
+		}
 
-	buf := make([]byte, n)
+		return content, content, content, nil
+	}
 
-	_, err = f.ReadAt(buf, 0)
+	head, tail, err := hashEnds(f, size)
+	if err != nil {
+		return "", "", "", err
+	}
+
+	content, err := hashContent(f, size)
+	if err != nil {
+		return "", "", "", err
+	}
+
+	return head, tail, content, nil
+}
+
+// hashEnds returns the SHA-256 of the first and last headTailWindow
+// bytes of f. It is called only for files at least headTailMin, which
+// is far larger than two windows, so the windows never overlap and both
+// reads are always full.
+func hashEnds(f *os.File, size int64) (string, string, error) {
+	buf := make([]byte, headTailWindow)
+
+	_, err := f.ReadAt(buf, 0)
 	if err != nil {
 		return "", "", err
 	}
 
 	h := sha256.Sum256(buf)
+	head := hex.EncodeToString(h[:])
 
-	// When the whole file fits in one chunk the tail window is exactly
+	_, err = f.ReadAt(buf, size-int64(headTailWindow))
-	// the bytes just read: reuse the head hash instead of issuing a
-	// second read for every small file.
-	if size <= int64(chunk) {
-		hh := hex.EncodeToString(h[:])
-
-		return hh, hh, nil
-	}
-
-	_, err = f.ReadAt(buf, size-n)
 	if err != nil {
 		return "", "", err
 	}
 
 	t := sha256.Sum256(buf)
 
-	return hex.EncodeToString(h[:]), hex.EncodeToString(t[:]), nil
+	return head, hex.EncodeToString(t[:]), nil
+}
+
+// hashContent returns the content-rung hash of f: the SHA-256 of the
+// whole file when it is smaller than wholeFileMax, or of sampled
+// windows when it is that size or larger.
+func hashContent(f *os.File, size int64) (string, error) {
+	if size >= int64(wholeFileMax) {
+		return hashSamples(f, size)
+	}
+
+	return hashWhole(f, size)
+}
+
+// hashWhole returns the SHA-256 of the entire file. A SectionReader is
+// used so the read is independent of the offset left by any end-window
+// reads. Reading fewer than size bytes means the file shrank between
+// the stat and the hash; that is an error rather than a hash of content
+// that no longer matches the recorded size.
+func hashWhole(f *os.File, size int64) (string, error) {
+	h := sha256.New()
+
+	n, err := io.Copy(h, io.NewSectionReader(f, 0, size))
+	if err != nil {
+		return "", err
+	}
+
+	if n != size {
+		return "", fmt.Errorf("read %d of %d bytes: %w", n, size,
+			io.ErrUnexpectedEOF)
+	}
+
+	return hex.EncodeToString(h.Sum(nil)), nil
+}
+
+// hashSamples feeds sampleWindow bytes at each gigabyte-aligned offset
+// (0, sampleStride, 2*sampleStride, ... while inside the file), in
+// order, into one hash, each window truncated at end of file. This is
+// the probabilistic large-file rung: two files of equal size agreeing
+// on every sample are reported as duplicates without every byte being
+// read. Because size is part of the signature, files of different sizes
+// never reach this comparison, so the sample boundaries always align.
+func hashSamples(f *os.File, size int64) (string, error) {
+	h := sha256.New()
+	buf := make([]byte, sampleWindow)
+
+	for off := int64(0); off < size; off += int64(sampleStride) {
+		n := min(int64(sampleWindow), size-off)
+
+		_, err := f.ReadAt(buf[:n], off)
+		if err != nil {
+			return "", err
+		}
+
+		h.Write(buf[:n])
+	}
+
+	return hex.EncodeToString(h.Sum(nil)), nil
 }

scan_test.go

@@ -53,7 +53,23 @@ func pattern(tag byte, n int) []byte {
 	return data
 }
 
-func TestHashHeadTail(t *testing.T) {
+// sig returns a file's full signature (head, tail, content), failing the
+// test on any error.
+func sig(t *testing.T, path string, size int64) (string, string, string) {
+	t.Helper()
+
+	head, tail, content, err := hashSignature(path, size)
+	if err != nil {
+		t.Fatalf("hashSignature %s: %v", path, err)
+	}
+
+	return head, tail, content
+}
+
+// TestHashSignatureBelowThreshold verifies that a file below headTailMin
+// is hashed in full and compared directly: head, tail, and content all
+// carry the whole-file SHA-256, with no separate end-window step.
+func TestHashSignatureBelowThreshold(t *testing.T) {
 	t.Parallel()
 
 	dir := t.TempDir()
@@ -62,13 +78,10 @@ func TestHashHeadTail(t *testing.T) {
 		name string
 		data []byte
 	}{
-		{"empty", nil},
 		{"one-byte", []byte("x")},
-		{"under-one-chunk", pattern(1, chunk-1)},
+		{"one-window", pattern(1, headTailWindow)},
-		{"exactly-one-chunk", pattern(2, chunk)},
+		{"several-windows", pattern(2, 3*headTailWindow)},
-		{"overlapping-reads", pattern(3, chunk+chunk/2)},
+		{"near-threshold", pattern(3, headTailMin-1)},
-		{"exactly-two-chunks", pattern(4, 2*chunk)},
-		{"beyond-two-chunks", pattern(5, 3*chunk)},
 	}
 	for _, c := range cases {
 		t.Run(c.name, func(t *testing.T) {
@@ -76,49 +89,240 @@ func TestHashHeadTail(t *testing.T) {
 
 			p := writeFile(t, dir, c.name, c.data)
 
-			head, tail, err := hashHeadTail(p, int64(len(c.data)))
+			head, tail, content := sig(t, p, int64(len(c.data)))
-			if err != nil {
-				t.Fatalf("hashHeadTail: %v", err)
-			}
 
-			n := min(chunk, len(c.data))
+			whole := hexSum(c.data)
-			if want := hexSum(c.data[:n]); head != want {
+			if head != whole || tail != whole || content != whole {
-				t.Errorf("head = %s, want %s", head, want)
+				t.Errorf("head=%s tail=%s content=%s, want all whole-file %s",
-			}
+					head, tail, content, whole)
-
-			if want := hexSum(c.data[len(c.data)-n:]); tail != want {
-				t.Errorf("tail = %s, want %s", tail, want)
 			}
 		})
 	}
 }
 
-func TestHashHeadTailErrors(t *testing.T) {
+// TestHashSignatureEnds exercises the head and tail rungs, which apply
+// only to files at least headTailMin. Sparse files keep the fixtures
+// cheap: a difference in the first window changes only head, a
+// difference in the last window changes only tail, and a difference
+// between the windows changes neither end hash but does change the
+// whole-file content rung (the file is below wholeFileMax).
+func TestHashSignatureEnds(t *testing.T) {
 	t.Parallel()
 
 	dir := t.TempDir()
 
-	_, _, err := hashHeadTail(filepath.Join(dir, "missing"), 1)
+	// Between headTailMin and wholeFileMax: the end-window gate is active
+	// and the content rung is a whole-file hash.
+	const size = int64(headTailMin + 2*1024*1024)
+
+	base := sparseFile(t, dir, "ends-base", size)
+	headDiff := sparseFile(t, dir, "ends-head", size)
+	tailDiff := sparseFile(t, dir, "ends-tail", size)
+	midDiff := sparseFile(t, dir, "ends-mid", size)
+
+	pokeAt(t, headDiff, 0, []byte{1})
+	pokeAt(t, tailDiff, size-1, []byte{1})
+	pokeAt(t, midDiff, size/2, []byte{1})
+
+	bHead, bTail, bContent := sig(t, base, size)
+
+	h, tl, c := sig(t, headDiff, size)
+	if h == bHead {
+		t.Error("a byte in the first window did not change head")
+	}
+
+	if tl != bTail {
+		t.Error("a byte in the first window changed tail")
+	}
+
+	if c == bContent {
+		t.Error("a byte in the first window did not change content")
+	}
+
+	h, tl, c = sig(t, tailDiff, size)
+	if tl == bTail {
+		t.Error("a byte in the last window did not change tail")
+	}
+
+	if h != bHead {
+		t.Error("a byte in the last window changed head")
+	}
+
+	if c == bContent {
+		t.Error("a byte in the last window did not change content")
+	}
+
+	h, tl, c = sig(t, midDiff, size)
+	if h != bHead || tl != bTail {
+		t.Error("a byte between the windows changed an end hash")
+	}
+
+	if c == bContent {
+		t.Error("whole-file content rung ignored a byte between the windows")
+	}
+}
+
+func TestHashSignatureErrors(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+
+	// A missing file: an error, and every hash left empty.
+	head, tail, content, err := hashSignature(filepath.Join(dir, "missing"), 1)
 	if err == nil {
 		t.Error("no error for a missing file")
 	}
 
+	if head != "" || tail != "" || content != "" {
+		t.Errorf("missing file returned hashes: %q %q %q", head, tail, content)
+	}
+
 	// A zero-length file has constant hashes and is never opened: even
 	// a missing path succeeds.
-	head, tail, err := hashHeadTail(filepath.Join(dir, "missing"), 0)
+	head, tail, content, err = hashSignature(filepath.Join(dir, "missing"), 0)
-	if err != nil || head != emptyHash || tail != emptyHash {
+	if err != nil ||
-		t.Errorf("empty: head=%q tail=%q err=%v, want constant hashes",
+		head != emptyHash || tail != emptyHash || content != emptyHash {
-			head, tail, err)
+		t.Errorf("empty: head=%q tail=%q content=%q err=%v, "+
+			"want constant hashes", head, tail, content, err)
 	}
 
 	// A file that shrank between the stat and hash passes: reading at
 	// the stat-reported size must fail rather than emit wrong hashes.
 	p := writeFile(t, dir, "shrunk", []byte("tiny"))
 
-	_, _, err = hashHeadTail(p, int64(2*chunk))
+	head, tail, content, err = hashSignature(p, int64(2*headTailWindow))
 	if err == nil {
 		t.Error("no error when the stat size exceeds the file size")
 	}
+
+	if head != "" || tail != "" || content != "" {
+		t.Errorf("shrunk file returned hashes: %q %q %q", head, tail, content)
+	}
+}
+
+// sparseFile creates a file that is logically size bytes long without
+// allocating blocks for the hole, so multi-gigabyte cases stay cheap.
+func sparseFile(t *testing.T, dir, name string, size int64) string {
+	t.Helper()
+
+	p := filepath.Join(dir, name)
+
+	f, err := os.Create(p) //nolint:gosec // test-controlled path
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	err = f.Truncate(size)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	err = f.Close()
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	return p
+}
+
+// pokeAt writes data into an existing file at off, leaving the rest of
+// the file (a sparse hole) untouched.
+func pokeAt(t *testing.T, path string, off int64, data []byte) {
+	t.Helper()
+
+	f, err := os.OpenFile(path, os.O_WRONLY, 0o600) //nolint:gosec // test path
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	_, err = f.WriteAt(data, off)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	err = f.Close()
+	if err != nil {
+		t.Fatal(err)
+	}
+}
+
+// contentHash returns just the content rung of a file's signature.
+func contentHash(t *testing.T, path string, size int64) string {
+	t.Helper()
+
+	_, _, content := sig(t, path, size)
+
+	return content
+}
+
+// TestContentRungBoundary checks the 50 MiB boundary between the two
+// content rungs: just below it the whole file is hashed and any byte
+// difference shows; at the boundary only the gigabyte-spaced samples are
+// hashed, so a difference outside a sample window is invisible.
+func TestContentRungBoundary(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+
+	// A byte that lands outside the single [0, sampleWindow) sample a
+	// sub-gigabyte file has, but well inside the file.
+	const off = 10 * 1024 * 1024
+
+	// Just under the boundary: the whole-file rung sees the poked byte.
+	under := int64(wholeFileMax - 1)
+	underBase := sparseFile(t, dir, "under-base", under)
+	underPoked := sparseFile(t, dir, "under-poked", under)
+
+	pokeAt(t, underPoked, off, []byte{1})
+
+	if contentHash(t, underBase, under) == contentHash(t, underPoked, under) {
+		t.Error("whole-file rung ignored a byte difference below wholeFileMax")
+	}
+
+	// At the boundary: only [0, sampleWindow) is sampled, so the poked
+	// byte at off is invisible and the two content hashes match.
+	at := int64(wholeFileMax)
+	atBase := sparseFile(t, dir, "at-base", at)
+	atPoked := sparseFile(t, dir, "at-poked", at)
+
+	pokeAt(t, atPoked, off, []byte{1})
+
+	if contentHash(t, atBase, at) != contentHash(t, atPoked, at) {
+		t.Error("sampled rung saw a byte outside every sample window")
+	}
+}
+
+// TestContentRungMultiGigabyte exercises the sampled rung across several
+// gigabytes using sparse files: a difference inside the third sample
+// window (at offset 2*sampleStride) changes the hash, while a difference
+// in the gap after it does not.
+func TestContentRungMultiGigabyte(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+
+	// Three sample windows (offsets 0, 1 GiB, 2 GiB) plus a trailing gap
+	// that no sample covers.
+	size := int64(2*sampleStride + 2*sampleWindow)
+	thirdSample := int64(2 * sampleStride)
+	gap := thirdSample + int64(sampleWindow)
+
+	base := sparseFile(t, dir, "g-base", size)
+	inSample := sparseFile(t, dir, "g-insample", size)
+	inGap := sparseFile(t, dir, "g-ingap", size)
+
+	pokeAt(t, inSample, thirdSample, []byte{1})
+	pokeAt(t, inGap, gap, []byte{1})
+
+	baseHash := contentHash(t, base, size)
+
+	if contentHash(t, inSample, size) == baseHash {
+		t.Error("sample at 2 GiB was not read: difference there was invisible")
+	}
+
+	if contentHash(t, inGap, size) != baseHash {
+		t.Error("a byte in an unsampled gap changed the content hash")
+	}
 }
 
 // collectWalk runs a walk over roots and returns the emitted records

trees.go

@@ -13,9 +13,10 @@ import (
 
 // fileSig is a file's duplicate signature; mtime is excluded.
 type fileSig struct {
-	size int64
+	size    int64
-	head string
+	head    string
-	tail string
+	tail    string
+	content string
 }
 
 // treeNode is one directory reconstructed from the scan stream.
@@ -122,7 +123,9 @@ func buildHierarchy(recs []scanRec) (*treeNode, []*treeNode) {
 			node.files = make(map[string]fileSig)
 		}
 
-		sig := fileSig{size: r.size, head: r.head, tail: r.tail}
+		sig := fileSig{
+			size: r.size, head: r.head, tail: r.tail, content: r.content,
+		}
 
 		// An unhashed record (its size was unique when last scanned)
 		// has unknown content: give it a signature no other file can
@@ -188,7 +191,7 @@ func (n *treeNode) compute() {
 	for name, sig := range n.files {
 		entries = append(entries,
 			"f\x00"+name+"\x00"+strconv.FormatInt(sig.size, 10)+
-				"\x00"+sig.head+"\x00"+sig.tail)
+				"\x00"+sig.head+"\x00"+sig.tail+"\x00"+sig.content)
 		n.fileCount++
 		n.totalSize += sig.size
 	}