sfdupes

Description

sfdupes is an MIT-licensed Go CLI tool by @sneak that quickly identifies candidate duplicate files — and, ultimately, entire duplicate directory trees — across very large filesystems without reading full file contents. Files are considered duplicates when they have identical size, identical SHA-256 of their first 1024 bytes, and identical SHA-256 of their last 1024 bytes. This is a strong candidate signal, not proof of identical content (the middle of the file is never read); the intended use is finding duplicate downloads and duplicated directory trees on multi-terabyte ZFS servers where reading every byte is 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.

This tool was created by @sneak to scratch an itch, using Claude Code/Fable.

This README is the complete and authoritative specification.

Getting Started

make build
export SFDUPES_DATABASE="$HOME/.local/share/sfdupes/db.sqlite"
./sfdupes scan /srv
./sfdupes report > dupes.tsv
./sfdupes trees > dupetrees.tsv

scan walks one or more filesystem trees and maintains one database record per regular file (path, size, mtime, head hash, tail 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 report. trees reads the same database and prints the duplicate-tree report. A missing/invalid subcommand — or a scan invocation with no PATH operand — prints a usage message and exits 2.

The database defaults to /var/lib/sfdupes/db.sqlite and can be placed anywhere by setting SFDUPES_DATABASE. The intended deployment is a daily sfdupes scan cron job, with the reporting commands run interactively whenever needed; their results are as fresh as the last completed scan.

Rationale

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 makes 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 not individual files but whole duplicated trees — duplicate extractions, duplicate downloads, copied project trees — which an operator can consider removing as a unit.

Design

Goals, in order:

1. Find whole duplicate trees, not just files. The end goal is to identify places where the exact same set of files and directories exists at two or more paths (duplicate extractions, duplicate 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 (first and last 1024 bytes). Scale target: ~10 million files, ~150 TB filesystem, possibly slow or busy disks (ZFS pool under resilver). Holding the full file list in memory is acceptable; reading file contents beyond 2 KiB per file is not.
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 the database alone and must never touch the scanned filesystem again. scan is designed to be cronned; the reports run at any time against the last completed scan.
4. Clean stream separation. Everything on stdout is machine-readable data. All progress, warnings, and summaries go to stderr. Never mix them.

Constraints

• Language: Go (module sneak.berlin/go/sfdupes). Binary name: sfdupes.
• Dependencies: standard library, github.com/spf13/cobra for the CLI, one progress-bar library (github.com/schollz/progressbar/v3), and one SQLite driver (modernc.org/sqlite, pure Go, so builds keep cgo disabled). github.com/spf13/viper is permitted if configuration-file support is ever needed, but is not currently used. No other third-party deps.
• Cross-compilation is not a concern. Builds run with cgo disabled (the Makefile exports CGO_ENABLED=0); the code must remain pure Go.
• Analysis modes (report, trees) must be deterministic: identical database contents, identical output, regardless of the order in which records were inserted.

Subcommands

Three subcommands, all implemented:

1. scan — walk the filesystem and synchronize the database: one signature record per regular file.
2. report — file-level duplicate report from the database.
3. trees — tree-level duplicate report: reconstruct the directory hierarchy from the database records, compute a Merkle-style digest per directory, and report maximal groups of identical trees.

sfdupes scan [--workers N] [-x] PATH...
sfdupes report > dupes.tsv
sfdupes trees > dupetrees.tsv

Database

All three subcommands operate on a single SQLite database file:

• Location: the value of the SFDUPES_DATABASE environment variable when set and non-empty, otherwise /var/lib/sfdupes/db.sqlite. There is no command-line flag.

• scan creates the database (and its parent directory) on first use. report and trees require an existing database; a missing database file is a fatal error (exit 1) telling the user to run scan first.

• The database uses WAL journal mode and a busy timeout, so running a report while a cron scan is in progress is safe. The filesystem is authoritative; the database is an eventually-consistent reflection of it. The update pass applies changes in batched transactions (keeping the WAL small and letting concurrent reports observe progress), so a report may see a scan's changes partially applied, and a scan that dies partway leaves a valid database that the next scan converges toward the filesystem.

• Schema (PRAGMA user_version is the schema version, currently 1; a database with any other version is a fatal error):

  CREATE TABLE files (
      path  BLOB PRIMARY KEY,  -- absolute path, raw bytes
      size  INTEGER NOT NULL,  -- bytes, from lstat
      mtime INTEGER NOT NULL,  -- Unix seconds, from lstat
      head  TEXT NOT NULL,     -- lowercase-hex SHA-256, first 1 KiB
      tail  TEXT NOT NULL      -- lowercase-hex SHA-256, last 1 KiB
  ) 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.

scan mode

scan requires one or more PATH operands naming the trees to scan. There is no default path; invoking scan with no operand is a usage error (usage message on stderr, exit 2). An operand may be a directory or a regular file; an operand that does not exist is a fatal error (exit 1). Because database records persist between runs and are keyed by absolute path, each operand is resolved to an absolute, lexically cleaned path (symlinks are not resolved) before walking, so results do not depend on the working directory. All operands belong to a single scan and are enumerated concurrently: every operand seeds the shared walk worker pool, and every pass runs once over the whole scan, so pass totals and ETAs are scan-wide. Overlapping operands (one containing another) are harmless — a file reached via multiple operands is deduplicated by path and produces one database record.

scan synchronizes the database with the filesystem state under the scanned operands:

• A file not yet in the database is hashed and inserted.
• A file already in the database is skipped without reading its contents when its lstat size equals the recorded size and its lstat mtime is not newer than the recorded mtime. This is what makes a daily rescan cheap.
• A file whose mtime is newer than recorded, or whose size differs, is re-hashed and its record updated.
• A database record whose path lies under one of the scanned operands but was not successfully processed this run is deleted. This removes records for deleted files. It also removes records for paths that failed to stat or hash this run: the database only ever contains signatures verified by the most recent scan that covered them (a subsequent successful scan re-adds such files).
• Database records outside the scanned operands are untouched, so disjoint trees can be scanned on different schedules into the same database.

scan runs four sequential passes over the whole scan. Parallelism lives strictly inside each pass; the passes themselves never overlap:

1. walk — enumerate the trees under all PATH operands concurrently with the worker pool: every operand seeds the shared queue, and each worker reads one directory at a time, collecting regular-file paths and handing discovered subdirectories back to the queue. Sequential directory enumeration is metadata-latency-bound and takes hours at tens of millions of files; per-directory parallelism is what makes the walk tractable on large or busy pools. Total unknown while running: show a live count, not a percentage.
2. stat — lstat every collected path with the worker pool (per-file parallelism), recording size and mtime.
3. hash — for each new or changed file (per the rules above), read the first min(1024, size) bytes and the last min(1024, size) bytes (the two reads overlap when size < 2048; for size == 0 hash the empty input) and compute the SHA-256 of each. Unchanged files are not read and do not appear in this pass's total, which is therefore exact for meaningful progress and ETA.
4. update — apply the scan's insertions, updates, and deletions to the database in batched transactions.

Rules for the walk:

• Only regular files. Skip directories, symlinks (do not follow, including symlink operands), sockets, FIFOs, and device nodes.
• Never descend into a directory named .zfs (ZFS snapshot pseudo-dirs; walking them would list every file once per snapshot).
• Filesystem boundaries are crossed by default. With -x (long form --one-file-system, following the GNU du/rsync convention), never descend into a directory on a different filesystem than its PATH operand; each operand is bounded by its own filesystem.
• On any per-path error (permission denied, file vanished between passes, unreadable): print a one-line warning to stderr, skip the path, and continue. Per-file errors never abort the run; the final summary reports how many were skipped. As specified above, a skipped path that has a database record from an earlier scan loses that record; an unreadable directory subtree likewise loses its records (accepted: the database mirrors what the latest scan could actually verify).

Concurrency: the walk, stat, and hash passes each use a worker pool (--workers, default runtime.NumCPU()); the walk parallelizes across directories, stat and hash across files, so raising --workers can speed up metadata-bound passes on busy pools. The main goroutine owns database writes and progress rendering; progress display must never block the workers.

scan writes nothing to stdout. The summary line on stderr reports the files seen this run broken down by disposition, plus skips:

scan: 123456 files seen (1200 added, 34 updated, 56 removed, 122166 unchanged), 3 skipped

(removed counts deleted database records, which are not part of the files-seen total.)

report mode

report reads every record from the database and takes no positional arguments.

report must never touch the filesystem being analyzed. It does not stat, open, or otherwise access any path that appears in the records; its only I/O is reading the database and writing stdout/stderr. It must produce identical output whether or not the scanned filesystem is still mounted.

Processing:

• Group records by the key (size, head_hash, tail_hash).
• Every group with two or more paths is a duplicate group.
• Within each group, sort paths lexicographically (byte order). The first path is the group's first; every other path is a dupe.
• Order groups by size descending (biggest reclaimable space first), tie-broken by first path ascending. Output must be fully deterministic for a given database state.

Report output format

TSV on stdout: a header line, then one row per duplicate file (N-1 rows for a group of N):

first	dupe	size
/srv/a/big.iso	/srv/b/big-copy.iso	4294967296
/srv/a/big.iso	/srv/c/big-copy2.iso	4294967296

Summary to stderr: records read, number of duplicate groups, number of dupe files, and total reclaimable bytes (sum of size over all dupe rows) in human units.

trees mode

trees reads the same database as report (no positional arguments) and reports entire duplicate directory trees: directories under which the exact same set of relative paths exists with the exact same file signatures.

trees must never touch the filesystem being analyzed — the same rule as report. The directory hierarchy is reconstructed purely from the paths in the records, split on /.

Definitions:

• A file's signature is (size, head_hash, tail_hash) — mtime is informational and excluded.
• A directory's digest is a SHA-256 Merkle digest computed bottom-up: serialize the directory's child entries — for a file child, its name and signature; for a subdirectory child, its name and that subdirectory's digest — sort the serialized entries byte-lexicographically, and hash the concatenation. Names are part of the digest: two trees whose files differ only in name are not duplicates.
• Two directories are duplicate trees when their digests are equal. Equal digests imply equal recursive file count and equal total byte size.

Known limitation (accepted): only regular files that appear in the database define a tree. Empty directories are invisible, and a file skipped during the scan (e.g. permission error) in one copy but not the other will make otherwise-identical trees compare as different.

Processing:

• Build the hierarchy, compute every directory's digest, and group directories by digest. Every group with two or more directories is a duplicate-tree group.
• Report only maximal trees. A group is suppressed when its members' parents are pairwise distinct directories that all share a single digest — such a group is wholly implied by its parents' (or a further ancestor's) group. Groups containing sibling directories, or members whose parents differ, are always reported.
• Within each group, sort paths lexicographically (byte order); the first path is first, every other path is a dupe.
• Order groups by total tree size descending, tie-broken by first path ascending. Output must be fully deterministic for a given input.

Trees output format

TSV on stdout: a header line, then one row per duplicate tree (N-1 rows for a group of N). files is the recursive regular-file count of one copy of the tree; size is the recursive total byte size of one copy:

first	dupe	files	size
/srv/a/project	/srv/backup/project	3417	104857600

Summary to stderr: records read, number of duplicate-tree groups, number of dupe trees, and total reclaimable bytes (sum of size over all dupe rows) in human units.

Progress

Use the progress-bar library for all scan-pass progress; rendering in the style of pv is the model. All progress goes to stderr.

Each scan pass gets its own bar. Required elements for the stat, hash, and update passes (known totals):

• elapsed time
• estimated time remaining
• a [m/n] x% display (items processed / total items, percent)
• current rate (items/s)

Example shape (exact layout is flexible, content is not):

hash: [1234567/9876543] 12% |████      | 8123 files/s elapsed 2:32 eta 17:54

The walk pass has no known total: show a live file count and elapsed time (spinner-style, no percentage or ETA).

Additional requirements:

• When stderr is not a TTY, do not emit ANSI redraws: print a plain one-line progress update no more often than every 5 seconds instead.
• Progress updates are driven from the main goroutine and must be non-blocking with respect to the worker pool.
• report and trees modes need no progress display, only their stderr summaries.

Error handling and exit codes

• 0: success, even if individual files were skipped with warnings.
• 1: fatal error (e.g., a PATH operand does not exist, the database cannot be created/opened/read/written, a missing database for report/trees, stdout write failure).
• 2: usage error (including scan with no PATH operand and report/trees with any positional argument).

Build

The Makefile is the single source of truth for all operations:

• make build — build the sfdupes binary (cgo disabled).
• make test — run the test suite (30-second timeout; reruns with -v on failure).
• make lint — run golangci-lint with the repo config.
• make fmt / make fmt-check — format Go sources / verify formatting without writing.
• make check — test, lint, and fmt-check; modifies nothing.
• make docker — build the Docker image, which runs make check as a build stage.
• make hooks — install the pre-commit hook.
• make clean — remove the binary and any legacy local files.dat.

Definition of done

All of the following, run in this directory, must pass:

1. make check passes (tests, lint, gofmt).

2. make docker succeeds.

3. Smoke test — create a throwaway tree in a temp dir (never test against real data):

   d=$(mktemp -d)
   export SFDUPES_DATABASE="$d/db.sqlite"
   mkdir -p "$d/a" "$d/b"
   head -c 2000 /dev/urandom > "$d/a/one.bin"
   cp "$d/a/one.bin" "$d/b/copy.bin"
   cp "$d/a/one.bin" "$d/b/copy2.bin"
   head -c 2000 /dev/urandom > "$d/a/unique.bin"     # same size, different content
   printf 'x' > "$d/tiny1"; printf 'x' > "$d/tiny2"  # 1-byte duplicates
   printf 'y' > "$d/tiny3"                           # 1-byte non-duplicate
   : > "$d/empty1"; : > "$d/empty2"                  # empty duplicates
   # duplicate trees: t1 and t2 are identical; t3 differs by one filename
   mkdir -p "$d/t1/sub" "$d/t2/sub" "$d/t3/sub"
   head -c 3000 /dev/urandom > "$d/t1/f1"
   head -c 100  /dev/urandom > "$d/t1/sub/f2"
   cp "$d/t1/f1" "$d/t2/f1"
   cp "$d/t1/sub/f2" "$d/t2/sub/f2"
   cp "$d/t1/f1" "$d/t3/f1"
   cp "$d/t1/sub/f2" "$d/t3/sub/f2renamed"
   ./sfdupes scan "$d"
   ./sfdupes report
   ./sfdupes trees
   # incremental behavior (scan a subtree; records elsewhere persist):
   ./sfdupes scan "$d/a"                  # everything unchanged, nothing hashed
   printf 'z' >> "$d/a/one.bin"           # modify: next scan re-hashes it
   rm "$d/a/unique.bin"                   # delete: next scan removes its record
   ./sfdupes scan "$d/a"                  # 1 updated, 1 removed
   ./sfdupes report
   

   (The scan database lives inside $d here purely for test hygiene; scanning $d therefore also records the SQLite file itself, which is harmless.)

   Expected from the first report: one.bin/copy.bin/copy2.bin form one group (two dupe rows, first is the lexicographically smallest path); t1/f1/t2/f1/t3/f1 form one group; t1/sub/f2/ t2/sub/f2/t3/sub/f2renamed form one group; tiny1/tiny2 pair; empty1/empty2 pair; unique.bin and tiny3 appear nowhere; groups ordered by size descending.

   Expected from trees: exactly one row — first $d/t1, dupe $d/t2, 2 files, 3100 bytes. $d/t1/sub vs $d/t2/sub is suppressed as non-maximal (implied by the t1/t2 group), and t3 appears nowhere (its file set differs by name).

   Expected from the second report (after the modify/delete rescan): one.bin has left its group (its content changed), so copy.bin/copy2.bin remain as one pair, and unique.bin is gone from the database.

   The test suite automates this scenario (see scan_test.go), plus a negative check: report and trees operate on the database alone and never touch the scanned filesystem.

TODO

Tracked in TODO.md.

Non-goals

• No full-content verification, no byte-for-byte compare, no deletion or linking of duplicates. The reports are advisory; acting on them is the user's job.
• No persistence beyond the SQLite database described above; no export/import formats.
• No daemon or filesystem watcher; scheduling rescans is cron's job.

License

MIT. See LICENSE.

Author

@sneak