Re-vendor the canonical files from sneak/prompts at c55a0cb (closes #95)

Every vendored file, REPO_POLICIES.md and every model script is the
copy at sneak/prompts c55a0cb, with this repository's own entries kept
after the canonical content. Lint and test are phases of the Dockerfile
that write no image, built uncached. make test runs the suite under the
race detector as nobody, because root reads the files the tests make
unreadable. Dockerfile.lint, script/verify-lint-image-pin and
make test-race are gone. Prettier runs on the host, from the node and
yarn that script/bootstrap installs. golangci-lint v2.14.0 raises no
findings. .claude/settings.json is deleted.

Deviation: the set comes from c55a0cb on next rather than dd4027b, as
the instructions on sneak/prompts#78 allow.

Model: opus-5-5

.editorconfig

@@ -13,3 +13,6 @@ indent_style = tab
 
 [*.go]
 indent_style = tab
+
+# This repository's own sections, such as one for another language it
+# uses, go below this comment, and a re-vendor keeps them.

.gitea/workflows/check.yml

@@ -1,11 +1,20 @@
 name: check
 on: [push]
+# Free the shared runner: a new push cancels only the same branch's older run.
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
 jobs:
     check:
         runs-on: ubuntu-latest
+        # Free the shared runner from a hung build.
+        timeout-minutes: 20
         steps:
             # actions/checkout v4.2.2, 2026-02-22
             - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+              # script/cibuild needs no token, so none is left in .git/config.
               with:
+                  persist-credentials: false
+                  # All history and tags, so git describe finds the version tag.
                   fetch-depth: 0
             - run: script/cibuild

.gitignore

@@ -27,7 +27,7 @@ node_modules/
 # Environment files. `*.env` covers bare `.env` and the `prod.env`
 # convention. Only the templates `example.env` and `sample.env` are
 # re-included below. A repository that commits any other template adds
-# its own negation after these lines, for example `!.env.example`.
+# its own negation at the end of this file, for example `!.env.example`.
 *.[eE][nN][vV]
 .[eE][nN][vV].*
 .[eE][nN][vV][rR][cC]
@@ -46,11 +46,13 @@ node_modules/
 [iI][dD]_[eE][dD]25519
 [iI][dD]_[eE][dD]25519_[sS][kK]
 
-# This repository's own entries, kept after the canonical content above.
+# This repository's own entries, such as its build outputs, go below
+# this comment, and a re-vendor keeps them. Anchor a binary built at the
+# root: `/myapp`, never `myapp`, which also ignores `cmd/myapp/`.
+/sfdupes
 *.log
 *.out
 *.test
-/sfdupes
 
 # A scan database lists every path it scanned.
 *.sqlite

.golangci.yml

@@ -25,6 +25,8 @@ linters:
     # silenced by disabling that name, not by enabling the successor.
     - wsl              # Deprecated, replaced by wsl_v5
     - gomodguard       # Deprecated, replaced by gomodguard_v2
+    # Misses findings at random in v2.14.0; back once a pinned release fixes it
+    - canonicalheader
   settings:
     lll:
       line-length: 88

README.md

@@ -312,29 +312,34 @@ All three subcommands operate on a single SQLite database file:
 
     ```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,  -- whole Unix seconds of the mtime, from lstat
-        head    TEXT NOT NULL,     -- lowercase-hex SHA-256; first 64 KiB, or whole file under 10 MiB
+        mtime_nsec INTEGER NOT NULL,  -- nanoseconds within that second, 0 to 999999999
-        tail    TEXT NOT NULL,     -- lowercase-hex SHA-256; last 64 KiB, or whole file under 10 MiB
+        head       TEXT NOT NULL,     -- lowercase-hex SHA-256; first 64 KiB, or whole file under 10 MiB
-        content TEXT NOT NULL      -- lowercase-hex SHA-256, whole file or samples
+        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;
     CREATE INDEX files_signature ON files (size, head, tail, content);
     ```
 
     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
+    UTF-8. `mtime` and `mtime_nsec` hold the file's mtime to the nanosecond:
-    duplicate key. For a file under 10 MiB `head`, `tail`, and `content` all
+    `mtime` the whole Unix seconds, rounded down, and `mtime_nsec` the
-    hold the whole-file hash (that range is hashed in full, with no end
+    nanoseconds past that second. Split this way they hold any mtime a
-    windows); for a larger file `head` and `tail` hold the first- and last-64
+    filesystem can record, one before 1678 or after 2262 included, which a
-    KiB hashes and `content` the whole-file or sampled hash. All three are empty
+    single 64-bit count of nanoseconds cannot. They are used only for change
-    strings when the file has never been hashed because its size was unique as
+    detection and are not part of the duplicate key. For a file under 10 MiB
-    of the last scan that covered it. For a file of 10 MiB or more, `content`
+    `head`, `tail`, and `content` all hold the whole-file hash (that range is
-    stays empty until the content phase of a scan (see "`scan` mode" below) has
+    hashed in full, with no end windows); for a larger file `head` and `tail`
-    read the file. A record with an empty `content` is never part of a duplicate
+    hold the first- and last-64 KiB hashes and `content` the whole-file or
-    group, though it still defines the file for tree reconstruction. The
+    sampled hash. All three are empty strings when the file has never been
-    `files_signature` index lets SQLite group the records by signature for
+    hashed because its size was unique as of the last scan that covered it. For
-    `report` without sorting the whole table.
+    a file of 10 MiB or more, `content` stays empty until the content phase of a
+    scan (see "`scan` mode" below) has read the file. A record with an empty
+    `content` is never part of a duplicate group, though it still defines the
+    file for tree reconstruction. The `files_signature` index lets SQLite group
+    the records by signature for `report` without sorting the whole table.
 
 ### Duplicate detection
 
@@ -421,6 +426,9 @@ operands:
   once its size, `head`, and `tail` match another record's.
 - A file whose mtime is newer than recorded, or whose size differs, is processed
   as if new: re-hashed, or recorded without hashes, per the shared-size rule.
+  Change detection compares the mtime to the nanosecond, as finely as the
+  filesystem records it, so a same-size rewrite counts as a change whenever the
+  filesystem gives it a later mtime than recorded, even within the same second.
 - 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
@@ -740,11 +748,12 @@ entrypoints are:
   come from the first of nix, apt, brew, or apk found on the host, and are
   presence-checked only. An installed node is used as it is; otherwise node
   22.17.0 is installed through nvm, which comes from a release archive whose
-  sha256 the script checks. yarn 1.22.22 comes through corepack, and
+  sha256 the script checks. A yarn already on `PATH` is used as it is; otherwise
-  `yarn install --frozen-lockfile` installs the prettier that `package.json` and
+  yarn 1.22.22 is activated through corepack, or installed with `npm` when there
-  `yarn.lock` pin. `golangci-lint` is never installed: it runs in Docker (see
+  is no corepack. `yarn install --frozen-lockfile` then installs the prettier
-  `script/lint`). `docker` is not installed either; testing, linting and the
+  that `package.json` and `yarn.lock` pin. `golangci-lint` is never installed:
-  image build need it. Ends with `go mod download`.
+  it runs in Docker (see `script/lint`). `docker` is not installed either;
+  testing, linting and the image build need it. Ends with `go mod download`.
 - `script/setup` — make a fresh clone ready for development: runs
   `script/bootstrap`, then `script/install-precommit`.
 - `script/projectname` — print this project's name (`sfdupes`). Scripts that
@@ -786,9 +795,8 @@ entrypoints are:
 - `script/precommit` — run by the git pre-commit hook: `go mod tidy` must be a
   no-op (a resulting change to `go.mod` or `go.sum` fails the commit), then
   `script/check`.
-- `script/install-precommit` — install the git pre-commit hook that runs
+- `script/install-precommit` — install the git pre-commit hook, as
-  `script/precommit`. The hook is written to the common git directory, so the
+  `.git/hooks/pre-commit`, that runs `script/precommit`.
-  main checkout and every worktree share it.
 
 Every `docker build` in `script/` passes `--no-cache`. On an unchanged tree
 Docker would serve the gate steps from its cache, and the build would pass

TODO.md

@@ -29,24 +29,33 @@
 
 # Completed Steps
 
-- re-vendor the canonical files from `sneak/prompts` commit `dd4027b`, with
+- re-vendor the canonical files and model scripts from `sneak/prompts` `next` at
-  `script/lint`, `script/test` and `REPO_POLICIES.md` from its `next` at
   `c55a0cb`: golangci-lint v2.14.0; lint and test are phases of the `Dockerfile`
   that write no image, and `make test` runs the suite under the race detector,
   so `Dockerfile.lint`, `script/verify-lint-image-pin` and `make test-race` are
   gone; every `docker build` in `script/` passes `--no-cache`; prettier runs on
   the host, from the node and yarn `script/bootstrap` installs, so the
   `prettier` and `markdown` stages are gone and the build stage installs `git`
-  and `make` itself; `.claude/settings.json` is deleted (2026-10-08,
+  and `make` itself; a new push cancels the workflow's older run on the same
-  https://git.eeqj.de/sneak/sfdupes/issues/95)
+  branch, and a run stops after 20 minutes; `.claude/settings.json` is deleted
+  (2026-10-08, https://git.eeqj.de/sneak/sfdupes/issues/95)
+
+- `scan` records mtime to the nanosecond, as whole seconds in `mtime` plus
+  `mtime_nsec`, and compares it at that resolution, so a same-size rewrite
+  within the same second is re-hashed (2026-10-07,
+  https://git.eeqj.de/sneak/sfdupes/issues/12)
 
 - cut the narration from `TODO.md` Completed Steps and from the comments in
-  `script/` and both Dockerfiles; §Workflow now branches from and merges to
+  `script/`, `Dockerfile` and `Dockerfile.lint` (gone since
-  `next` (2026-10-04, https://git.eeqj.de/sneak/sfdupes/issues/49)
+  https://git.eeqj.de/sneak/sfdupes/issues/95); §Workflow now branches from and
+  merges to `next` (2026-10-04, https://git.eeqj.de/sneak/sfdupes/issues/49)
 
-- `make test-race` runs the test suite under the race detector in a cgo-enabled
+- `make test-race` ran the test suite under the race detector in a cgo-enabled
   container, outside `make check` (2026-10-04,
-  https://git.eeqj.de/sneak/sfdupes/issues/18)
+  https://git.eeqj.de/sneak/sfdupes/issues/18). Since
+  https://git.eeqj.de/sneak/sfdupes/issues/95 `make test` itself runs the suite
+  under the race detector, in the `Dockerfile`'s Debian-based `test` phase, and
+  `make test-race` is gone
 
 - a bare `docker build .` failed, naming `script/cibuild` and `script/docker`,
   rather than serve the gates from cache (2026-10-04,
@@ -99,9 +108,12 @@
 - README documents install, Docker, a daily cron scan and how to read and check
   the reports (2026-10-04, https://git.eeqj.de/sneak/sfdupes/issues/54)
 
-- the `Dockerfile` build stage keeps the Go module cache out of `builder`'s home
+- the `Dockerfile` build stage kept the Go module cache out of `builder`'s home
-  and copies the sources with `--chown`, so no `chown -R` walks them
+  and copied the sources with `--chown`, so no `chown -R` walked them
-  (2026-10-04, https://git.eeqj.de/sneak/sfdupes/issues/43)
+  (2026-10-04, https://git.eeqj.de/sneak/sfdupes/issues/43). Since
+  https://git.eeqj.de/sneak/sfdupes/issues/95 there is no `builder` user and
+  nothing changes owner: the build stage only compiles, as root, and the tests
+  run as `nobody` in the `test` phase
 
 - `--version` prints `sfdupes VERSION` to stdout; README documents it and
   `--help` (2026-10-04, https://git.eeqj.de/sneak/sfdupes/issues/15)
@@ -165,82 +177,45 @@
 
 - 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): both pins are now the policy
+  https://git.eeqj.de/sneak/sfdupes/issues/25): both pins became the policy
   `# image:vX.Y.Z, YYYY-MM-DD` comment over a bare `FROM image@sha256:...`,
-  without the false `(Debian-based)` note or the tag; digest unchanged.
+  without the false `(Debian-based)` note or the tag. Since
-  `script/verify-lint-image-pin` still matches the tagless form, and a tag on
+  https://git.eeqj.de/sneak/sfdupes/issues/95 the `Dockerfile`'s `lint` phase
-  one side only is caught as a plain mismatch.
+  holds the only golangci-lint pin, in that form, so `Dockerfile.lint` and
+  `script/verify-lint-image-pin`, which compared the two pins, are gone.
 
 - run all linting in Docker via `Dockerfile.lint` and `script/lint` (2026-08-10,
   branch `next`, closes https://git.eeqj.de/sneak/sfdupes/issues/46): per the
-  owner ruling the linter is never installed on a host. `Dockerfile.lint` copies
+  owner ruling the linter is never installed on a host, and
-  the repo into the digest-pinned `golangci/golangci-lint:v2.12.2` image and
+  `golangci-lint config verify` runs before `golangci-lint run`.
-  runs `golangci-lint config verify` and `golangci-lint run` as build steps;
+  `script/bootstrap` stopped installing or pinning the linter, and
-  `script/lint` builds it. `script/bootstrap` no longer installs or pins the
+  `script/verify-linter-pin` was retired. Since
-  linter, and warns rather than fails when `docker` is absent;
+  https://git.eeqj.de/sneak/sfdupes/issues/95 both commands run in the
-  `ENV PATH=/home/builder/go/bin:$PATH` went with its `go install`.
+  `Dockerfile`'s `lint` phase, which `script/lint` builds alone and the build
-  `script/verify-linter-pin` is retired; `script/verify-lint-image-pin`, a gate
+  stage depends on through `COPY --from=lint /src/go.sum /dev/null`;
-  in both files, compares their two `FROM` lines and restates neither pin.
+  `Dockerfile.lint` and `script/verify-lint-image-pin` are gone. Nothing inside
-  Traps: nothing inside an image build may shell out to docker, so the
+  an image build may run docker, so the phase calls `golangci-lint` directly.
-  `Dockerfile` lint stage calls `golangci-lint` directly and the build stage
-  runs `make test` and `make fmt-check` instead of `make check`, through `make`
-  because the Makefile's `export CGO_ENABLED = 0` only reaches what it invokes.
-  `COPY --from=lint /src/go.sum /dev/null` replaces the copied linter binary as
-  the only edge making the build stage wait for lint; dropping it would end
-  fail-fast linting under a still-green build. `golangci-lint config verify`,
-  included per the ruling, validates from an embedded schema with no network
-  call, but `go mod download` above the gates still needs the network on a cold
-  cache. Verified: `make lint` green with no `golangci-lint` on `PATH`; two
-  back-to-back `script/lint` runs on an untouched tree both ran the linter
-  (27.7s and 28.7s in the lint step, `COPY . .` `CACHED` above); a planted
-  unused variable failed `script/lint`, and failed `make docker` at `[lint 9/9]`
-  with the build stage stopped at `[builder 3/12]`; the drift guard fails on a
-  tag-only, a digest-only and an unreadable reference, naming both sides; under
-  `--network none` config verify passes a valid config and rejects an invalid
-  one; `make docker` green in 5m35s with all six gates run (lint 37.6s, test
-  25.2s reporting `ok sneak.berlin/go/sfdupes 1.938s coverage: 88.5%`, not
-  `(cached)`); in the builder image with the Go test cache off, `--user 0:0`
-  still fails `TestScanHardlinkRunFailsTogether` where the unprivileged user
-  passes. Noted for follow-up, not fixed here: `golangci-lint` warns that
-  `gomodguard` is deprecated since v2.12.0 in favour of `gomodguard_v2`.
 
 - install the Docker build stage's prerequisites by running `script/bootstrap`
   instead of `apk add --no-cache make` inline (2026-08-09, branch
-  `dockerfile-bootstrap`, closes https://git.eeqj.de/sneak/sfdupes/issues/42):
+  `dockerfile-bootstrap`, closes https://git.eeqj.de/sneak/sfdupes/issues/42),
-  the stage copies `script/` plus `go.mod`/`go.sum` and runs `script/bootstrap`,
+  with `script/verify-linter-pin` failing the build unless the linter copied
-  which ends in `go mod download`, so the separate call to it is gone.
+  from the lint stage was the version `script/bootstrap` pinned. Builds then
-  `COPY --from=lint /usr/bin/golangci-lint` stays and moves above the bootstrap
+  took up to 5m14s cold, mostly in a `chown -R` of the module cache, filed as
-  layer: it is the only edge making this stage depend on the lint stage, so
+  https://git.eeqj.de/sneak/sfdupes/issues/43. Since
-  deleting it would end fail-fast linting silently. A new
+  https://git.eeqj.de/sneak/sfdupes/issues/95 the build stage installs `git` and
-  `script/verify-linter-pin`, run in the build stage before bootstrap, fails the
+  `make` with `apk add --no-cache` and only compiles; the `lint` and `test`
-  build naming both versions unless that copied binary is the version
+  phases are the gates
-  `script/bootstrap` pins; a pin it cannot read is a hard failure, not a skip.
-  `$GOPATH/bin` joins `PATH`, where bootstrap's `go install` lands. The `chown`
-  and `USER builder` still precede `make check`. Verified: the guard fails the
-  build with both versions named when the lint stage's linter is faked to
-  another version, and passes an unmodified build; bootstrap runs clean under
-  Alpine's `sh` and `apk`, finding the copied linter already at the pin; a
-  second build served the bootstrap and dependency layers `CACHED` while both
-  gates ran; a planted `unused` finding failed the build at the lint gate in
-  48.9s with the build stage's `make check` never starting; and the suite run in
-  the image as `--user 0:0` fails `TestScanHardlinkRunFailsTogether`, so the
-  drop to the unprivileged user is still needed. That last check needs the Go
-  test cache off: as root it first reported `ok ... (cached)`, reusing the
-  build-time result. Build times on a noisy shared host: 2m13s on an unchanged
-  tree, 2m17s and 4m29s after a source change, 5m14s cold, which breaches the
-  policy ceiling; `chown -R builder:builder /src /home/builder` walks the module
-  cache and alone varied from 77s to 210s across those builds, and `main`
-  measured 5m03s cold with a 209s `chown`. Filed as
-  https://git.eeqj.de/sneak/sfdupes/issues/43
 - bust the Docker layer cache for the gate steps, so `script/cibuild` and
   `script/docker` cannot report a green they did not earn (2026-08-09, branch
   `cibuild-cache-bust`, closes https://git.eeqj.de/sneak/sfdupes/issues/32): the
   `Dockerfile` copies the tree before its gates, so on an unchanged tree Docker
-  served them from cache and the build exited 0 having run nothing. Every
+  served them from cache and the build exited 0 having run nothing. The fix was
-  `docker build` in `script/` now passes `--no-cache` instead
+  a `CHECK_EPOCH` build argument; since
-  (https://git.eeqj.de/sneak/sfdupes/issues/95). Run as root, the tests fail
+  https://git.eeqj.de/sneak/sfdupes/issues/95 every `docker build` in `script/`
+  passes `--no-cache` instead. Run as root, the tests fail
   `TestScanHardlinkRunFailsTogether`, because root reads through the `chmod(0)`
-  the test relies on, so they run as an unprivileged user
+  the test relies on, so the `test` phase runs them as `nobody`
 - check the installed golangci-lint version in `script/bootstrap` instead of
   only its presence (2026-08-09, branch `bootstrap-version-check`, closes
   https://git.eeqj.de/sneak/sfdupes/issues/24): the version lives only in

db.go

@@ -11,6 +11,7 @@ import (
 	"path/filepath"
 	"slices"
 	"strconv"
+	"time"
 
 	"golang.org/x/sys/unix"
 	// The pure-Go SQLite driver, registered as "sqlite"; keeps cgo
@@ -40,15 +41,18 @@ const dbDirPerm = 0o755
 const lockFilePerm = 0o600
 
 // createTableSQL is the schema applied to a fresh database. Paths are
-// BLOBs because Unix paths are raw bytes, not guaranteed UTF-8.
+// BLOBs because Unix paths are raw bytes, not guaranteed UTF-8. mtime
+// holds whole Unix seconds and mtime_nsec the nanoseconds within that
+// second.
 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,
+    mtime_nsec INTEGER NOT NULL,
-    tail    TEXT NOT NULL,
+    head       TEXT NOT NULL,
-    content TEXT NOT NULL
+    tail       TEXT NOT NULL,
+    content    TEXT NOT NULL
 ) WITHOUT ROWID
 `
 
@@ -61,10 +65,11 @@ CREATE INDEX files_signature ON files (size, head, tail, content)
 // upsertSQL inserts one file record, replacing any existing record for
 // the same path.
 const upsertSQL = `
-INSERT INTO files (path, size, mtime, head, tail, content)
+INSERT INTO files (path, size, mtime, mtime_nsec, head, tail, content)
-VALUES (?, ?, ?, ?, ?, ?)
+VALUES (?, ?, ?, ?, ?, ?, ?)
 ON CONFLICT (path) DO UPDATE SET
     size = excluded.size, mtime = excluded.mtime,
+    mtime_nsec = excluded.mtime_nsec,
     head = excluded.head, tail = excluded.tail,
     content = excluded.content
 `
@@ -356,8 +361,8 @@ func userVersion(ctx context.Context, db *sql.DB) (int, error) {
 // which is the order of the primary key, so SQLite does not sort.
 func loadFileRows(ctx context.Context, db *sql.DB, fn func(r scanRec)) error {
 	rows, err := db.QueryContext(ctx,
-		"SELECT path, size, mtime, head, tail, content FROM files "+
+		"SELECT path, size, mtime, mtime_nsec, head, tail, content "+
-			"ORDER BY path")
+			"FROM files ORDER BY path")
 	if err != nil {
 		return fmt.Errorf("read records: %w", err)
 	}
@@ -366,17 +371,19 @@ func loadFileRows(ctx context.Context, db *sql.DB, fn func(r scanRec)) error {
 
 	for rows.Next() {
 		var (
-			path []byte
+			path      []byte
-			r    scanRec
+			sec, nsec int64
+			r         scanRec
 		)
 
-		err = rows.Scan(&path, &r.size, &r.mtime, &r.head, &r.tail,
+		err = rows.Scan(&path, &r.size, &sec, &nsec, &r.head, &r.tail,
 			&r.content)
 		if err != nil {
 			return fmt.Errorf("read record: %w", err)
 		}
 
 		r.path = string(path)
+		r.mtime = time.Unix(sec, nsec)
 		fn(r)
 	}
 
@@ -466,10 +473,10 @@ func loadDupeRows(ctx context.Context, db *sql.DB,
 // values, and skipping the hash columns keeps the scan's in-memory
 // index small on multi-million-file databases.
 func loadFileMeta(ctx context.Context, db *sql.DB,
-	fn func(path string, size, mtime int64, hashed bool),
+	fn func(path string, size int64, mtime time.Time, hashed bool),
 ) error {
 	rows, err := db.QueryContext(ctx,
-		"SELECT path, size, mtime, head <> '' FROM files")
+		"SELECT path, size, mtime, mtime_nsec, head <> '' FROM files")
 	if err != nil {
 		return fmt.Errorf("read records: %w", err)
 	}
@@ -478,17 +485,17 @@ func loadFileMeta(ctx context.Context, db *sql.DB,
 
 	for rows.Next() {
 		var (
-			path        []byte
+			path            []byte
-			size, mtime int64
+			size, sec, nsec int64
-			hashed      int64
+			hashed          int64
 		)
 
-		err = rows.Scan(&path, &size, &mtime, &hashed)
+		err = rows.Scan(&path, &size, &sec, &nsec, &hashed)
 		if err != nil {
 			return fmt.Errorf("read record: %w", err)
 		}
 
-		fn(string(path), size, mtime, hashed != 0)
+		fn(string(path), size, time.Unix(sec, nsec), hashed != 0)
 	}
 
 	err = rows.Err()
@@ -507,7 +514,7 @@ func loadFileMeta(ctx context.Context, db *sql.DB,
 // memory; the rows come ordered by size, head, and tail, so each
 // group's rows arrive together.
 const contentCandidatesSQL = `
-SELECT f.path, f.size, f.mtime, f.head, f.tail, f.content <> ''
+SELECT f.path, f.size, f.mtime, f.mtime_nsec, f.head, f.tail, f.content <> ''
 FROM files AS f
 JOIN (
     SELECT size, head, tail
@@ -533,17 +540,20 @@ func loadContentCandidates(ctx context.Context, db *sql.DB,
 
 	for rows.Next() {
 		var (
-			path   []byte
+			path      []byte
-			r      scanRec
+			sec, nsec int64
-			hashed int64
+			r         scanRec
+			hashed    int64
 		)
 
-		err = rows.Scan(&path, &r.size, &r.mtime, &r.head, &r.tail, &hashed)
+		err = rows.Scan(&path, &r.size, &sec, &nsec, &r.head, &r.tail,
+			&hashed)
 		if err != nil {
 			return fmt.Errorf("read record: %w", err)
 		}
 
 		r.path = string(path)
+		r.mtime = time.Unix(sec, nsec)
 		fn(r, hashed != 0)
 	}
 
@@ -627,8 +637,8 @@ func execUpserts(ctx context.Context, tx *sql.Tx, upserts []scanRec,
 	defer func() { _ = st.Close() }()
 
 	for _, r := range upserts {
-		_, err = st.ExecContext(ctx,
+		_, err = st.ExecContext(ctx, []byte(r.path), r.size,
-			[]byte(r.path), r.size, r.mtime, r.head, r.tail, r.content)
+			r.mtime.Unix(), r.mtime.Nanosecond(), r.head, r.tail, r.content)
 		if err != nil {
 			return fmt.Errorf("upsert %s: %w", r.path, err)
 		}

db_test.go

@@ -10,6 +10,7 @@ import (
 	"slices"
 	"strings"
 	"testing"
+	"time"
 )
 
 // testDBPath returns a database path inside a fresh temp dir.
@@ -260,10 +261,13 @@ func TestApplyChangesRoundTrip(t *testing.T) {
 	// written.
 	recs := []scanRec{
 		{
-			size: 2, mtime: 20, head: "h2", tail: "t2", content: "c2",
+			size: 2, mtime: time.Unix(20, 999_999_999), head: "h2", tail: "t2",
-			path: "/a/tab\tnew\nline",
+			content: "c2", path: "/a/tab\tnew\nline",
+		},
+		{
+			size: 1, mtime: time.Unix(10, 0), head: "h1", tail: "t1",
+			content: "c1", path: "/a/x",
 		},
-		{size: 1, mtime: 10, head: "h1", tail: "t1", content: "c1", path: "/a/x"},
 	}
 
 	err := applyChanges(t.Context(), db, recs, nil,
@@ -281,7 +285,8 @@ func TestApplyChangesRoundTrip(t *testing.T) {
 	// An upsert for an existing path updates in place; a delete
 	// removes exactly its path.
 	upd := scanRec{
-		size: 3, mtime: 30, head: "h3", tail: "t3", content: "c3", path: "/a/x",
+		size: 3, mtime: time.Unix(30, 0), head: "h3", tail: "t3", content: "c3",
+		path: "/a/x",
 	}
 
 	err = applyChanges(t.Context(), db, []scanRec{upd},
@@ -308,7 +313,7 @@ func TestApplyChangesBatching(t *testing.T) {
 	recs := make([]scanRec, 0, n)
 	for i := range n {
 		recs = append(recs, scanRec{
-			size: int64(i), mtime: 1, head: "h", tail: "t",
+			size: int64(i), mtime: time.Unix(1, 0), head: "h", tail: "t",
 			path: fmt.Sprintf("/batch/%07d", i),
 		})
 	}

report.go

@@ -7,6 +7,7 @@ import (
 	"io"
 	"os"
 	"strings"
+	"time"
 )
 
 // ioBufSize is the buffer size for the buffered stdout writers.
@@ -21,7 +22,7 @@ const minGroupSize = 2
 // only and used by scan for change detection.
 type scanRec struct {
 	size    int64
-	mtime   int64
+	mtime   time.Time
 	head    string
 	tail    string
 	content string

report_test.go

@@ -11,6 +11,7 @@ import (
 	"slices"
 	"strings"
 	"testing"
+	"time"
 )
 
 // awkwardDir is a directory name holding every byte the reports escape.
@@ -313,8 +314,14 @@ func TestDupeGroupsMtimeExcluded(t *testing.T) {
 	// mtime is informational only; records differing only in mtime
 	// still group together.
 	recs := []scanRec{
-		{size: 9, mtime: 100, head: "h", tail: "t", content: "c", path: "/m/1"},
+		{
-		{size: 9, mtime: 200, head: "h", tail: "t", content: "c", path: "/m/2"},
+			size: 9, mtime: time.Unix(100, 0), head: "h", tail: "t",
+			content: "c", path: "/m/1",
+		},
+		{
+			size: 9, mtime: time.Unix(200, 0), head: "h", tail: "t",
+			content: "c", path: "/m/2",
+		},
 	}
 
 	groups := dupeGroupsOf(t, recs)

scan.go

@@ -17,6 +17,7 @@ import (
 	"strings"
 	"sync"
 	"syscall"
+	"time"
 )
 
 // The duplicate ladder (see hashSignature and README "Duplicate
@@ -68,7 +69,7 @@ var errInterrupted = errors.New("scan interrupted")
 type fileRec struct {
 	path  string
 	size  int64
-	mtime int64
+	mtime time.Time
 	dev   uint64
 	ino   uint64
 }
@@ -79,7 +80,7 @@ type fileRec struct {
 // they would dominate the scan's memory.
 type fileMeta struct {
 	size   int64
-	mtime  int64
+	mtime  time.Time
 	hashed bool
 }
 
@@ -369,7 +370,7 @@ func (s *scanState) loadIndex(ctx context.Context, roots []string) error {
 	s.existing = make(map[string]fileMeta)
 
 	return loadFileMeta(ctx, s.db,
-		func(path string, size, mtime int64, hashed bool) {
+		func(path string, size int64, mtime time.Time, hashed bool) {
 			prog.increment()
 
 			if underAnyRoot(path, roots) {
@@ -415,7 +416,7 @@ func (s *scanState) walkPhase(
 		old, ok := s.existing[ev.rec.path]
 
 		switch {
-		case !ok || old.size != ev.rec.size || old.mtime < ev.rec.mtime:
+		case !ok || old.size != ev.rec.size || mtimeAfter(ev.rec.mtime, old.mtime):
 			changed = append(changed, ev.rec)
 		case old.hashed:
 			delete(s.existing, ev.rec.path)
@@ -807,7 +808,7 @@ func unchangedFile(r scanRec) (fileRec, bool, error) {
 	}
 
 	if !fi.Mode().IsRegular() || fi.Size() != r.size ||
-		fi.ModTime().Unix() > r.mtime {
+		mtimeAfter(fi.ModTime(), r.mtime) {
 		return fileRec{}, false, nil
 	}
 
@@ -818,6 +819,16 @@ func unchangedFile(r scanRec) (fileRec, bool, error) {
 	}, true, nil
 }
 
+// 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 {
@@ -966,7 +977,7 @@ func seedRoot(ctx context.Context, root string,
 	sendEvent(ctx, events, walkEvent{rec: fileRec{
 		path:  root,
 		size:  fi.Size(),
-		mtime: fi.ModTime().Unix(),
+		mtime: fi.ModTime(),
 		dev:   dev,
 		ino:   ino,
 	}})
@@ -1124,7 +1135,7 @@ func emitFile(ctx context.Context, p string, e fs.DirEntry,
 	sendEvent(ctx, events, walkEvent{rec: fileRec{
 		path:  p,
 		size:  info.Size(),
-		mtime: info.ModTime().Unix(),
+		mtime: info.ModTime(),
 		dev:   dev,
 		ino:   ino,
 	}})

scan_test.go

@@ -20,6 +20,8 @@ import (
 	"syscall"
 	"testing"
 	"time"
+
+	"golang.org/x/sys/unix"
 )
 
 // writeFile creates a file with the given content and returns its path.
@@ -581,6 +583,65 @@ func TestScanContentHashedStalePartners(t *testing.T) {
 	}
 }
 
+// TestScanContentSameSecondRewrite is TestScanContentStalePartners for
+// a stored file rewritten in place at the same size with an mtime later
+// in the same second than recorded: the file counts as changed, so
+// neither it nor its match inside the operand is read.
+func TestScanContentSameSecondRewrite(t *testing.T) {
+	t.Parallel()
+
+	db := openTestDB(t)
+	dirA := t.TempDir()
+	changed := sparseFileWithoutMatch(t, dirA, "changed", headTailMin)
+
+	first := time.Date(2026, 1, 2, 3, 4, 5, 100_000_000, time.UTC)
+
+	err := os.Chtimes(changed, first, first)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	syncTree(t, db, dirA)
+
+	before := dbRecords(t, db)
+
+	// Rewrite one byte in place, keeping the size.
+	pokeAt(t, changed, headTailMin/2, []byte{1})
+
+	later := first.Add(500 * time.Millisecond)
+
+	err = os.Chtimes(changed, later, later)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	dirB := t.TempDir()
+	sparseFile(t, dirB, "changed-copy", headTailMin)
+
+	st := syncTree(t, db, dirB)
+	if st != (scanStats{walked: 1, added: 1}) {
+		t.Errorf("stats = %+v, want 1 added and nothing skipped", st)
+	}
+
+	recs := dbRecords(t, db)
+	for _, r := range recs {
+		if r.content != "" {
+			t.Errorf("%s: content = %q, want none: its only match is stale",
+				r.path, r.content)
+		}
+	}
+
+	for _, old := range before {
+		if r := recordByPath(t, recs, old.path); r != old {
+			t.Errorf("record = %+v, want it left as %+v", r, old)
+		}
+	}
+
+	if groups := dupeGroups(t, db); len(groups) != 0 {
+		t.Errorf("groups = %+v, want none", groups)
+	}
+}
+
 // TestScanContentReadFailure checks that a failed content read is
 // counted as skipped and leaves the record without a content hash, and
 // that a later scan tries the read again.
@@ -783,8 +844,8 @@ func TestWalk(t *testing.T) {
 			t.Errorf("%s: size = %d, want 1..3", r.path, r.size)
 		}
 
-		if r.mtime <= 0 {
+		if r.mtime.Unix() <= 0 {
-			t.Errorf("%s: mtime = %d, want positive", r.path, r.mtime)
+			t.Errorf("%s: mtime = %v, want after 1970", r.path, r.mtime)
 		}
 	}
 }
@@ -1285,11 +1346,172 @@ func TestSyncScanMtimeBump(t *testing.T) {
 		t.Fatalf("mtime-bump stats = %+v, want 1 updated", st)
 	}
 
-	if r := recordByPath(t, dbRecords(t, db), a); r.mtime != future.Unix() {
+	if r := recordByPath(t, dbRecords(t, db), a); !r.mtime.Equal(future) {
-		t.Fatalf("mtime = %d, want %d", r.mtime, future.Unix())
+		t.Fatalf("mtime = %v, want %v", r.mtime, future)
 	}
 }
 
+// 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,
+	data []byte,
+) {
+	t.Helper()
+
+	r := recordByPath(t, dbRecords(t, db), path)
+	if want := hexSum(data); r.head != want || r.tail != want ||
+		r.content != want {
+		t.Fatalf("head, tail, content = %q, %q, %q, want %q for each",
+			r.head, r.tail, r.content, want)
+	}
+}
+
+// TestSyncScanSameSecondRewrite rewrites a file in place at the same
+// size with an mtime later in the same second as the recorded one: the
+// next scan must notice the change and re-hash the file.
+func TestSyncScanSameSecondRewrite(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	a := writeFile(t, dir, "a.bin", pattern(1, 500))
+
+	// b.bin shares the size of a.bin, so a.bin is hashed.
+	writeFile(t, dir, "b.bin", pattern(2, 500))
+
+	first := time.Date(2026, 1, 2, 3, 4, 5, 100_000_000, time.UTC)
+
+	err := os.Chtimes(a, first, first)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	syncTree(t, db, dir)
+
+	rewritten := pattern(3, 500)
+	writeFile(t, dir, "a.bin", rewritten)
+
+	later := first.Add(500 * time.Millisecond)
+
+	err = os.Chtimes(a, later, later)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	st := syncTree(t, db, dir)
+	if st != (scanStats{walked: 2, updated: 1, unchanged: 1}) {
+		t.Fatalf("rescan stats = %+v, want 1 updated 1 unchanged", st)
+	}
+
+	assertWholeFileHashed(t, db, a, rewritten)
+}
+
+// TestSyncScanOperandSameSecondRewrite is TestSyncScanSameSecondRewrite
+// for files given to scan as operands, which scan stats without reading
+// their directory.
+func TestSyncScanOperandSameSecondRewrite(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	a := writeFile(t, dir, "a.bin", pattern(1, 500))
+
+	// b.bin shares the size of a.bin, so a.bin is hashed.
+	b := writeFile(t, dir, "b.bin", pattern(2, 500))
+
+	first := time.Date(2026, 1, 2, 3, 4, 5, 100_000_000, time.UTC)
+
+	err := os.Chtimes(a, first, first)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	syncTree(t, db, a, b)
+
+	rewritten := pattern(3, 500)
+	writeFile(t, dir, "a.bin", rewritten)
+
+	later := first.Add(500 * time.Millisecond)
+
+	err = os.Chtimes(a, later, later)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	st := syncTree(t, db, a, b)
+	if st != (scanStats{walked: 2, updated: 1, unchanged: 1}) {
+		t.Fatalf("rescan stats = %+v, want 1 updated 1 unchanged", st)
+	}
+
+	assertWholeFileHashed(t, db, a, rewritten)
+}
+
+// TestSyncScanRewriteAfter2262 runs assertLateRewriteRehashed with an
+// mtime after 2262, a time too late to count in nanoseconds in an int64.
+func TestSyncScanRewriteAfter2262(t *testing.T) {
+	t.Parallel()
+
+	assertLateRewriteRehashed(t, time.Date(2300, 1, 2, 3, 4, 5, 0, time.UTC))
+}
+
+// TestSyncScanRewritePastTimeLimit runs assertLateRewriteRehashed with an
+// mtime one second past the latest a time.Time holds without wrapping it
+// to a time far in the past.
+func TestSyncScanRewritePastTimeLimit(t *testing.T) {
+	t.Parallel()
+
+	assertLateRewriteRehashed(t, time.Unix(9223371974719179008, 0))
+}
+
+// assertLateRewriteRehashed scans a directory, rewrites a file in it in
+// place at the same size, sets its mtime to late, and fails unless the
+// next scan re-hashes the file. It skips where late does not fit the
+// platform's timespec or the filesystem does not store it.
+func assertLateRewriteRehashed(t *testing.T, late time.Time) {
+	t.Helper()
+
+	dir := t.TempDir()
+	db := openTestDB(t)
+	a := writeFile(t, dir, "a.bin", pattern(1, 500))
+
+	// b.bin shares the size of a.bin, so a.bin is hashed.
+	writeFile(t, dir, "b.bin", pattern(2, 500))
+
+	syncTree(t, db, dir)
+
+	rewritten := pattern(3, 500)
+	writeFile(t, dir, "a.bin", rewritten)
+
+	// os.Chtimes cannot set such a time: it converts through UnixNano.
+	ts, err := unix.TimeToTimespec(late)
+	if err != nil {
+		t.Skipf("an mtime %d seconds after 1970 does not fit this platform's "+
+			"timespec: %v", late.Unix(), err)
+	}
+
+	err = unix.UtimesNano(a, []unix.Timespec{ts, ts})
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	fi, err := os.Lstat(a)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	if fi.ModTime().Unix() != late.Unix() {
+		t.Skipf("the filesystem stored the mtime as %d seconds after 1970, "+
+			"not %d", fi.ModTime().Unix(), late.Unix())
+	}
+
+	st := syncTree(t, db, dir)
+	if st != (scanStats{walked: 2, updated: 1, unchanged: 1}) {
+		t.Fatalf("rescan stats = %+v, want 1 updated 1 unchanged", st)
+	}
+
+	assertWholeFileHashed(t, db, a, rewritten)
+}
+
 func TestSyncScanAddRemove(t *testing.T) {
 	t.Parallel()
 
@@ -1335,9 +1557,7 @@ func TestSyncScanSizeChange(t *testing.T) {
 
 	writeFile(t, dir, "f", pattern(1, 200))
 
-	mt := time.Unix(old.mtime, 0)
+	err := os.Chtimes(p, old.mtime, old.mtime)
-
-	err := os.Chtimes(p, mt, mt)
 	if err != nil {
 		t.Fatal(err)
 	}

script/check

@@ -1,6 +1,8 @@
 #!/bin/sh
 # script/check: run all checks (test, lint, fmt-check). Our own
-# extension to scripts-to-rule-them-all. Must not modify any files.
+# extension to scripts-to-rule-them-all. test and lint are Docker
+# phases; fmt-check is native, because a formatter writes the working
+# tree. Must not modify any files.
 set -eu
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd -P)"

script/cibuild

@@ -14,15 +14,17 @@ main() {
     cd "$ROOT"
     "$SCRIPT_DIR/bootstrap"
     "$SCRIPT_DIR/check"
-    # Own line: a failing command substitution inside an argument does
+    # The version and the tag each get their own line: a failing
-    # not trip `set -e`, so the inline form degrades silently to an
+    # command substitution inside an argument does not trip `set -e`,
-    # empty constant. The VERSION build argument takes precedence over
+    # so the inline form degrades silently to an empty constant. The
-    # the version a build stage derives from the .git in the context.
+    # VERSION build argument takes precedence over the version a build
+    # stage derives from the .git in the context.
     version="$(git describe --tags --always --dirty 2>/dev/null || true)"
     [ -n "$version" ] || version="unknown"
+    tag="$("$SCRIPT_DIR/projectname")"
     docker build --no-cache \
         --build-arg VERSION="$version" \
-        -t "$("$SCRIPT_DIR/projectname")" .
+        -t "$tag" .
 }
 
 main "$@"

script/docker

@@ -10,15 +10,17 @@ ROOT="$(cd "$SCRIPT_DIR/.." && pwd -P)"
 
 main() {
     cd "$ROOT"
-    # Own line: a failing command substitution inside an argument does
+    # The version and the tag each get their own line: a failing
-    # not trip `set -e`, so the inline form degrades silently to an
+    # command substitution inside an argument does not trip `set -e`,
-    # empty constant. The VERSION build argument takes precedence over
+    # so the inline form degrades silently to an empty constant. The
-    # the version a build stage derives from the .git in the context.
+    # VERSION build argument takes precedence over the version a build
+    # stage derives from the .git in the context.
     version="$(git describe --tags --always --dirty 2>/dev/null || true)"
     [ -n "$version" ] || version="unknown"
+    tag="$("$SCRIPT_DIR/projectname")"
     docker build --no-cache \
         --build-arg VERSION="$version" \
-        -t "$("$SCRIPT_DIR/projectname")" .
+        -t "$tag" .
 }
 
 main "$@"

script/install-precommit

@@ -1,19 +1,15 @@
 #!/bin/sh
 # script/install-precommit: install the git pre-commit hook that runs
 # script/precommit. Our own extension to scripts-to-rule-them-all.
-# Hooks are shared between the main checkout and all worktrees, so
-# resolve the common git dir instead of assuming .git is a directory.
 set -eu
 
 ROOT="$(cd "$(dirname "$0")/.." && pwd -P)"
 
 main() {
     cd "$ROOT"
-    hooks_dir="$(git rev-parse --git-common-dir)/hooks"
+    hook=".git/hooks/pre-commit"
-    mkdir -p "$hooks_dir"
+    printf '#!/bin/sh\nset -e\nscript/precommit\n' > .git/hooks/pre-commit
-    hook="$hooks_dir/pre-commit"
+    chmod +x .git/hooks/pre-commit
-    printf '#!/bin/sh\nset -e\nscript/precommit\n' > "$hook"
-    chmod +x "$hook"
     echo "pre-commit hook installed: runs script/precommit"
 }
 

script/precommit

@@ -1,13 +1,13 @@
 #!/bin/sh
 # script/precommit: run by the git pre-commit hook; fails the commit if
-# checks fail. Our own extension to scripts-to-rule-them-all. Go extra:
+# checks fail. Our own extension to scripts-to-rule-them-all.
-# go mod tidy must be a no-op before the checks run.
 set -eu
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 ROOT="$(cd "$SCRIPT_DIR/.." && pwd -P)"
 
 main() {
+    # Go extra: go mod tidy must be a no-op before the checks run.
     cd "$ROOT"
     go mod tidy
     if ! git diff --exit-code -- go.mod go.sum; then

script/setup

@@ -1,6 +1,6 @@
 #!/bin/sh
 # script/setup: set up the repo for development after a fresh clone:
-# installs dependencies (script/bootstrap) and the git pre-commit hook.
+# installs dependencies and the git pre-commit hook.
 set -eu
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd -P)"