fetch: destination directory, skip files already present, save the manifest, require a signer (closes #101)

fetch takes --dest (default .) and writes every file there through the
existing symlink and hard-link guards, which now work relative to that
directory. A file already there with the listed size and hash is
skipped; a leftover temp file is still replaced. Once every file
verifies, the manifest is saved as index.mf through the same temp file
and rename, so check runs on the result; a manifest that lists index.mf
or its temp name at the top of the tree is refused, since saving would
replace that file. --require-signature is shared with check and
enforced through verifyRequiredSigner. Both refusals come before any
file is downloaded or anything is written.

Model: opus-5-5

Dockerfile

@@ -9,7 +9,8 @@ RUN go mod download
 COPY . .
 
 # Go half of fmt-check only: this image has no node, so no prettier. The
-# markdown half runs in the mdfmt stage below.
+# markdown half runs in the mdfmt stage below. The image has no gofumpt
+# either; script/gofumpt builds the version it pins with `go run`.
 RUN make fmt-check-go
 # The linter directly, not `make lint`: script/lint builds this stage, and
 # there is no docker inside this build.

Makefile

@@ -46,7 +46,7 @@ fmt-check:
 # Halves of fmt-check, for environments that have only one toolchain:
 # the Docker lint stage has Go but no node, the markdown stage the reverse.
 fmt-check-go:
-	@script/fmt-check-go
+	@script/gofumpt --check
 
 fmt-check-md:
 	@script/prettier --check

README.md

@@ -40,7 +40,7 @@ tree by URL:
 bin/mfer gen .
 
 # Verify the files on disk against the manifest. Exits nonzero if any file
-# is missing or corrupted.
+# it lists is missing or corrupted; warns about files it does not list.
 bin/mfer check index.mf
 
 # Download and cryptographically verify a tree published over HTTP into
@@ -93,16 +93,19 @@ provide:
 - `script/lint` — run `golangci-lint` in Docker: builds only the `lint` stage of
   the `Dockerfile` (the Go format check, then the linter), uncached so it runs
   every time, then removes the image
-- `script/fmt` — format all code and docs (writes): `gofumpt` and
+- `script/fmt` — format all code and docs (writes): `script/gofumpt --write` and
   `script/prettier --write`
+- `script/gofumpt` — run `gofumpt` over every Go file in the repository in the
+  given mode, `--write` or `--check`, at the one version it pins (built on
+  demand by `go run`, so nothing installs it); `script/fmt`, `script/fmt-check`
+  and the Docker lint stage (`make fmt-check-go`) all go through it, so they
+  cannot disagree about Go formatting
 - `script/prettier` — run prettier over the repository's canonical file set
   (Markdown and JSON, minus `.prettierignore`) in the given mode, `--write` or
   `--check`; the single definition of that file set, so `script/fmt` and
   `script/fmt-check` cannot disagree about it
-- `script/fmt-check` — check formatting without writing: `script/fmt-check-go`
+- `script/fmt-check` — check formatting without writing:
-  plus `script/prettier --check`
+  `script/gofumpt --check` plus `script/prettier --check`
-- `script/fmt-check-go` — the Go half of `script/fmt-check`, on its own, for the
-  Docker lint stage, whose image has no node
 - `script/check` — run `script/test`, `script/lint`, and `script/fmt-check`
 - `script/docker` — build the Docker image tagged with the project name
 - `script/cibuild` — CI entrypoint: builds the image with the same command as
@@ -253,13 +256,18 @@ are now tracked only in the [issues](https://git.eeqj.de/sneak/mfer/issues).
 - `mfer check` / `mfer check .`
     - verifies checksums of all files in manifest, displaying error and exiting
       nonzero if any files are missing or corrupted
+    - warns about each file under the base directory that the manifest does not
+      list, hidden files included; with `--no-extra-files` each one is a failure
+      instead
 - `mfer fetch https://example.com/stuff/`
     - fetches `/stuff/index.mf` and downloads all files listed in manifest into
       the current directory, or the one given with `--dest`, and assures
       cryptographic integrity of downloaded files. A file already there with the
       size and hash the manifest lists is skipped. Once every file is in place,
       the manifest is saved there as `index.mf`, so `mfer check` can verify the
-      tree later.
+      tree later. A manifest that lists `index.mf` (in any letter case) or
+      `.index.mf.tmp` at the top of the tree is refused before any file is
+      downloaded, since saving the manifest would replace it.
 - `mfer fetch --require-signature <fingerprint> https://example.com/stuff/`
     - as above, but first refuses a manifest not signed by the key with that
       fingerprint, as `mfer check --require-signature` does, before downloading

internal/cli/check.go

@@ -206,16 +206,21 @@ func countCheckFailures(
 }
 
 // findExtraFiles reports files present on disk but absent from the
-// manifest, counting each as a failure.
+// manifest, and anything the search cannot read: each is a failure under
+// --no-extra-files, otherwise a warning.
 func findExtraFiles(ctx *cli.Context, chk *mfer.Checker, failures *int64) error {
 	extraResults := make(chan mfer.Result, 1)
 	extraDone := make(chan struct{})
 
 	go func() {
 		for result := range extraResults {
-			*failures++
+			if ctx.Bool("no-extra-files") {
+				*failures++
 
-			log.Infof("%s: %s (%s)", result.Status, result.Path, result.Message)
+				log.Infof("%s: %s (%s)", result.Status, result.Path, result.Message)
+			} else {
+				log.Warnf("%s: %s (%s)", result.Status, result.Path, result.Message)
+			}
 		}
 
 		close(extraDone)
@@ -270,12 +275,9 @@ func runCheck(ctx *cli.Context, chk *mfer.Checker, showProgress bool) (int64, er
 	// Wait for results processing to complete
 	<-done
 
-	// Check for extra files if requested
+	err = findExtraFiles(ctx, chk, &failures)
-	if ctx.Bool("no-extra-files") {
+	if err != nil {
-		err = findExtraFiles(ctx, chk, &failures)
+		return 0, err
-		if err != nil {
-			return 0, err
-		}
 	}
 
 	return failures, nil

internal/cli/entry_test.go

@@ -705,30 +705,155 @@ func TestNoExtraFilesWithSubdirectory(t *testing.T) {
 		"check should fail when extra files exist in subdirectory")
 }
 
-func TestCheckWithoutNoExtraFilesIgnoresExtra(t *testing.T) {
+// TestCheckWarnsAboutUnlistedFiles adds one file the manifest does not list
+// to a tree that had none: it gets one warning and the check passes, unless
+// --no-extra-files makes it a failure. --quiet hides the warning, not the
+// failure.
+func TestCheckWarnsAboutUnlistedFiles(t *testing.T) {
 	t.Parallel()
 
-	fs := afero.NewMemMapFs()
+	for name, unlisted := range map[string]string{
+		"regular file":             "extra.txt",
+		"dotfile":                  ".hidden",
+		"file in hidden directory": ".git/config",
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
 
-	// Create test file
+			fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll(testDir, 0o755))
+			require.NoError(t, fs.MkdirAll(testDir, 0o755))
-	writeTestFile(t, fs, testFile1, "hello")
+			writeTestFile(t, fs, testFile1, "hello")
 
-	// Generate manifest
+			opts := testOpts([]string{
-	opts := testOpts([]string{testApp, cmdGenerate, "-q", "-o", testManifest, testDir}, fs)
+				testApp, cmdGenerate, "-q", "-o", testManifest, testDir,
-	exitCode := runCLI(opts)
+			}, fs)
-	require.Equal(t, 0, exitCode)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
 
-	// Add extra file
+			check := func(flags ...string) (int, string) {
-	writeTestFile(t, fs, "/testdir/extra.txt", "extra")
+				args := append([]string{testApp, cmdCheck, testFlagBase, testDir}, flags...)
+				opts := testOpts(append(args, testManifest), fs)
+
+				return runCLI(opts), testStderr(t, opts)
+			}
+
+			exitCode, stderr := check()
+			assert.Equal(t, 0, exitCode, "stderr: %s", stderr)
+			assert.NotContains(t, stderr, "not in manifest")
+
+			writeTestFile(t, fs, filepath.Join(testDir, unlisted), "unlisted")
+
+			exitCode, stderr = check()
+			assert.Equal(t, 0, exitCode, "stderr: %s", stderr)
+			assert.Equal(t, 1, strings.Count(stderr, "not in manifest"), stderr)
+			assert.Contains(t, stderr, unlisted)
+
+			exitCode, stderr = check("-q")
+			assert.Equal(t, 0, exitCode, "stderr: %s", stderr)
+			assert.NotContains(t, stderr, "not in manifest")
+
+			exitCode, stderr = check(testFlagNoExtra)
+			assert.Equal(t, 1, exitCode, "stderr: %s", stderr)
+			assert.Contains(t, stderr, unlisted)
+
+			exitCode, _ = check("-q", testFlagNoExtra)
+			assert.Equal(t, 1, exitCode)
+		})
+	}
+}
+
+// TestCheckNeverReportsManifest keeps the manifest inside the checked tree,
+// under several names and path spellings, and names the tree both directly
+// and through a symlink: the manifest is never reported, even under
+// --no-extra-files. The manifest is recognized by file identity, which needs
+// the real filesystem.
+func TestCheckNeverReportsManifest(t *testing.T) {
+	t.Parallel()
+
+	// Manifest paths are relative to the checked tree.
+	for name, manifest := range map[string]string{
+		"default name":                 defaultManifestName,
+		"hidden name":                  ".index.mf",
+		"other name in a subdirectory": "sub/listing.mf",
+		"path spelled through ..":      "sub/../index.mf",
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			// A temp dir holding data/tree and link, a symlink to data.
+			root := t.TempDir()
+			tree := filepath.Join(root, "data", "tree")
+			// Not filepath.Join, which would clean away a "..".
+			manifestPath := tree + "/" + manifest
+
+			fs := afero.NewOsFs()
+			require.NoError(t, fs.MkdirAll(filepath.Join(tree, "sub"), 0o750))
+			require.NoError(t,
+				os.Symlink(filepath.Join(root, "data"), filepath.Join(root, "link")))
+			writeTestFile(t, fs, filepath.Join(tree, testFileTxt), "hello")
+
+			opts := testOpts([]string{
+				testApp, cmdGenerate, "-q", "-o", manifestPath, tree,
+			}, fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			for _, base := range []string{tree, filepath.Join(root, "link", "tree")} {
+				opts = testOpts([]string{
+					testApp, cmdCheck, testFlagNoExtra, testFlagBase, base, manifestPath,
+				}, fs)
+				assert.Equal(t, 0, runCLI(opts),
+					"base %s, stderr: %s", base, testStderr(t, opts))
+				assert.NotContains(t, testStderr(t, opts), "not in manifest")
+			}
+		})
+	}
+}
+
+// unlistableDirFs is a filesystem on which one directory cannot be listed.
+type unlistableDirFs struct {
+	afero.Fs
+
+	dir string
+}
+
+//nolint:ireturn // Open must return afero.File to satisfy afero.Fs.
+func (f unlistableDirFs) Open(name string) (afero.File, error) {
+	if name == f.dir {
+		return nil, os.ErrPermission
+	}
+
+	return f.Fs.Open(name)
+}
+
+// TestCheckWithUnlistableDirectory has a directory under the base that
+// cannot be listed, followed by an unlisted file: both are warned about and
+// the check still passes, unless --no-extra-files is given.
+func TestCheckWithUnlistableDirectory(t *testing.T) {
+	t.Parallel()
+
+	mem := afero.NewMemMapFs()
+	require.NoError(t, mem.MkdirAll("/testdir/locked", 0o755))
+	writeTestFile(t, mem, testFile1, "hello")
+
+	opts := testOpts([]string{
+		testApp, cmdGenerate, "-q", "-o", testManifest, testDir,
+	}, mem)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	// Directories are searched in name order, so this comes after "locked".
+	writeTestFile(t, mem, "/testdir/unlisted.txt", "unlisted")
+
+	fs := unlistableDirFs{Fs: mem, dir: "/testdir/locked"}
+
+	opts = testOpts([]string{testApp, cmdCheck, testFlagBase, testDir, testManifest}, fs)
+	assert.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+	assert.Contains(t, testStderr(t, opts), os.ErrPermission.Error())
+	assert.Contains(t, testStderr(t, opts), "unlisted.txt")
 
-	// Check WITHOUT --no-extra-files (should pass - extra files ignored)
 	opts = testOpts([]string{
-		testApp, cmdCheck, "-q", testFlagBase, testDir, testManifest,
+		testApp, cmdCheck, testFlagNoExtra, testFlagBase, testDir, testManifest,
 	}, fs)
-	exitCode = runCLI(opts)
+	assert.Equal(t, 1, runCLI(opts), "stderr: %s", testStderr(t, opts))
-	assert.Equal(t, 0, exitCode,
+	assert.Contains(t, testStderr(t, opts), "unlisted.txt")
-		"check without --no-extra-files should ignore extra files")
 }
 
 func TestGenerateAtomicWriteNoTempFileOnSuccess(t *testing.T) {

internal/cli/fetch.go

@@ -91,6 +91,10 @@ var (
 	// errHashMismatch indicates a downloaded file whose hash matches no
 	// manifest hash.
 	errHashMismatch = errors.New("hash mismatch")
+	// errManifestNameListed indicates a manifest that lists a file where
+	// fetch saves the manifest.
+	errManifestNameListed = errors.New(
+		"manifest lists a file where fetch saves the manifest")
 )
 
 // DownloadProgress reports the progress of a single file download.
@@ -407,7 +411,8 @@ func (mfa *CLIApp) fetchManifestOperation(ctx *cli.Context) error {
 }
 
 // fetchManifest downloads the manifest at manifestURL and parses it,
-// enforcing --require-signature if it is given. It returns the manifest as
+// enforcing --require-signature if it is given and refusing a manifest
+// that lists a file where it will be saved. It returns the manifest as
 // downloaded, to be saved once the files are in place, and the files it
 // lists.
 func fetchManifest(
@@ -446,11 +451,36 @@ func fetchManifest(
 	}
 
 	files := manifest.Files()
+
+	err = checkManifestNameUnlisted(files)
+	if err != nil {
+		return nil, nil, err
+	}
+
 	log.Infof("manifest contains %d files", len(files))
 
 	return manifestData, files, nil
 }
 
+// checkManifestNameUnlisted returns an error if files lists a file or
+// directory at the top of the tree under the name fetch saves the
+// manifest as, or under that name's temp file. Saving the manifest would
+// replace or remove it, or fail once every file was downloaded, leaving a
+// tree check rejects. Names are compared ignoring case, since on a
+// case-insensitive filesystem INDEX.MF and index.mf are one file.
+func checkManifestNameUnlisted(files []*mfer.MFFilePath) error {
+	for _, f := range files {
+		top, _, _ := strings.Cut(filepath.Clean(f.GetPath()), string(filepath.Separator))
+
+		if strings.EqualFold(top, defaultManifestName) ||
+			strings.EqualFold(top, tempPathFor(defaultManifestName)) {
+			return fmt.Errorf("%w: %s", errManifestNameListed, f.GetPath())
+		}
+	}
+
+	return nil
+}
+
 // verifyFetchedSigner enforces --require-signature on the fetched manifest
 // exactly as check does. verifyRequiredSigner takes a Checker, which loads
 // its manifest from a file, so the manifest is handed to it as a file in

internal/cli/fetch_test.go

@@ -13,6 +13,7 @@ import (
 	"net/http/httptest"
 	"os"
 	"path/filepath"
+	"slices"
 	"strconv"
 	"sync"
 	"sync/atomic"
@@ -513,24 +514,51 @@ func TestFetchProgress(t *testing.T) {
 	assert.Equal(t, content, downloaded)
 }
 
-// TestFetchRefusesSymlinks runs fetch into a destination directory that
+// TestFetchRefusesSymlinks runs fetch with --dest naming a directory other
-// holds a symlink pointing outside it, in each of the three places fetch
+// than the current one, which holds a symlink pointing outside it, in each
-// writes: a parent directory, the temp file, and the file itself, which
+// place fetch writes: a parent directory, the temp file, the file itself,
-// the temp file is renamed onto; and once as a directory inside a plain
+// which the temp file is renamed onto, and the saved manifest's temp file
-// directory. The fetch must fail and nothing outside may change.
+// and final name; and once as a directory inside a plain directory. The
+// fetch must fail, and neither the outside directory nor the current one
+// may change.
 //
 //nolint:paralleltest // changes the process-global working directory
 func TestFetchRefusesSymlinks(t *testing.T) {
+	// What a link standing for a file points to: a file outside that does
+	// not exist yet.
+	const newFile = "new.txt"
+
 	tests := []struct {
-		name   string
+		name    string
-		entry  string // the manifest's only file
+		entry   string // the manifest's only file
-		link   string // symlink placed in the destination directory
+		link    string // symlink placed in the destination directory
-		target string // what link points to, relative to the outside directory
+		target  string // what link points to, relative to the outside directory
+		failure string // what fetch reports it was doing when it found link
 	}{
-		{"parent directory", "sub/deeper/file.txt", "sub", "."},
+		{
-		{"directory inside a plain directory", "docs/data/passwd", "docs/data", "."},
+			"parent directory", "sub/deeper/file.txt", "sub", ".",
-		{"temp file", testFileTxt, ".file.txt.tmp", "new.txt"},
+			"failed to download sub/deeper/file.txt",
-		{"file", testFileTxt, testFileTxt, "new.txt"},
+		},
+		{
+			"directory inside a plain directory", "docs/data/passwd", "docs/data", ".",
+			"failed to download docs/data/passwd",
+		},
+		{
+			"temp file", testFileTxt, ".file.txt.tmp", newFile,
+			"failed to download " + testFileTxt,
+		},
+		{
+			"file", testFileTxt, testFileTxt, newFile,
+			"failed to download " + testFileTxt,
+		},
+		{
+			"manifest temp file", testFileTxt, tempPathFor(defaultManifestName), newFile,
+			"failed to save manifest",
+		},
+		{
+			"manifest", testFileTxt, defaultManifestName, newFile,
+			"failed to save manifest",
+		},
 	}
 
 	for _, tt := range tests {
@@ -545,23 +573,61 @@ func TestFetchRefusesSymlinks(t *testing.T) {
 			defer server.Close()
 
 			outside := t.TempDir()
+			cwd := chdirTemp(t)
+			dest := t.TempDir()
+			link := filepath.Join(dest, tt.link)
 
-			chdirTemp(t)
+			require.NoError(t, os.MkdirAll(filepath.Dir(link), 0o750))
-			require.NoError(t, os.MkdirAll(filepath.Dir(tt.link), 0o750))
+			require.NoError(t, os.Symlink(filepath.Join(outside, tt.target), link))
-			require.NoError(t, os.Symlink(filepath.Join(outside, tt.target), tt.link))
 
-			opts := testOpts([]string{testApp, cmdFetch, "-q", server.URL}, afero.NewOsFs())
+			opts := testOpts([]string{
+				testApp, cmdFetch, "-q", "--" + flagDest, dest, server.URL,
+			}, afero.NewOsFs())
 			assert.Equal(t, 1, runCLI(opts))
-			assert.Contains(t, testStderr(t, opts), "failed to download "+tt.entry+
+			assert.Contains(t, testStderr(t, opts),
-				": symlink in path not allowed: "+tt.link)
+				tt.failure+": symlink in path not allowed: "+link)
 
 			written, err := os.ReadDir(outside)
 			require.NoError(t, err)
 			assert.Empty(t, written, "fetch wrote outside the destination")
+
+			written, err = os.ReadDir(cwd)
+			require.NoError(t, err)
+			assert.Empty(t, written, "fetch wrote to the current directory")
 		})
 	}
 }
 
+// TestFetchDoesNotSkipThroughSymlink runs fetch with --dest holding a
+// symlink to a directory outside it, where the file the manifest lists
+// through that symlink already sits with the listed content. fetch must
+// not take that file as already present: it must fail on the symlink, as
+// the download would, and leave the outside file alone.
+func TestFetchDoesNotSkipThroughSymlink(t *testing.T) {
+	t.Parallel()
+
+	content := []byte("fetched")
+	files := map[string][]byte{"sub/" + testFileTxt: content}
+
+	server := httptest.NewServer(fetchTestHandler(manifestOf(t, files), files))
+	defer server.Close()
+
+	outside := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(outside, testFileTxt), content, 0o600))
+
+	dest := t.TempDir()
+	link := filepath.Join(dest, "sub")
+	require.NoError(t, os.Symlink(outside, link))
+
+	opts := testOpts([]string{
+		testApp, cmdFetch, "-q", "--" + flagDest, dest, server.URL,
+	}, afero.NewOsFs())
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts),
+		"failed to download sub/"+testFileTxt+": symlink in path not allowed: "+link)
+	assert.Equal(t, map[string][]byte{testFileTxt: content}, filesUnder(t, outside))
+}
+
 // TestFetchReplacesHardLinkAtTempName runs fetch into a destination
 // directory that holds, at the temp file's name, a hard link to a file
 // outside it. To fetch that is an ordinary leftover from an interrupted
@@ -1061,8 +1127,9 @@ func TestFetchRequireSignature(t *testing.T) {
 	files := map[string][]byte{testFileTxt: []byte("signed file")}
 
 	t.Run("unsigned", func(t *testing.T) {
-		assertFetchRefused(t, manifestOf(t, files), files, msgFpA,
+		assertFetchRefused(t, manifestOf(t, files), files,
-			"manifest is not signed, but signature from "+msgFpA+" is required")
+			"manifest is not signed, but signature from "+msgFpA+" is required",
+			"--"+flagRequireSignature, msgFpA)
 	})
 
 	t.Run("signed", func(t *testing.T) {
@@ -1072,8 +1139,9 @@ func TestFetchRequireSignature(t *testing.T) {
 			ExtractEmbeddedSigningKeyFP(context.Background())
 		require.NoError(t, err)
 
-		assertFetchRefused(t, manifest, files, msgFpB,
+		assertFetchRefused(t, manifest, files,
-			"embedded signing key fingerprint "+signer+" does not match required "+msgFpB)
+			"embedded signing key fingerprint "+signer+" does not match required "+msgFpB,
+			"--"+flagRequireSignature, msgFpB)
 
 		server := httptest.NewServer(fetchTestHandler(manifest, files))
 		defer server.Close()
@@ -1089,12 +1157,49 @@ func TestFetchRequireSignature(t *testing.T) {
 	})
 }
 
+// TestFetchRefusesListedManifestName fetches manifests that list, at the
+// top of the tree, the name fetch saves the manifest under or that name's
+// temp file: as a file, as a directory, in capitals, and with a leading
+// "./". Saving the manifest would replace or remove what is listed there,
+// so fetch must refuse the manifest before it creates the destination or
+// requests any file.
+func TestFetchRefusesListedManifestName(t *testing.T) {
+	t.Parallel()
+
+	for _, listed := range []string{
+		defaultManifestName,
+		tempPathFor(defaultManifestName),
+		defaultManifestName + "/" + testFileTxt,
+		"INDEX.MF",
+		"./" + defaultManifestName,
+	} {
+		t.Run(listed, func(t *testing.T) {
+			t.Parallel()
+
+			// Built directly rather than scanned, since a scan lists no
+			// hidden files and never a path starting with "./".
+			content := []byte("listed")
+			builder := mfer.NewBuilder()
+			_, err := builder.AddFile(mfer.RelFilePath(listed), mfer.FileSize(len(content)),
+				mfer.ModTime(time.Now()), bytes.NewReader(content), nil)
+			require.NoError(t, err)
+
+			var manifest bytes.Buffer
+			require.NoError(t, builder.Build(context.Background(), &manifest))
+
+			assertFetchRefused(t, manifest.Bytes(), map[string][]byte{listed: content},
+				"manifest lists a file where fetch saves the manifest: "+listed)
+		})
+	}
+}
+
 // assertFetchRefused serves manifest, a manifest of files, and fetches it
-// with --require-signature signer into a directory that does not exist
+// with flags into a directory that does not exist yet. fetch must fail
-// yet. fetch must fail with message after requesting only the manifest,
+// with message after requesting only the manifest, and must not create
-// and must not create the directory.
+// the directory.
 func assertFetchRefused(
-	t *testing.T, manifest []byte, files map[string][]byte, signer, message string,
+	t *testing.T, manifest []byte, files map[string][]byte,
+	message string, flags ...string,
 ) {
 	t.Helper()
 
@@ -1119,13 +1224,12 @@ func assertFetchRefused(
 
 	dest := filepath.Join(t.TempDir(), "mirror")
 
-	opts := testOpts([]string{
+	opts := testOpts(slices.Concat(
-		testApp, cmdFetch, "-q", "--" + flagDest, dest,
+		[]string{testApp, cmdFetch, "-q", "--" + flagDest, dest}, flags, []string{server.URL},
-		"--" + flagRequireSignature, signer, server.URL,
+	), afero.NewOsFs())
-	}, afero.NewOsFs())
 	assert.Equal(t, 1, runCLI(opts))
 	assert.Contains(t, testStderr(t, opts), message)
-	assert.NoDirExists(t, dest, "fetch wrote before checking the signer")
+	assert.NoDirExists(t, dest, "fetch created the destination before refusing")
 
 	mu.Lock()
 	defer mu.Unlock()

internal/cli/mfer.go

@@ -240,7 +240,7 @@ func (mfa *CLIApp) checkCommand() *cli.Command {
 			},
 			&cli.BoolFlag{
 				Name:  "no-extra-files",
-				Usage: "Fail if files exist in base directory that are not in manifest",
+				Usage: "Fail, instead of warning, if files in base directory are not in manifest",
 			},
 			requireSignatureFlag(),
 		),

mfer/checker.go

@@ -77,9 +77,9 @@ type Checker struct {
 	fs       afero.Fs
 	// manifestPaths is a set of paths in the manifest for quick lookup
 	manifestPaths map[RelFilePath]struct{}
-	// manifestRelPath is the relative path of the manifest file from
+	// manifestInfo is the manifest file, which FindExtraFiles leaves out,
-	// basePath (for exclusion)
+	// matched with os.SameFile.
-	manifestRelPath RelFilePath
+	manifestInfo os.FileInfo
 	// signature info from the manifest
 	signature     []byte
 	signer        []byte
@@ -133,26 +133,20 @@ func NewChecker(opts *CheckerOptions) (*Checker, error) {
 		manifestPaths[RelFilePath(f.GetPath())] = struct{}{}
 	}
 
-	// Compute manifest's relative path from basePath for exclusion in FindExtraFiles
+	manifestInfo, err := fs.Stat(opts.ManifestPath)
-	absManifest, err := filepath.Abs(opts.ManifestPath)
 	if err != nil {
 		return nil, err
 	}
 
-	manifestRel, err := filepath.Rel(abs, absManifest)
-	if err != nil {
-		manifestRel = ""
-	}
-
 	return &Checker{
-		basePath:        AbsFilePath(abs),
+		basePath:      AbsFilePath(abs),
-		files:           files,
+		files:         files,
-		fs:              fs,
+		fs:            fs,
-		manifestPaths:   manifestPaths,
+		manifestPaths: manifestPaths,
-		manifestRelPath: RelFilePath(manifestRel),
+		manifestInfo:  manifestInfo,
-		signature:       m.pbOuter.GetSignature(),
+		signature:     m.pbOuter.GetSignature(),
-		signer:          m.pbOuter.GetSigner(),
+		signer:        m.pbOuter.GetSigner(),
-		signingPubKey:   m.pbOuter.GetSigningPubKey(),
+		signingPubKey: m.pbOuter.GetSigningPubKey(),
 	}, nil
 }
 
@@ -273,20 +267,27 @@ func (c *Checker) Check(
 	return nil
 }
 
-// FindExtraFiles walks the filesystem and reports files not in the manifest.
+// FindExtraFiles walks the filesystem and reports files not in the manifest,
-// Results are sent to the results channel. The channel is closed when done.
+// hidden files and directories included. The manifest file itself is not
-// Hidden files/directories (starting with .) are skipped, as they are excluded
+// reported. Anything the search cannot read, such as a directory that cannot
-// from manifests by default. The manifest file itself is also skipped.
+// be listed, is reported with StatusError and the search goes on. Results are
+// sent to the results channel. The channel is closed when done.
 func (c *Checker) FindExtraFiles(ctx context.Context, results chan<- Result) error {
 	if results != nil {
 		defer close(results)
 	}
 
-	walkFn := func(walkPath string, info os.FileInfo, err error) error {
+	// The search does not follow symlinks, so a base directory named
-		if err != nil {
+	// through one is resolved first. If that fails, the base is searched as
-			return err
+	// named and the search reports the problem.
-		}
+	root := string(c.basePath)
 
+	resolved, err := filepath.EvalSymlinks(root)
+	if err == nil {
+		root = resolved
+	}
+
+	walkFn := func(walkPath string, info os.FileInfo, walkErr error) error {
 		select {
 		case <-ctx.Done():
 			return ctx.Err()
@@ -294,15 +295,22 @@ func (c *Checker) FindExtraFiles(ctx context.Context, results chan<- Result) err
 		}
 
 		// Get relative path
-		rel, err := filepath.Rel(string(c.basePath), walkPath)
+		rel, err := filepath.Rel(root, walkPath)
 		if err != nil {
 			return err
 		}
 
-		// Skip hidden files and directories (dotfiles)
+		relPath := RelFilePath(rel)
-		if IsHiddenPath(filepath.ToSlash(rel)) {
+
-			if info.IsDir() {
+		// Report what cannot be read, such as a directory that cannot be
-				return filepath.SkipDir
+		// listed, and go on with the rest.
+		if walkErr != nil {
+			if results != nil {
+				results <- Result{
+					Path:    relPath,
+					Status:  StatusError,
+					Message: walkErr.Error(),
+				}
 			}
 
 			return nil
@@ -313,10 +321,17 @@ func (c *Checker) FindExtraFiles(ctx context.Context, results chan<- Result) err
 			return nil
 		}
 
-		relPath := RelFilePath(rel)
+		// A symlink is compared by what it points to, so a manifest reached
+		// through one is not reported either.
+		if info.Mode()&os.ModeSymlink != 0 {
+			target, statErr := c.fs.Stat(walkPath)
+			if statErr == nil {
+				info = target
+			}
+		}
 
-		// Skip the manifest file itself
+		// Skip the manifest file itself, however its path is spelled
-		if relPath == c.manifestRelPath {
+		if os.SameFile(info, c.manifestInfo) {
 			return nil
 		}
 
@@ -334,7 +349,7 @@ func (c *Checker) FindExtraFiles(ctx context.Context, results chan<- Result) err
 		return nil
 	}
 
-	return afero.Walk(c.fs, string(c.basePath), walkFn)
+	return afero.Walk(c.fs, root, walkFn)
 }
 
 func (c *Checker) checkFile(entry *MFFilePath, checkedBytes *FileSize) Result {

mfer/checker_test.go

@@ -21,8 +21,6 @@ const (
 	testExistsFile   = "exists.txt"
 	testManifestPath = "/manifest.mf"
 	testDataDir      = "/data"
-	// testDataManifestPath is a manifest kept inside the checked tree.
-	testDataManifestPath = testDataDir + "/index.mf"
 )
 
 func TestStatusString(t *testing.T) {
@@ -459,50 +457,120 @@ func TestFindExtraFiles(t *testing.T) {
 	assert.Equal(t, "not in manifest", extras[0].Message)
 }
 
-func TestFindExtraFilesSkipsManifestAndDotfiles(t *testing.T) {
+// TestFindExtraFilesReportsHiddenFilesButNotManifest keeps the manifest
+// inside the checked tree: hidden files and directories are reported, the
+// manifest is not. The manifest is recognized by file identity, which needs
+// the real filesystem.
+func TestFindExtraFilesReportsHiddenFilesButNotManifest(t *testing.T) {
 	t.Parallel()
 
-	fs := afero.NewMemMapFs()
+	dir := t.TempDir()
-	manifestFiles := map[string][]byte{
+	manifestPath := filepath.Join(dir, "index.mf")
-		testFile1: []byte("in manifest"),
+
-	}
+	fs := afero.NewOsFs()
-	createTestManifest(t, fs, testDataManifestPath, manifestFiles)
+	createTestManifest(t, fs, manifestPath, map[string][]byte{
-	createFilesOnDisk(t, fs, map[string][]byte{
 		testFile1: []byte("in manifest"),
 	})
-	// Create dotfile and manifest that should be skipped
+
-	require.NoError(t, afero.WriteFile(fs, "/data/.hidden", []byte("hidden"), 0o644))
+	unlisted := []RelFilePath{"extra.txt", ".hidden", ".git/config"}
-	require.NoError(t, afero.WriteFile(fs, "/data/.config/settings", []byte("cfg"), 0o644))
+	for _, p := range append([]RelFilePath{testFile1}, unlisted...) {
-	// Create a real extra file
+		path := filepath.Join(dir, string(p))
-	require.NoError(t, fs.MkdirAll(testDataDir, 0o755))
+		require.NoError(t, fs.MkdirAll(filepath.Dir(path), 0o750))
-	require.NoError(t, afero.WriteFile(fs, "/data/extra.txt", []byte("extra"), 0o644))
+		require.NoError(t, afero.WriteFile(fs, path, []byte("x"), 0o600))
+	}
 
 	chk, err := NewChecker(&CheckerOptions{
-		ManifestPath: testDataManifestPath,
+		ManifestPath: manifestPath,
-		BasePath:     testDataDir,
+		BasePath:     dir,
 		Fs:           fs,
 	})
 	require.NoError(t, err)
 
 	results := make(chan Result, 10)
-	err = chk.FindExtraFiles(context.Background(), results)
+	require.NoError(t, chk.FindExtraFiles(context.Background(), results))
+
+	var extras []RelFilePath
+	for r := range results {
+		extras = append(extras, r.Path)
+	}
+
+	assert.ElementsMatch(t, unlisted, extras)
+}
+
+// TestFindExtraFilesSkipsManifestReachedThroughSymlink checks a tree whose
+// index.mf is a symlink to the manifest kept outside the tree: the symlink is
+// not reported.
+func TestFindExtraFilesSkipsManifestReachedThroughSymlink(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	tree := filepath.Join(dir, "tree")
+	manifestPath := filepath.Join(dir, "real.mf")
+	linkPath := filepath.Join(tree, "index.mf")
+
+	fs := afero.NewOsFs()
+	createTestManifest(t, fs, manifestPath, map[string][]byte{testFile1: []byte("x")})
+	require.NoError(t, fs.MkdirAll(tree, 0o750))
+	require.NoError(t,
+		afero.WriteFile(fs, filepath.Join(tree, testFile1), []byte("x"), 0o600))
+	require.NoError(t, os.Symlink(manifestPath, linkPath))
+
+	chk, err := NewChecker(&CheckerOptions{
+		ManifestPath: linkPath,
+		BasePath:     tree,
+		Fs:           fs,
+	})
 	require.NoError(t, err)
 
-	var extras []Result
+	results := make(chan Result, 10)
+	require.NoError(t, chk.FindExtraFiles(context.Background(), results))
+
+	var extras []RelFilePath
 	for r := range results {
-		extras = append(extras, r)
+		extras = append(extras, r.Path)
 	}
 
-	// Should only report extra.txt, not .hidden, .config/settings, or index.mf
+	assert.Empty(t, extras)
-	for _, e := range extras {
+}
-		t.Logf("extra: %s", e.Path)
+
+// TestFindExtraFilesSearchesBaseNamedThroughSymlink names the checked tree
+// through a symlink to it: the files in the tree are searched, and the
+// symlink itself is not reported.
+func TestFindExtraFilesSearchesBaseNamedThroughSymlink(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	tree := filepath.Join(dir, "tree")
+	link := filepath.Join(dir, "link")
+	manifestPath := filepath.Join(dir, "index.mf")
+
+	fs := afero.NewOsFs()
+	createTestManifest(t, fs, manifestPath, map[string][]byte{testFile1: []byte("x")})
+	require.NoError(t, fs.MkdirAll(tree, 0o750))
+
+	for _, name := range []string{testFile1, testFile2} {
+		require.NoError(t,
+			afero.WriteFile(fs, filepath.Join(tree, name), []byte("x"), 0o600))
 	}
 
-	assert.Len(t, extras, 1)
+	require.NoError(t, os.Symlink(tree, link))
 
-	if len(extras) > 0 {
+	chk, err := NewChecker(&CheckerOptions{
-		assert.Equal(t, RelFilePath("extra.txt"), extras[0].Path)
+		ManifestPath: manifestPath,
+		BasePath:     link,
+		Fs:           fs,
+	})
+	require.NoError(t, err)
+
+	results := make(chan Result, 10)
+	require.NoError(t, chk.FindExtraFiles(context.Background(), results))
+
+	var extras []RelFilePath
+	for r := range results {
+		extras = append(extras, r.Path)
 	}
+
+	assert.Equal(t, []RelFilePath{testFile2}, extras)
 }
 
 func TestFindExtraFilesContextCancellation(t *testing.T) {
@@ -649,77 +717,6 @@ func TestCheckMissingFileDetectedWithoutFallback(t *testing.T) {
 	assert.Equal(t, 0, statusCounts[StatusError], "no files should be ERROR")
 }
 
-func TestFindExtraFilesSkipsDotfiles(t *testing.T) {
-	t.Parallel()
-
-	// Regression test for #16: FindExtraFiles should not report dotfiles
-	// or the manifest file itself as extra files.
-	fs := afero.NewMemMapFs()
-	files := map[string][]byte{
-		testFile1: []byte("in manifest"),
-	}
-	createTestManifest(t, fs, testDataManifestPath, files)
-	createFilesOnDisk(t, fs, files)
-
-	// Add dotfiles and manifest file on disk
-	require.NoError(t, afero.WriteFile(fs, "/data/.hidden", []byte("dotfile"), 0o644))
-	require.NoError(t, fs.MkdirAll("/data/.git", 0o755))
-	require.NoError(t,
-		afero.WriteFile(fs, "/data/.git/config", []byte("git config"), 0o644))
-
-	chk, err := NewChecker(&CheckerOptions{
-		ManifestPath: testDataManifestPath,
-		BasePath:     testDataDir,
-		Fs:           fs,
-	})
-	require.NoError(t, err)
-
-	results := make(chan Result, 10)
-	err = chk.FindExtraFiles(context.Background(), results)
-	require.NoError(t, err)
-
-	var extras []Result
-	for r := range results {
-		extras = append(extras, r)
-	}
-
-	// Should report NO extra files — dotfiles and manifest should be skipped
-	assert.Empty(t, extras,
-		"FindExtraFiles should not report dotfiles or manifest file as extra; got: %v",
-		extras)
-}
-
-func TestFindExtraFilesSkipsManifestFile(t *testing.T) {
-	t.Parallel()
-
-	// The manifest file itself should never be reported as extra
-	fs := afero.NewMemMapFs()
-	files := map[string][]byte{
-		testFile1: []byte("content"),
-	}
-	createTestManifest(t, fs, testDataManifestPath, files)
-	createFilesOnDisk(t, fs, files)
-
-	chk, err := NewChecker(&CheckerOptions{
-		ManifestPath: testDataManifestPath,
-		BasePath:     testDataDir,
-		Fs:           fs,
-	})
-	require.NoError(t, err)
-
-	results := make(chan Result, 10)
-	err = chk.FindExtraFiles(context.Background(), results)
-	require.NoError(t, err)
-
-	var extras []Result
-	for r := range results {
-		extras = append(extras, r)
-	}
-
-	assert.Empty(t, extras,
-		"manifest file should not be reported as extra; got: %v", extras)
-}
-
 func TestCheckEmptyManifest(t *testing.T) {
 	t.Parallel()
 

script/fmt

@@ -7,8 +7,9 @@ ROOT="$(cd "$SCRIPT_DIR/.." && pwd -P)"
 
 main() {
     cd "$ROOT"
-    gofumpt -l -w mfer internal cmd
+    # Go, then Markdown and JSON, through the same scripts script/fmt-check
-    # Markdown and JSON, over the same file set script/fmt-check verifies.
+    # uses, so both see the same files and the same tool versions.
+    "$SCRIPT_DIR/gofumpt" --write
     "$SCRIPT_DIR/prettier" --write
 }
 

script/fmt-check

@@ -1,13 +1,13 @@
 #!/bin/sh
 # script/fmt-check: check formatting (read-only). Same scope as
-# script/fmt, but fails instead of writing: Go via script/fmt-check-go,
+# script/fmt, but fails instead of writing: Go via script/gofumpt,
 # Markdown and JSON via script/prettier.
 set -eu
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 
 main() {
-    "$SCRIPT_DIR/fmt-check-go"
+    "$SCRIPT_DIR/gofumpt" --check
     "$SCRIPT_DIR/prettier" --check
 }
 

script/fmt-check-go

@@ -1,18 +0,0 @@
-#!/bin/sh
-# script/fmt-check-go: check Go formatting (read-only). Split out from
-# script/fmt-check so the Docker lint stage, whose image has no node and
-# therefore no prettier, can run the Go half on its own.
-set -eu
-
-ROOT="$(cd "$(dirname "$0")/.." && pwd -P)"
-
-main() {
-    cd "$ROOT"
-    if [ -n "$(gofmt -l .)" ]; then
-        echo "gofmt: files need formatting:" >&2
-        gofmt -l . >&2
-        exit 1
-    fi
-}
-
-main "$@"

script/gofumpt

@@ -0,0 +1,44 @@
+#!/bin/sh
+# script/gofumpt: run gofumpt over this repo's Go files.
+#
+# Takes exactly one mode argument, --write or --check, and runs the same
+# gofumpt version over the same files in both modes. script/fmt and
+# script/fmt-check both go through here, and so does the Docker lint
+# stage (make fmt-check-go), so what gets formatted and what gets
+# verified cannot drift apart.
+set -eu
+
+ROOT="$(cd "$(dirname "$0")/.." && pwd -P)"
+
+# gofumpt v0.12.0, 2026-10-04. `go run` fetches and builds exactly this
+# version, so neither a developer machine nor the lint image needs
+# gofumpt installed.
+GOFUMPT="mvdan.cc/gofumpt@v0.12.0"
+
+usage() {
+    echo "usage: script/gofumpt --write|--check" >&2
+    exit 2
+}
+
+main() {
+    [ "$#" -eq 1 ] || usage
+    cd "$ROOT"
+    # Every Go file in the repo. gofumpt holds generated files, such as
+    # mfer/mf.pb.go, to gofmt's rules only.
+    case "$1" in
+        --write) go run "$GOFUMPT" -l -w . ;;
+        --check)
+            # Own line: a failing command inside `[ -n "$(...)" ]` does
+            # not trip `set -e`, so a gofumpt that never ran would pass.
+            unformatted="$(go run "$GOFUMPT" -l .)"
+            if [ -n "$unformatted" ]; then
+                echo "gofumpt: files need formatting (run make fmt):" >&2
+                echo "$unformatted" >&2
+                exit 1
+            fi
+            ;;
+        *) usage ;;
+    esac
+}
+
+main "$@"