Enforce real timeouts on gpg subprocess calls (closes #62)

Every gpg run now has a one-minute deadline (gpgTimeout) on top of its
caller's context and is killed when either ends. A timeout is reported
as "gpg timed out" under the failing operation instead of "signal:
killed". Builder.Build and Checker.ExtractEmbeddedSigningKeyFP take a
context, so ToManifest's context now reaches signing and the
contextcheck suppression calling signing non-cancellable is gone.
Manifest loading takes no context, so its signature check is bounded by
the timeout alone. Killing gpg itself is enough: the gpg-agent it starts
runs detached and holds none of its output.

Model: opus-5-5

.dockerignore

@@ -1,4 +1,64 @@
+# .dockerignore does NOT use .gitignore semantics. Docker matches with
+# moby/patternmatcher: filepath.Match plus `**`, so `*` does not cross
+# `/` and an unprefixed pattern is anchored at the context root. Every
+# depth-independent pattern therefore needs `**/`, or `config/.env` and
+# `certs/server.key` still ship while this file reads as solved. Only
+# genuinely root-anchored entries go unprefixed. Never transplant these
+# into .gitignore, where `**/` is wrong.
+#
+# Matching is case-sensitive, so secrets use character ranges rather
+# than an ALL-CAPS twin, which would still miss `Server.Key`.
+#
+# Extend with this repo's own host-built artifacts, written anchored:
+# `/myapp`, never `**/myapp`, which also matches `cmd/myapp/` and
+# deletes the package directory from the context.
+
+# .git is sent without its config. Without a VERSION build argument the
+# stage that compiles runs `git describe --tags --always` on .git, which
+# does not need .git/config; that file can hold a credential, such as a
+# password in a remote URL or the token the CI checkout step stores there.
+.git/config
+
+# Agent scratch: one full checkout of the repo per in-flight agent.
+# Anchored because it occurs once where agents run at the repo root.
+# KNOWN GAP: a repo running agents in subdirectories still ships
+# `services/api/.claude/` and must add its own anchored entry.
+.claude
+
+# Environment files. `*.env` covers bare `.env` and the `prod.env`
+# convention. Re-include a committed template with a negation if the
+# build needs one: `!docs/example.env`.
+**/*.[eE][nN][vV]
+**/.[eE][nN][vV].*
+**/.[eE][nN][vV][rR][cC]
+
+# Private keys and the bundles carrying them. Public certificates
+# (*.crt, *.cer) are deliberately absent: they are legitimate inputs.
+**/*.[pP][eE][mM]
+**/*.[kK][eE][yY]
+**/*.[pP]12
+**/*.[pP][fF][xX]
+**/[iI][dD]_[rR][sS][aA]
+**/[iI][dD]_[dD][sS][aA]
+**/[iI][dD]_[eE][cC][dD][sS][aA]
+**/[iI][dD]_[eE][dD]25519
+
+# Dependencies: restored inside the image, never copied in.
+**/node_modules
+
+# OS metadata.
+**/.DS_Store
+**/Thumbs.db
+
+# Editor state: never a build input, and it churns COPY.
+**/*.swp
+**/*.swo
+**/*~
+**/*.bak
+**/.idea
+**/.vscode
+**/*.sublime-*
+
+# This repo's own host-built archives (Makefile).
 *.tmp
 *.dockerimage
-.git
-node_modules

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[Makefile]
+indent_style = tab

.gitignore

@@ -10,5 +10,24 @@ modcache.tzst
 # Generated manifest files
 .index.mf
 
-# Stale files
+# Secrets
-.drone.yml
+.env
+.env.*
+*.key
+*.pem
+
+# OS files
+.DS_Store
+Thumbs.db
+
+# Editor files
+*.swp
+*.swo
+*~
+.idea/
+.vscode/
+
+# Go build artifacts
+*.log
+*.out
+*.test

Dockerfile

@@ -48,7 +48,26 @@ COPY . .
 RUN touch mfer/mf.pb.go
 
 RUN make test
-RUN cd cmd/mfer && go build -tags urfave_cli_no_docs -o /mfer .
+
+# A build context sent as a tar archive, as upaas sends it, keeps its files'
+# owners, and git refuses to read a checkout owned by another user.
+RUN git config --system --add safe.directory /src
+
+# The revision `mfer version` prints, stamped into main.Gitrev: the VERSION
+# build argument when one is given (script/docker passes one), otherwise
+# `git describe --tags --always` of the .git the build context carries: the
+# tag on a tagged commit, tag-N-gHASH on a commit after one, the short commit
+# when no tag is reachable. git ships in this base image. A context that
+# carries .git and still yields no version fails the build.
+ARG VERSION
+RUN version="${VERSION:-$(git describe --tags --always)}"; \
+    if [ -e .git ] && { [ -z "$version" ] || [ "$version" = dev ] || \
+        [ "$version" = unknown ]; }; then \
+        echo "no version could be derived although the build context carries .git" >&2; \
+        exit 1; \
+    fi; \
+    cd cmd/mfer && \
+    go build -tags urfave_cli_no_docs -ldflags "-X main.Gitrev=$version" -o /mfer .
 
 FROM scratch
 COPY --from=builder /mfer /mfer

TODO.md

@@ -24,8 +24,31 @@ only thing left of the `chore/align-repo-policies` branch is the list below.
 
 # Completed Steps
 
-- 2026-09-21: fixed the `-v` collision between `--verbose` and `--version`;
+- 2026-10-03: every gpg run is killed after one minute or when its caller's
-  verbose owns `-v`, and version answers to `--version` and `-V` (#64)
+  context ends, and a timeout reads as "gpg timed out" under the failing
+  operation; `Builder.Build` and `Checker.ExtractEmbeddedSigningKeyFP` take a
+  context, which reaches gpg (#62)
+- 2026-10-03: `fetch` removes whatever sits at a file's temp name and then
+  creates the temp file only if that name is free, so a hard link left there
+  cannot make it write into a file outside the destination directory (#115)
+- 2026-10-03: `fetch` refuses any manifest path that runs through a symlink
+  already in the destination directory, checked before each of its writes
+  (directories, temp file, rename), so such a symlink cannot send a write
+  outside it (#86)
+- 2026-10-02: a plain `docker build .` of a clone now stamps the tag or short
+  commit into `mfer version` instead of nothing: `.dockerignore` sends `.git`
+  (not `.git/config`), and the build stage takes the `VERSION` build argument,
+  otherwise `git describe --tags --always`, failing if `.git` is present and no
+  version comes out. `script/docker` is the canonical copy, which passes
+  `VERSION`; `bin/gitrev.sh` uses `--tags` too (#112)
+- 2026-09-21: validate manifest entry paths on deserialize so untrusted `.mf`
+  files cannot make `Checker` stat or read outside `basePath` (#61)
+- 2026-09-21: rewrote `script/test` to the canonical pattern (30s timeout,
+  `-race -cover`, quiet-first with verbose-on-failure rerun) and fixed the
+  process-global logger data race it surfaced (#67)
+- 2026-09-21: added the canonical `.editorconfig`, made `.gitignore` cover
+  secrets, OS, editor, and Go artifacts, and removed the dead Drone CI
+  references from `.gitignore` and `bin/gitrev.sh` (#72)
 - 2026-08-09: added `.prettierrc`/`.prettierignore`, gave `script/fmt` and
   `script/fmt-check` one shared prettier file set via `script/prettier`, dropped
   the `|| true` that hid prettier failures, and added a node-based Dockerfile
@@ -64,7 +87,6 @@ only thing left of the `chore/align-repo-policies` branch is the list below.
     - Move FORMAT.md from repo root to docs/ and update the AGENTS.md reference
     - Pin Makefile-installed Go tools (`protoc-gen-go@v1.28.1`,
       `golangci-lint@v2.12.2`) by module hash, not mutable tag
-    - Set `make test` timeout to 30s (currently 10s)
     - Add explicit README "Rationale" heading (content exists under other
       names); name the author in the README Description first line
     - Reconcile root-level AGENTS.md with directory-hygiene policy (keep or
@@ -94,8 +116,7 @@ only thing left of the `chore/align-repo-policies` branch is the list below.
     - Add decompression size limit via io.LimitReader in deserializeInner()
     - Fix errors.Is dead code in checker; make AddFile verify totalRead == size
     - Export manifest type or define a public interface (pending)
-    - Replace GPG subprocess with pure-Go crypto (pending); add timeouts to
+    - Replace GPG subprocess with pure-Go crypto (pending)
-      remaining subprocess calls
 - CLI:
     - Kebab-case primary flag names; fix fetch URL construction with
       url.JoinPath; add http.Client timeout and retry with backoff to fetch;

bin/gitrev.sh

@@ -1,12 +1,7 @@
 #!/bin/bash
 #
-if [[ ! -z "$DRONE_COMMIT_SHA" ]]; then
-    echo "${DRONE_COMMIT_SHA:0:7}"
-    exit 0
-fi
-
 if [[ ! -z "$GITREV" ]]; then
     echo $GITREV
 else
-    git describe --always --dirty=-dirty
+    git describe --tags --always --dirty=-dirty
 fi

internal/cli/check.go

@@ -2,6 +2,7 @@
 package cli
 
 import (
+	"context"
 	"encoding/hex"
 	"errors"
 	"fmt"
@@ -126,7 +127,9 @@ func (mfa *CLIApp) fetchManifestToTemp(url string) (string, error) {
 
 // verifyRequiredSigner enforces the --require-signature fingerprint
 // against the manifest's embedded signing key.
-func verifyRequiredSigner(chk *mfer.Checker, requiredSigner string) error {
+func verifyRequiredSigner(
+	ctx context.Context, chk *mfer.Checker, requiredSigner string,
+) error {
 	// Validate fingerprint format: must be exactly 40 hex characters
 	if len(requiredSigner) != fingerprintHexLen {
 		return fmt.Errorf("%w, got %d", errInvalidFingerprint, len(requiredSigner))
@@ -145,7 +148,7 @@ func verifyRequiredSigner(chk *mfer.Checker, requiredSigner string) error {
 	// Extract fingerprint from the embedded public key (not from the
 	// signer field). This validates the key is importable and gets its
 	// actual fingerprint.
-	embeddedFP, err := chk.ExtractEmbeddedSigningKeyFP()
+	embeddedFP, err := chk.ExtractEmbeddedSigningKeyFP(ctx)
 	if err != nil {
 		return fmt.Errorf(
 			"failed to extract fingerprint from embedded signing key: %w", err)
@@ -303,7 +306,7 @@ func (mfa *CLIApp) checkManifestOperation(ctx *cli.Context) error {
 	// Check signature requirement
 	requiredSigner := ctx.String("require-signature")
 	if requiredSigner != "" {
-		err = verifyRequiredSigner(chk, requiredSigner)
+		err = verifyRequiredSigner(ctx.Context, chk, requiredSigner)
 		if err != nil {
 			return err
 		}

internal/cli/entry_test.go

@@ -27,7 +27,6 @@ const (
 	testManifest    = "/manifest.mf"
 	testFlagBase    = "--base"
 	testFlagNoExtra = "--no-extra-files"
-	testFlagVersion = "--version"
 )
 
 var errSimulatedWrite = errors.New("simulated write failure")
@@ -103,7 +102,7 @@ func TestVersionCommand(t *testing.T) {
 	t.Parallel()
 
 	fs := afero.NewMemMapFs()
-	opts := testOpts([]string{testApp, cmdVersion}, fs)
+	opts := testOpts([]string{testApp, "version"}, fs)
 
 	exitCode := runCLI(opts)
 
@@ -114,69 +113,6 @@ func TestVersionCommand(t *testing.T) {
 	assert.Contains(t, stdout, "abc123")
 }
 
-// TestVFlagCollision covers the -v/--verbose vs --version flag interaction
-// (issue #64). Verbose owns -v; version answers to --version and -V. None of
-// these invocations may produce a parser error, and the two ways of asking
-// for the version must print the same thing.
-func TestVFlagCollision(t *testing.T) {
-	t.Parallel()
-
-	// Invocations that must print the version and exit 0.
-	versionCases := map[string][]string{
-		"long version flag":        {testApp, testFlagVersion},
-		"short version flag":       {testApp, "-V"},
-		"verbose then version":     {testApp, "-v", testFlagVersion},
-		"long verbose and version": {testApp, "--verbose", testFlagVersion},
-	}
-
-	for name, args := range versionCases {
-		t.Run(name, func(t *testing.T) {
-			t.Parallel()
-
-			opts := testOpts(args, afero.NewMemMapFs())
-			exitCode := runCLI(opts)
-
-			assert.Equal(t, 0, exitCode, "stderr: %s", testStderr(t, opts))
-			assert.Contains(t, testStdout(t, opts), mfer.Version)
-			assert.NotContains(t, testStderr(t, opts), "two forms of the same flag")
-		})
-	}
-
-	// Invocations that must enable verbose and exit 0 without a parser error.
-	verboseCases := map[string][]string{
-		"short verbose flag": {testApp, "-v"},
-		"long verbose flag":  {testApp, "--verbose"},
-	}
-
-	for name, args := range verboseCases {
-		t.Run(name, func(t *testing.T) {
-			t.Parallel()
-
-			opts := testOpts(args, afero.NewMemMapFs())
-			exitCode := runCLI(opts)
-
-			assert.Equal(t, 0, exitCode, "stderr: %s", testStderr(t, opts))
-			assert.Contains(t, testStdout(t, opts), cmdGenerate,
-				"root should show help listing subcommands")
-			assert.Empty(t, testStderr(t, opts))
-		})
-	}
-}
-
-// TestVersionFlagAndCommandMatch asserts that "mfer --version" and
-// "mfer version" produce identical output (issue #64).
-func TestVersionFlagAndCommandMatch(t *testing.T) {
-	t.Parallel()
-
-	flagOpts := testOpts([]string{testApp, testFlagVersion}, afero.NewMemMapFs())
-	require.Equal(t, 0, runCLI(flagOpts))
-
-	cmdOpts := testOpts([]string{testApp, cmdVersion}, afero.NewMemMapFs())
-	require.Equal(t, 0, runCLI(cmdOpts))
-
-	assert.Equal(t, testStdout(t, flagOpts), testStdout(t, cmdOpts))
-}
-
 func TestHelpCommand(t *testing.T) {
 	t.Parallel()
 
@@ -190,7 +126,7 @@ func TestHelpCommand(t *testing.T) {
 	stdout := testStdout(t, opts)
 	assert.Contains(t, stdout, cmdGenerate)
 	assert.Contains(t, stdout, cmdCheck)
-	assert.Contains(t, stdout, "fetch")
+	assert.Contains(t, stdout, cmdFetch)
 }
 
 func TestGenerateCommand(t *testing.T) {
@@ -743,11 +679,13 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 	fs := afero.NewMemMapFs()
 	rng := rand.New(rand.NewSource(42)) //nolint:gosec // deterministic test data
 
-	// Create many small files with random names to generate a ~1MB manifest
+	// Create many small files with random names so the manifest has many
-	// Each manifest entry is roughly 50-60 bytes, so we need ~20000 files
+	// entries and random single-byte flips land at varied offsets. Each
+	// manifest entry is roughly 50-60 bytes. Kept modest so the suite stays
+	// within its wall-clock budget under -race.
 	require.NoError(t, fs.MkdirAll(testDir, 0o755))
 
-	numFiles := 20000
+	numFiles := 1500
 	for range numFiles {
 		// Generate random filename
 		filename := fmt.Sprintf("/testdir/%08x%08x%08x.dat",
@@ -763,11 +701,11 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 	exitCode := runCLI(opts)
 	require.Equal(t, 0, exitCode, "generate should succeed")
 
-	// Read the valid manifest and verify it's approximately 1MB
+	// Read the valid manifest and verify it has real size.
 	validManifest, err := afero.ReadFile(fs, testManifest)
 	require.NoError(t, err)
-	require.GreaterOrEqual(t, len(validManifest), 1024*1024,
+	require.GreaterOrEqual(t, len(validManifest), 64*1024,
-		"manifest should be at least 1MB, got %d bytes", len(validManifest))
+		"manifest should be at least 64KB, got %d bytes", len(validManifest))
 	t.Logf("manifest size: %d bytes (%d files)", len(validManifest), numFiles)
 
 	// First corruption: truncate the manifest
@@ -790,8 +728,8 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 	exitCode = runCLI(opts)
 	require.Equal(t, 0, exitCode, "check should pass with valid manifest")
 
-	// Now do 500 random corruption iterations
+	// Now do 100 random corruption iterations
-	for i := range 500 {
+	for i := range 100 {
 		// Corrupt: write a random byte at a random offset
 		corrupted := make([]byte, len(validManifest))
 		copy(corrupted, validManifest)

internal/cli/fetch.go

@@ -36,6 +36,11 @@ const (
 	// traversal bit for group and other must stay set.
 	dirPerms os.FileMode = 0o755
 
+	// filePerms is the permission mode, before the umask, for downloaded
+	// files. It is the mode os.Create uses; like dirPerms, it keeps group
+	// and other read access.
+	filePerms os.FileMode = 0o666
+
 	// Bitrate unit thresholds in bits per second.
 	bpsPerGbps = 1e9
 	bpsPerMbps = 1e6
@@ -53,6 +58,9 @@ var (
 	// errPathTraversal indicates a manifest path escaping the target
 	// directory.
 	errPathTraversal = errors.New("path traversal not allowed")
+	// errSymlinkInPath indicates a manifest path running through a
+	// symlink that already exists in the target directory.
+	errSymlinkInPath = errors.New("symlink in path not allowed")
 	// errSizeMismatch indicates a downloaded file with an unexpected
 	// size.
 	errSizeMismatch = errors.New("size mismatch")
@@ -274,6 +282,35 @@ func sanitizePath(p string) (string, error) {
 	return cleaned, nil
 }
 
+// checkNoSymlinks returns an error if any part of the relative path p
+// already exists as a symlink. sanitizePath checks p only as text, so
+// without this a symlink inside the target directory could send a write
+// to p outside of it. Parts that do not exist yet are fine: fetch creates
+// them as plain directories and files. Call it immediately before each
+// write: a symlink created after it returns is not caught.
+func checkNoSymlinks(p string) error {
+	current := ""
+
+	for _, part := range strings.Split(p, string(filepath.Separator)) {
+		current = filepath.Join(current, part)
+
+		info, err := os.Lstat(current)
+		if errors.Is(err, os.ErrNotExist) {
+			return nil
+		}
+
+		if err != nil {
+			return fmt.Errorf("failed to check %s for a symlink: %w", current, err)
+		}
+
+		if info.Mode()&os.ModeSymlink != 0 {
+			return fmt.Errorf("%w: %s", errSymlinkInPath, current)
+		}
+	}
+
+	return nil
+}
+
 // resolveManifestURL takes a URL and returns the manifest URL.
 // If the URL already ends with .mf, it's returned as-is.
 // Otherwise, index.mf is appended.
@@ -419,7 +456,12 @@ func downloadFile(
 	// Create parent directories if needed
 	dir := filepath.Dir(localPath)
 	if dir != "" && dir != "." {
-		err := os.MkdirAll(dir, dirPerms)
+		err = checkNoSymlinks(dir)
+		if err != nil {
+			return err
+		}
+
+		err = os.MkdirAll(dir, dirPerms)
 		if err != nil {
 			return fmt.Errorf("failed to create directory %s: %w", dir, err)
 		}
@@ -447,15 +489,25 @@ func downloadFile(
 		totalBytes = expectedSize
 	}
 
-	// Create temp file.
+	err = checkNoSymlinks(tmpPath)
+	if err != nil {
+		return err
+	}
+
+	// Remove whatever is at tmpPath, such as a leftover from an
+	// interrupted run, rather than write into it: it may be a hard link
+	// to a file outside the target directory, and removing a hard link
+	// removes only this name. If the removal fails, O_EXCL below makes
+	// the create fail.
+	_ = os.Remove(tmpPath)
+
+	// Create the temp file only if nothing is at tmpPath (O_EXCL).
 	//
-	// G304: tmpPath is derived from localPath, which sanitizePath above
+	// G304: tmpPath is a relative path that sanitizePath keeps inside the
-	// constrains lexically to a relative path that does not escape the
+	// target directory as text, and checkNoSymlinks just found no symlink
-	// destination directory. That is a purely lexical guarantee: it does
+	// in it.
-	// not resolve symlinks, so a pre-existing symlink inside the
+	out, err := os.OpenFile( //nolint:gosec // G304: see comment above
-	// destination tree can still redirect this write outside of it
+		tmpPath, os.O_RDWR|os.O_CREATE|os.O_EXCL, filePerms)
-	// (tracked in issue #86).
-	out, err := os.Create(tmpPath) //nolint:gosec // G304: see comment above
 	if err != nil {
 		return fmt.Errorf("failed to create temp file: %w", err)
 	}
@@ -519,6 +571,11 @@ func finishDownload(
 		return err
 	}
 
+	err = checkNoSymlinks(localPath)
+	if err != nil {
+		return err
+	}
+
 	// Rename temp file to final path
 	err = os.Rename(tmpPath, localPath)
 	if err != nil {

internal/cli/fetch_test.go

@@ -440,3 +440,86 @@ func TestFetchProgress(t *testing.T) {
 	require.NoError(t, err)
 	assert.Equal(t, content, downloaded)
 }
+
+// TestFetchRefusesSymlinks runs fetch into a destination directory that
+// holds a symlink pointing outside it, in each of the three places fetch
+// writes: a parent directory, the temp file, and the file itself, which
+// the temp file is renamed onto; and once as a directory inside a plain
+// directory. The fetch must fail and nothing outside may change.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestFetchRefusesSymlinks(t *testing.T) {
+	tests := []struct {
+		name   string
+		entry  string // the manifest's only file
+		link   string // symlink placed in the destination directory
+		target string // what link points to, relative to the outside directory
+	}{
+		{"parent directory", "sub/deeper/file.txt", "sub", "."},
+		{"directory inside a plain directory", "docs/data/passwd", "docs/data", "."},
+		{"temp file", testFileTxt, ".file.txt.tmp", "new.txt"},
+		{"file", testFileTxt, testFileTxt, "new.txt"},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			content := []byte("fetched")
+			sourceFs := afero.NewMemMapFs()
+			require.NoError(t, sourceFs.MkdirAll(filepath.Dir("/"+tt.entry), 0o755))
+			require.NoError(t, afero.WriteFile(sourceFs, "/"+tt.entry, content, 0o644))
+
+			server := httptest.NewServer(fetchTestHandler(
+				scanToManifest(t, sourceFs), map[string][]byte{tt.entry: content}))
+			defer server.Close()
+
+			outside := t.TempDir()
+
+			chdirTemp(t)
+			require.NoError(t, os.MkdirAll(filepath.Dir(tt.link), 0o750))
+			require.NoError(t, os.Symlink(filepath.Join(outside, tt.target), tt.link))
+
+			opts := testOpts([]string{testApp, cmdFetch, "-q", server.URL}, afero.NewOsFs())
+			assert.Equal(t, 1, runCLI(opts))
+			assert.Contains(t, testStderr(t, opts), "failed to download "+tt.entry+
+				": symlink in path not allowed: "+tt.link)
+
+			written, err := os.ReadDir(outside)
+			require.NoError(t, err)
+			assert.Empty(t, written, "fetch wrote outside the destination")
+		})
+	}
+}
+
+// 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
+// earlier run: it must replace it and succeed, and the outside file must
+// not change.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestFetchReplacesHardLinkAtTempName(t *testing.T) {
+	content := []byte("fetched")
+	sourceFs := afero.NewMemMapFs()
+	require.NoError(t, afero.WriteFile(sourceFs, "/"+testFileTxt, content, 0o644))
+
+	server := httptest.NewServer(fetchTestHandler(
+		scanToManifest(t, sourceFs), map[string][]byte{testFileTxt: content}))
+	defer server.Close()
+
+	outsideFile := filepath.Join(t.TempDir(), "secret.txt")
+	require.NoError(t, os.WriteFile(outsideFile, []byte("outside"), 0o600))
+
+	chdirTemp(t)
+	require.NoError(t, os.Link(outsideFile, ".file.txt.tmp"))
+
+	opts := testOpts([]string{testApp, cmdFetch, "-q", server.URL}, afero.NewOsFs())
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+	fetched, err := os.ReadFile(testFileTxt)
+	require.NoError(t, err)
+	assert.Equal(t, content, fetched)
+
+	outside, err := os.ReadFile(outsideFile) //nolint:gosec // test-controlled path
+	require.NoError(t, err)
+	assert.Equal(t, "outside", string(outside), "fetch wrote outside the destination")
+}

internal/cli/freshen.go

@@ -1,6 +1,7 @@
 package cli
 
 import (
+	"context"
 	"crypto/sha256"
 	"errors"
 	"fmt"
@@ -304,7 +305,7 @@ func (h *freshenHasher) processEntry(e *freshenEntry) error {
 // writeFreshenedManifest writes the manifest atomically (write to a
 // temp file, then rename over the target).
 func writeFreshenedManifest(
-	afs afero.Fs, builder *mfer.Builder, manifestPath string,
+	ctx context.Context, afs afero.Fs, builder *mfer.Builder, manifestPath string,
 ) error {
 	tmpPath := manifestPath + ".tmp"
 
@@ -313,7 +314,7 @@ func writeFreshenedManifest(
 		return fmt.Errorf("failed to create temp file: %w", err)
 	}
 
-	err = builder.Build(outFile)
+	err = builder.Build(ctx, outFile)
 	_ = outFile.Close()
 
 	if err != nil {
@@ -530,7 +531,7 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 	}
 
 	// Write updated manifest atomically (write to temp, then rename)
-	err = writeFreshenedManifest(mfa.Fs, hasher.builder, manifestPath)
+	err = writeFreshenedManifest(ctx.Context, mfa.Fs, hasher.builder, manifestPath)
 	if err != nil {
 		return err
 	}

internal/cli/mfer.go

@@ -18,7 +18,7 @@ const (
 	cmdGenerate = "generate"
 	cmdCheck    = "check"
 	cmdExport   = "export"
-	cmdVersion  = "version"
+	cmdFetch    = "fetch"
 
 	flagProgress = "progress"
 
@@ -68,12 +68,6 @@ func (mfa *CLIApp) VersionString() string {
 	return mfer.Version
 }
 
-// printVersion writes the version line shared by the --version flag and the
-// version subcommand, so both produce identical output.
-func (mfa *CLIApp) printVersion() {
-	_, _ = fmt.Fprintf(mfa.Stdout, "%s version %s\n", mfa.appname, mfa.VersionString())
-}
-
 func (mfa *CLIApp) printBanner() {
 	if log.GetLevel() <= log.InfoLevel {
 		_, _ = fmt.Fprintln(mfa.Stdout, banner)
@@ -272,10 +266,10 @@ func (mfa *CLIApp) exportCommand() *cli.Command {
 
 func (mfa *CLIApp) versionCommand() *cli.Command {
 	return &cli.Command{
-		Name:  cmdVersion,
+		Name:  "version",
 		Usage: "Show version",
 		Action: func(_ *cli.Context) error {
-			mfa.printVersion()
+			_, _ = fmt.Fprintln(mfa.Stdout, mfa.VersionString())
 
 			return nil
 		},
@@ -307,7 +301,7 @@ func (mfa *CLIApp) listCommand() *cli.Command {
 
 func (mfa *CLIApp) fetchCommand() *cli.Command {
 	return &cli.Command{
-		Name:  "fetch",
+		Name:  cmdFetch,
 		Usage: "fetch manifest and referenced files",
 		Action: func(c *cli.Context) error {
 			mfa.setVerbosity(c)
@@ -331,20 +325,6 @@ func (mfa *CLIApp) run(args []string) {
 	log.SetOutput(mfa.Stdout, mfa.Stderr)
 	log.Init()
 
-	// -v means verbose, not version. urfave/cli's built-in version flag
-	// claims -v by default, colliding with the -v verbose alias used here and
-	// on every subcommand; that collision makes "mfer -v --version" fail to
-	// parse. Verbose is the more common meaning of -v in tools that offer
-	// both, so verbose keeps -v and the version flag takes the capital -V.
-	// VersionFlag and VersionPrinter are urfave/cli package globals; run() is
-	// serialized in tests, so assigning them here is safe.
-	cli.VersionFlag = &cli.BoolFlag{
-		Name:    cmdVersion,
-		Aliases: []string{"V"},
-		Usage:   "print the version",
-	}
-	cli.VersionPrinter = func(_ *cli.Context) { mfa.printVersion() }
-
 	mfa.app = &cli.App{
 		Name:                 mfa.appname,
 		Usage:                "Manifest generator",
@@ -352,13 +332,11 @@ func (mfa *CLIApp) run(args []string) {
 		EnableBashCompletion: true,
 		Writer:               mfa.Stdout,
 		ErrWriter:            mfa.Stderr,
-		Flags:                commonFlags(),
 		Action: func(c *cli.Context) error {
 			if c.Args().Len() > 0 {
 				return fmt.Errorf("%w %q", errUnknownCommand, c.Args().First())
 			}
 
-			mfa.setVerbosity(c)
 			mfa.printBanner()
 
 			return cli.ShowAppHelp(c)
@@ -380,6 +358,6 @@ func (mfa *CLIApp) run(args []string) {
 	if err != nil {
 		mfa.exitCode = 1
 
-		log.WithError(err).Debugf("exiting")
+		log.Errorf("%s", err)
 	}
 }

internal/log/log.go

@@ -112,13 +112,16 @@ func DisableStyling() {
 }
 
 // Init initializes the logger with the CLI handler and default log level.
+//
+// It reconfigures the process-global apex/log logger under the write lock so
+// the global is never mutated while another goroutine holds the read lock to
+// read it in emit. Without this, parallel callers (e.g. the test suite) race
+// Init's SetLevel/SetHandler against concurrent log calls.
 func Init() {
-	mu.RLock()
+	mu.Lock()
+	defer mu.Unlock()
 
-	w := stderr
+	log.SetHandler(acli.New(stderr))
-
-	mu.RUnlock()
-	log.SetHandler(acli.New(w))
 	log.SetLevel(log.DebugLevel) // Let apex/log pass everything; we filter ourselves
 }
 
@@ -130,74 +133,66 @@ func isEnabled(l Level) bool {
 	return l >= currentLevel
 }
 
+// emit calls fn while holding the read lock if messages at level l are
+// enabled. Holding the read lock across the apex/log call keeps the global
+// logger from being read while Init reconfigures it under the write lock.
+func emit(l Level, fn func()) {
+	mu.RLock()
+	defer mu.RUnlock()
+
+	if l >= currentLevel {
+		fn()
+	}
+}
+
 // Fatalf logs a formatted message at fatal level.
 func Fatalf(format string, args ...any) {
-	if isEnabled(FatalLevel) {
+	emit(FatalLevel, func() { log.Fatalf(format, args...) })
-		log.Fatalf(format, args...)
-	}
 }
 
 // Fatal logs a message at fatal level.
 func Fatal(arg string) {
-	if isEnabled(FatalLevel) {
+	emit(FatalLevel, func() { log.Fatal(arg) })
-		log.Fatal(arg)
-	}
 }
 
 // Errorf logs a formatted message at error level.
 func Errorf(format string, args ...any) {
-	if isEnabled(ErrorLevel) {
+	emit(ErrorLevel, func() { log.Errorf(format, args...) })
-		log.Errorf(format, args...)
-	}
 }
 
 // Error logs a message at error level.
 func Error(arg string) {
-	if isEnabled(ErrorLevel) {
+	emit(ErrorLevel, func() { log.Error(arg) })
-		log.Error(arg)
-	}
 }
 
 // Warnf logs a formatted message at warn level.
 func Warnf(format string, args ...any) {
-	if isEnabled(WarnLevel) {
+	emit(WarnLevel, func() { log.Warnf(format, args...) })
-		log.Warnf(format, args...)
-	}
 }
 
 // Warn logs a message at warn level.
 func Warn(arg string) {
-	if isEnabled(WarnLevel) {
+	emit(WarnLevel, func() { log.Warn(arg) })
-		log.Warn(arg)
-	}
 }
 
 // Infof logs a formatted message at info level.
 func Infof(format string, args ...any) {
-	if isEnabled(InfoLevel) {
+	emit(InfoLevel, func() { log.Infof(format, args...) })
-		log.Infof(format, args...)
-	}
 }
 
 // Info logs a message at info level.
 func Info(arg string) {
-	if isEnabled(InfoLevel) {
+	emit(InfoLevel, func() { log.Info(arg) })
-		log.Info(arg)
-	}
 }
 
 // Verbosef logs a formatted message at verbose level.
 func Verbosef(format string, args ...any) {
-	if isEnabled(VerboseLevel) {
+	emit(VerboseLevel, func() { log.Infof(format, args...) })
-		log.Infof(format, args...)
-	}
 }
 
 // Verbose logs a message at verbose level.
 func Verbose(arg string) {
-	if isEnabled(VerboseLevel) {
+	emit(VerboseLevel, func() { log.Info(arg) })
-		log.Info(arg)
-	}
 }
 
 // Debugf logs a formatted message at debug level with caller location.
@@ -216,7 +211,10 @@ func Debug(arg string) {
 
 // DebugReal logs at debug level with caller info from the specified stack depth.
 func DebugReal(arg string, cs int) {
-	if !isEnabled(DebugLevel) {
+	mu.RLock()
+	defer mu.RUnlock()
+
+	if DebugLevel < currentLevel {
 		return
 	}
 
@@ -275,11 +273,6 @@ func GetLevel() Level {
 	return currentLevel
 }
 
-// WithError returns a log entry with the error attached.
-func WithError(e error) *log.Entry {
-	return log.Log.WithError(e)
-}
-
 // Progressf prints a progress message that overwrites the current line.
 // Use ProgressDone() when progress is complete to move to the next line.
 func Progressf(format string, args ...any) {

mfer/builder.go

@@ -3,6 +3,7 @@
 package mfer
 
 import (
+	"context"
 	"crypto/sha256"
 	"errors"
 	"fmt"
@@ -281,8 +282,9 @@ func (b *Builder) SetSigningOptions(opts *SigningOptions) {
 	b.signingOptions = opts
 }
 
-// Build finalizes the manifest and writes it to the writer.
+// Build finalizes the manifest and writes it to the writer. ctx bounds the
-func (b *Builder) Build(w io.Writer) error {
+// gpg runs that sign the manifest when signing options are set.
+func (b *Builder) Build(ctx context.Context, w io.Writer) error {
 	b.mu.Lock()
 	defer b.mu.Unlock()
 
@@ -308,13 +310,13 @@ func (b *Builder) Build(w io.Writer) error {
 	}
 
 	// Generate outer wrapper
-	err := m.generateOuter()
+	err := m.generateOuter(ctx)
 	if err != nil {
 		return fmt.Errorf("build: generate outer: %w", err)
 	}
 
 	// Generate final output
-	err = m.generate()
+	err = m.generate(ctx)
 	if err != nil {
 		return fmt.Errorf("build: generate: %w", err)
 	}

mfer/builder_test.go

@@ -3,6 +3,7 @@ package mfer
 
 import (
 	"bytes"
+	"context"
 	"strings"
 	"testing"
 	"time"
@@ -113,7 +114,7 @@ func TestBuilderBuild(t *testing.T) {
 
 	var buf bytes.Buffer
 
-	err = b.Build(&buf)
+	err = b.Build(context.Background(), &buf)
 	require.NoError(t, err)
 
 	// Should have magic bytes
@@ -177,7 +178,7 @@ func TestBuilderDeterministicOutput(t *testing.T) {
 
 		var buf bytes.Buffer
 
-		err := b.Build(&buf)
+		err := b.Build(context.Background(), &buf)
 		require.NoError(t, err)
 
 		return buf.Bytes()
@@ -325,7 +326,7 @@ func TestBuilderBuildRoundTrip(t *testing.T) {
 	}
 
 	var buf bytes.Buffer
-	require.NoError(t, b.Build(&buf))
+	require.NoError(t, b.Build(context.Background(), &buf))
 
 	m, err := NewManifestFromReader(&buf)
 	require.NoError(t, err)
@@ -383,7 +384,7 @@ func TestManifestString(t *testing.T) {
 	require.NoError(t, err)
 
 	var buf bytes.Buffer
-	require.NoError(t, b.Build(&buf))
+	require.NoError(t, b.Build(context.Background(), &buf))
 
 	m, err := NewManifestFromReader(&buf)
 	require.NoError(t, err)
@@ -397,7 +398,7 @@ func TestBuilderBuildEmpty(t *testing.T) {
 
 	var buf bytes.Buffer
 
-	err := b.Build(&buf)
+	err := b.Build(context.Background(), &buf)
 	require.NoError(t, err)
 
 	// Should still produce valid manifest with 0 files
@@ -416,7 +417,7 @@ func TestBuilderOmitsCreatedAtByDefault(t *testing.T) {
 	require.NoError(t, err)
 
 	var buf bytes.Buffer
-	require.NoError(t, b.Build(&buf))
+	require.NoError(t, b.Build(context.Background(), &buf))
 
 	m, err := NewManifestFromReader(&buf)
 	require.NoError(t, err)
@@ -438,7 +439,7 @@ func TestBuilderIncludesCreatedAtWhenRequested(t *testing.T) {
 	require.NoError(t, err)
 
 	var buf bytes.Buffer
-	require.NoError(t, b.Build(&buf))
+	require.NoError(t, b.Build(context.Background(), &buf))
 
 	m, err := NewManifestFromReader(&buf)
 	require.NoError(t, err)
@@ -464,7 +465,7 @@ func TestBuilderDeterministicFileOrder(t *testing.T) {
 		}
 
 		var buf bytes.Buffer
-		require.NoError(t, b.Build(&buf))
+		require.NoError(t, b.Build(context.Background(), &buf))
 		m, err := NewManifestFromReader(&buf)
 		require.NoError(t, err)
 

mfer/checker.go

@@ -164,12 +164,12 @@ func (c *Checker) SigningPubKey() []byte {
 // ExtractEmbeddedSigningKeyFP imports the manifest's embedded public key into a
 // temporary keyring and extracts its fingerprint. This validates the key and
 // returns its actual fingerprint from the key material itself.
-func (c *Checker) ExtractEmbeddedSigningKeyFP() (string, error) {
+func (c *Checker) ExtractEmbeddedSigningKeyFP(ctx context.Context) (string, error) {
 	if len(c.signingPubKey) == 0 {
 		return "", errNoSigningPubKey
 	}
 
-	return gpgExtractPubKeyFingerprint(c.signingPubKey)
+	return gpgExtractPubKeyFingerprint(ctx, c.signingPubKey)
 }
 
 // Check verifies all files against the manifest.
@@ -312,6 +312,10 @@ func (c *Checker) FindExtraFiles(ctx context.Context, results chan<- Result) err
 }
 
 func (c *Checker) checkFile(entry *MFFilePath, checkedBytes *FileSize) Result {
+	// entry.GetPath() is safe to join here: a manifest's entry paths are
+	// validated against the path invariants when it is loaded (see
+	// deserializeInner) or built (see Builder.AddFile), so a traversal or
+	// absolute path can never reach this point.
 	absPath := filepath.Join(string(c.basePath), entry.GetPath())
 	relPath := RelFilePath(entry.GetPath())
 

mfer/checker_test.go

@@ -61,7 +61,7 @@ func createTestManifest(
 	}
 
 	var buf bytes.Buffer
-	require.NoError(t, builder.Build(&buf))
+	require.NoError(t, builder.Build(context.Background(), &buf))
 	require.NoError(t, afero.WriteFile(fs, manifestPath, buf.Bytes(), 0o644))
 }
 

mfer/deserialize.go

@@ -2,6 +2,7 @@ package mfer
 
 import (
 	"bytes"
+	"context"
 	"crypto/sha256"
 	"errors"
 	"fmt"
@@ -25,6 +26,7 @@ var (
 	errDecompressedTooLarge = errors.New("decompressed data exceeds maximum allowed size")
 	errUUIDMismatch         = errors.New("outer and inner UUID mismatch")
 	errInvalidFileFormat    = errors.New("invalid file format")
+	errInvalidManifestPath  = errors.New("manifest contains invalid path")
 )
 
 // validateUUID checks that the byte slice is a valid UUID (16 bytes, parseable).
@@ -91,7 +93,9 @@ func (m *manifest) verifyOuterIntegrity() error {
 		)
 	}
 
+	// Loading a manifest takes no context; gpgTimeout still bounds gpg.
 	err = gpgVerify(
+		context.Background(),
 		[]byte(sigString),
 		m.pbOuter.GetSignature(),
 		m.pbOuter.GetSigningPubKey(),
@@ -181,6 +185,19 @@ func (m *manifest) deserializeInner() error {
 		return errUUIDMismatch
 	}
 
+	// Enforce the manifest path invariants on every entry as it is loaded,
+	// so that no consumer of a manifest — Checker today, any restore or
+	// extract path tomorrow — acts on a traversal or absolute path from an
+	// untrusted .mf. Reject loudly on the first offender rather than
+	// dropping entries, which would let a hostile manifest hide files from a
+	// check.
+	for _, f := range m.pbInner.GetFiles() {
+		err = ValidatePath(f.GetPath())
+		if err != nil {
+			return fmt.Errorf("%w: %w", errInvalidManifestPath, err)
+		}
+	}
+
 	log.Infof("loaded manifest with %d files", len(m.pbInner.GetFiles()))
 
 	return nil

mfer/deserialize_path_test.go

@@ -0,0 +1,146 @@
+//nolint:testpackage // white-box tests exercise unexported internals
+package mfer
+
+import (
+	"bytes"
+	"context"
+	"crypto/sha256"
+	"fmt"
+	"testing"
+
+	"github.com/google/uuid"
+	"github.com/klauspost/compress/zstd"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"google.golang.org/protobuf/encoding/protowire"
+	"google.golang.org/protobuf/proto"
+)
+
+// craftInnerBytes builds the wire bytes of an inner MFFile holding a single
+// file entry whose path is exactly pathBytes. It writes the wire form by hand
+// so a hostile path — including one that is not valid UTF-8 — can be embedded
+// without proto.Marshal's own UTF-8 enforcement rejecting it first.
+func craftInnerBytes(id uuid.UUID, pathBytes string) []byte {
+	entry := protowire.AppendTag(nil, 1, protowire.BytesType) // MFFilePath.path
+	entry = protowire.AppendString(entry, pathBytes)
+
+	inner := protowire.AppendTag(nil, 100, protowire.VarintType) // MFFile.version
+	inner = protowire.AppendVarint(inner, uint64(MFFile_VERSION_ONE))
+	inner = protowire.AppendTag(inner, 101, protowire.BytesType) // MFFile.files
+	inner = protowire.AppendBytes(inner, entry)
+	inner = protowire.AppendTag(inner, 102, protowire.BytesType) // MFFile.uuid
+	inner = protowire.AppendBytes(inner, id[:])
+
+	return inner
+}
+
+// wrapInner wraps inner MFFile wire bytes in a complete, well-formed .mf
+// envelope (magic prefix, zstd-compressed payload, matching hash and UUID) so
+// that deserialization reaches path validation rather than failing earlier on
+// an integrity check.
+func wrapInner(t *testing.T, id uuid.UUID, innerData []byte) []byte {
+	t.Helper()
+
+	var cbuf bytes.Buffer
+
+	zw, err := zstd.NewWriter(&cbuf, zstd.WithEncoderLevel(zstd.SpeedBestCompression))
+	require.NoError(t, err)
+
+	_, err = zw.Write(innerData)
+	require.NoError(t, err)
+	require.NoError(t, zw.Close())
+
+	compressed := cbuf.Bytes()
+	sum := sha256.Sum256(compressed)
+
+	outer := &MFFileOuter{
+		InnerMessage:    compressed,
+		Size:            int64(len(innerData)),
+		Sha256:          sum[:],
+		Uuid:            id[:],
+		Version:         MFFileOuter_VERSION_ONE,
+		CompressionType: MFFileOuter_COMPRESSION_ZSTD,
+	}
+
+	ob, err := proto.Marshal(outer)
+	require.NoError(t, err)
+
+	return append([]byte(MAGIC), ob...)
+}
+
+func TestDeserializeRejectsInvalidEntryPaths(t *testing.T) {
+	t.Parallel()
+
+	tests := []struct {
+		name string
+		path string
+	}{
+		{"parent traversal", "../escape"},
+		{"interior traversal", "a/../../escape"},
+		{"absolute path", "/etc/passwd"},
+		{"backslash path", `a\b`},
+		{"double slash", "a//b"},
+		{"empty path", ""},
+		{"invalid utf-8", "abc\xff"},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+
+			id := uuid.New()
+			data := wrapInner(t, id, craftInnerBytes(id, tt.path))
+
+			_, err := NewManifestFromReader(bytes.NewReader(data))
+			require.Error(t, err)
+
+			if tt.path == "abc\xff" {
+				// A path that is not valid UTF-8 cannot survive the proto3
+				// string decoder, which rejects it before path validation
+				// runs; the manifest is still refused at load time.
+				return
+			}
+
+			require.ErrorIs(t, err, errInvalidManifestPath)
+
+			if tt.path != "" {
+				// ValidatePath quotes the path with %q; assert against the
+				// same rendering so escaped characters (e.g. a backslash)
+				// still match.
+				assert.Contains(t, err.Error(), fmt.Sprintf("%q", tt.path),
+					"error must name the offending path")
+			}
+		})
+	}
+}
+
+func TestDeserializeValidManifestRoundTrips(t *testing.T) {
+	t.Parallel()
+
+	hash := make([]byte, 34) // multihash: 2-byte prefix + 32-byte SHA-256
+
+	b := NewBuilder()
+	require.NoError(t, b.AddFileWithHash("dir/file.txt", 123, ModTime{}, hash))
+
+	var buf bytes.Buffer
+	require.NoError(t, b.Build(context.Background(), &buf))
+
+	m, err := NewManifestFromReader(bytes.NewReader(buf.Bytes()))
+	require.NoError(t, err)
+
+	files := m.Files()
+	require.Len(t, files, 1)
+	assert.Equal(t, "dir/file.txt", files[0].GetPath())
+	assert.Equal(t, int64(123), files[0].GetSize())
+}
+
+// TestValidatePathRejectsInvalidUTF8 pins the ValidatePath rule that a manifest
+// path must be valid UTF-8, independent of the proto decoder that also enforces
+// it on the wire.
+func TestValidatePathRejectsInvalidUTF8(t *testing.T) {
+	t.Parallel()
+
+	err := ValidatePath("abc\xff")
+	require.ErrorIs(t, err, errPathNotUTF8)
+	assert.Contains(t, err.Error(), "UTF-8")
+}

mfer/errmsg_test.go

@@ -2,6 +2,7 @@
 package mfer
 
 import (
+	"context"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
@@ -80,6 +81,7 @@ func TestSerializeInternalErrorMessagesVerbatim(t *testing.T) {
 	t.Parallel()
 
 	m := &manifest{}
-	require.EqualError(t, m.generate(), "internal error: pbInner not set")
+	require.EqualError(t, m.generate(context.Background()),
-	require.EqualError(t, m.generateOuter(), "internal error")
+		"internal error: pbInner not set")
+	require.EqualError(t, m.generateOuter(context.Background()), "internal error")
 }

mfer/gpg.go

@@ -10,9 +10,15 @@ import (
 	"os/exec"
 	"path/filepath"
 	"strings"
+	"time"
 )
 
 const (
+	// gpgTimeout bounds every gpg run, which can otherwise wait forever on
+	// a passphrase prompt or a stalled gpg-agent. A minute leaves a person
+	// time to type a passphrase or touch a smartcard.
+	gpgTimeout = time.Minute
+
 	// privateDirPerms is the permission mode for temporary GPG home
 	// directories.
 	privateDirPerms os.FileMode = 0o700
@@ -66,8 +72,17 @@ func gpgArgs(opts []string, positional ...string) []string {
 }
 
 // runGPG runs the gpg binary in batch mode with the given arguments and
-// optional stdin, returning captured stdout and stderr.
+// optional stdin, returning captured stdout and stderr. gpg is killed when
-func runGPG(stdin io.Reader, args ...string) (*bytes.Buffer, *bytes.Buffer, error) {
+// ctx ends or gpgTimeout passes, whichever comes first.
+func runGPG(
+	ctx context.Context, stdin io.Reader, args ...string,
+) (*bytes.Buffer, *bytes.Buffer, error) {
+	// exec.CommandContext kills only gpg itself, and that is enough: a
+	// gpg-agent that gpg starts runs detached in its own session and does
+	// not hold gpg's output open, so Run returns as soon as gpg dies.
+	ctx, cancel := context.WithTimeout(ctx, gpgTimeout)
+	defer cancel()
+
 	fullArgs := append([]string{"--batch", "--no-tty"}, args...)
 
 	// G204: the executable name is a compile-time constant. The arguments
@@ -76,7 +91,7 @@ func runGPG(stdin io.Reader, args ...string) (*bytes.Buffer, *bytes.Buffer, erro
 	// option or after the "--" end-of-options marker inserted by gpgArgs,
 	// and therefore cannot be reinterpreted by gpg as an option.
 	cmd := exec.CommandContext( //nolint:gosec // G204: see comment above
-		context.Background(), "gpg", fullArgs...)
+		ctx, "gpg", fullArgs...)
 	cmd.Stdin = stdin
 
 	var stdout, stderr bytes.Buffer
@@ -85,6 +100,14 @@ func runGPG(stdin io.Reader, args ...string) (*bytes.Buffer, *bytes.Buffer, erro
 	cmd.Stderr = &stderr
 
 	err := cmd.Run()
+	if err != nil && ctx.Err() != nil {
+		// gpg was killed because ctx ended, which Run reports only as
+		// "signal: killed"; return the reason instead.
+		err = ctx.Err()
+		if errors.Is(err, context.DeadlineExceeded) {
+			err = fmt.Errorf("gpg timed out: %w", err)
+		}
+	}
 
 	return &stdout, &stderr, err
 }
@@ -105,8 +128,8 @@ func parseFingerprint(colonOutput string) (string, bool) {
 
 // gpgSign creates a detached signature of the data using the specified key.
 // Returns the armored detached signature.
-func gpgSign(data []byte, keyID GPGKeyID) ([]byte, error) {
+func gpgSign(ctx context.Context, data []byte, keyID GPGKeyID) ([]byte, error) {
-	stdout, stderr, err := runGPG(bytes.NewReader(data),
+	stdout, stderr, err := runGPG(ctx, bytes.NewReader(data),
 		"--detach-sign",
 		gpgOptArmor,
 		"--local-user", string(keyID),
@@ -120,8 +143,8 @@ func gpgSign(data []byte, keyID GPGKeyID) ([]byte, error) {
 
 // gpgExportPublicKey exports the public key for the specified key ID.
 // Returns the armored public key.
-func gpgExportPublicKey(keyID GPGKeyID) ([]byte, error) {
+func gpgExportPublicKey(ctx context.Context, keyID GPGKeyID) ([]byte, error) {
-	stdout, stderr, err := runGPG(nil,
+	stdout, stderr, err := runGPG(ctx, nil,
 		gpgArgs([]string{"--export", gpgOptArmor}, string(keyID))...,
 	)
 	if err != nil {
@@ -136,8 +159,8 @@ func gpgExportPublicKey(keyID GPGKeyID) ([]byte, error) {
 }
 
 // gpgGetKeyFingerprint gets the full fingerprint for a key ID.
-func gpgGetKeyFingerprint(keyID GPGKeyID) ([]byte, error) {
+func gpgGetKeyFingerprint(ctx context.Context, keyID GPGKeyID) ([]byte, error) {
-	stdout, stderr, err := runGPG(nil,
+	stdout, stderr, err := runGPG(ctx, nil,
 		gpgArgs([]string{"--with-colons", "--fingerprint"}, string(keyID))...,
 	)
 	if err != nil {
@@ -157,7 +180,7 @@ func gpgGetKeyFingerprint(keyID GPGKeyID) ([]byte, error) {
 // gpgExtractPubKeyFingerprint imports a public key into a temporary keyring
 // and extracts its fingerprint. This verifies the key is valid and returns
 // the actual fingerprint from the key material.
-func gpgExtractPubKeyFingerprint(pubKey []byte) (string, error) {
+func gpgExtractPubKeyFingerprint(ctx context.Context, pubKey []byte) (string, error) {
 	// Create temporary directory for GPG operations
 	tmpDir, err := os.MkdirTemp("", "mfer-gpg-fingerprint-*")
 	if err != nil {
@@ -181,7 +204,7 @@ func gpgExtractPubKeyFingerprint(pubKey []byte) (string, error) {
 	}
 
 	// Import the public key into the temporary keyring
-	_, importStderr, err := runGPG(nil,
+	_, importStderr, err := runGPG(ctx, nil,
 		gpgArgs([]string{gpgOptHomedir, tmpDir, "--import"}, pubKeyFile)...,
 	)
 	if err != nil {
@@ -191,7 +214,7 @@ func gpgExtractPubKeyFingerprint(pubKey []byte) (string, error) {
 	}
 
 	// List keys to get fingerprint
-	listStdout, listStderr, err := runGPG(nil,
+	listStdout, listStderr, err := runGPG(ctx, nil,
 		"--homedir", tmpDir,
 		"--with-colons",
 		"--fingerprint",
@@ -212,7 +235,7 @@ func gpgExtractPubKeyFingerprint(pubKey []byte) (string, error) {
 
 // gpgVerify verifies a detached signature against data using the provided public key.
 // It creates a temporary keyring to import the public key for verification.
-func gpgVerify(data, signature, pubKey []byte) error {
+func gpgVerify(ctx context.Context, data, signature, pubKey []byte) error {
 	// Create temporary directory for GPG operations
 	tmpDir, err := os.MkdirTemp("", "mfer-gpg-verify-*")
 	if err != nil {
@@ -252,7 +275,7 @@ func gpgVerify(data, signature, pubKey []byte) error {
 	}
 
 	// Import the public key into the temporary keyring
-	_, importStderr, err := runGPG(nil,
+	_, importStderr, err := runGPG(ctx, nil,
 		gpgArgs([]string{gpgOptHomedir, tmpDir, "--import"}, pubKeyFile)...,
 	)
 	if err != nil {
@@ -262,7 +285,7 @@ func gpgVerify(data, signature, pubKey []byte) error {
 	}
 
 	// Verify the signature
-	_, verifyStderr, err := runGPG(nil,
+	_, verifyStderr, err := runGPG(ctx, nil,
 		gpgArgs([]string{gpgOptHomedir, tmpDir, gpgOptVerify},
 			sigFile, dataFile)...,
 	)

mfer/gpg_test.go

@@ -4,11 +4,13 @@ package mfer
 import (
 	"bytes"
 	"context"
+	"io"
 	"os"
 	"os/exec"
 	"path/filepath"
 	"strings"
 	"testing"
+	"time"
 
 	"github.com/spf13/afero"
 	"github.com/stretchr/testify/assert"
@@ -43,8 +45,11 @@ Expire-Date: 0
 	paramsFile := filepath.Join(gpgHome, "key-params")
 	require.NoError(t, os.WriteFile(paramsFile, []byte(keyParams), 0o600))
 
+	ctx, cancel := context.WithTimeout(context.Background(), gpgTimeout)
+	defer cancel()
+
 	//nolint:gosec // paramsFile is a test-controlled path inside t.TempDir()
-	cmd := exec.CommandContext(context.Background(), "gpg",
+	cmd := exec.CommandContext(ctx, "gpg",
 		"--batch", "--gen-key", paramsFile)
 
 	cmd.Env = append(os.Environ(), "GNUPGHOME="+gpgHome)
@@ -55,7 +60,7 @@ Expire-Date: 0
 	}
 
 	// Get the key fingerprint
-	cmd = exec.CommandContext(context.Background(), "gpg",
+	cmd = exec.CommandContext(ctx, "gpg",
 		"--list-keys", "--with-colons", "test@mfer.test")
 
 	cmd.Env = append(os.Environ(), "GNUPGHOME="+gpgHome)
@@ -90,7 +95,7 @@ func TestGPGSign(t *testing.T) {
 	t.Setenv("GNUPGHOME", gpgHome)
 
 	data := []byte("test data to sign")
-	sig, err := gpgSign(data, keyID)
+	sig, err := gpgSign(context.Background(), data, keyID)
 	require.NoError(t, err)
 	assert.NotEmpty(t, sig)
 	assert.Contains(t, string(sig), "-----BEGIN PGP SIGNATURE-----")
@@ -101,7 +106,7 @@ func TestGPGExportPublicKey(t *testing.T) {
 	keyID, gpgHome := testGPGEnv(t)
 	t.Setenv("GNUPGHOME", gpgHome)
 
-	pubKey, err := gpgExportPublicKey(keyID)
+	pubKey, err := gpgExportPublicKey(context.Background(), keyID)
 	require.NoError(t, err)
 	assert.NotEmpty(t, pubKey)
 	assert.Contains(t, string(pubKey), "-----BEGIN PGP PUBLIC KEY BLOCK-----")
@@ -112,7 +117,7 @@ func TestGPGGetKeyFingerprint(t *testing.T) {
 	keyID, gpgHome := testGPGEnv(t)
 	t.Setenv("GNUPGHOME", gpgHome)
 
-	fingerprint, err := gpgGetKeyFingerprint(keyID)
+	fingerprint, err := gpgGetKeyFingerprint(context.Background(), keyID)
 	require.NoError(t, err)
 	assert.NotEmpty(t, fingerprint)
 	// The fingerprint should be 40 hex chars
@@ -146,12 +151,12 @@ func TestGPGOptionLikeKeyIDIsNotAnOption(t *testing.T) {
 	_, gpgHome := testGPGEnv(t)
 	t.Setenv("GNUPGHOME", gpgHome)
 
-	pubKey, err := gpgExportPublicKey(GPGKeyID("--version"))
+	pubKey, err := gpgExportPublicKey(context.Background(), GPGKeyID("--version"))
 	require.Error(t, err)
 	require.ErrorIs(t, err, errGPGKeyNotFound)
 	assert.NotContains(t, string(pubKey), "gpg (GnuPG)")
 
-	fpr, err := gpgGetKeyFingerprint(GPGKeyID("--version"))
+	fpr, err := gpgGetKeyFingerprint(context.Background(), GPGKeyID("--version"))
 	require.Error(t, err)
 	assert.NotContains(t, string(fpr), "gpg (GnuPG)")
 }
@@ -162,7 +167,8 @@ func TestGPGSignInvalidKey(t *testing.T) {
 	t.Setenv("GNUPGHOME", gpgHome)
 
 	data := []byte("test data")
-	_, err := gpgSign(data, GPGKeyID("NONEXISTENT_KEY_ID_12345"))
+	_, err := gpgSign(context.Background(), data,
+		GPGKeyID("NONEXISTENT_KEY_ID_12345"))
 	assert.Error(t, err)
 }
 
@@ -185,7 +191,7 @@ func TestBuilderWithSigning(t *testing.T) {
 	// Build the manifest
 	var buf bytes.Buffer
 
-	err = b.Build(&buf)
+	err = b.Build(context.Background(), &buf)
 	require.NoError(t, err)
 
 	// Parse the manifest and verify signature fields are populated
@@ -251,14 +257,14 @@ func TestGPGVerify(t *testing.T) {
 	t.Setenv("GNUPGHOME", gpgHome)
 
 	data := []byte("test data to sign and verify")
-	sig, err := gpgSign(data, keyID)
+	sig, err := gpgSign(context.Background(), data, keyID)
 	require.NoError(t, err)
 
-	pubKey, err := gpgExportPublicKey(keyID)
+	pubKey, err := gpgExportPublicKey(context.Background(), keyID)
 	require.NoError(t, err)
 
 	// Verify the signature
-	err = gpgVerify(data, sig, pubKey)
+	err = gpgVerify(context.Background(), data, sig, pubKey)
 	require.NoError(t, err)
 }
 
@@ -267,15 +273,15 @@ func TestGPGVerifyInvalidSignature(t *testing.T) {
 	t.Setenv("GNUPGHOME", gpgHome)
 
 	data := []byte("test data to sign")
-	sig, err := gpgSign(data, keyID)
+	sig, err := gpgSign(context.Background(), data, keyID)
 	require.NoError(t, err)
 
-	pubKey, err := gpgExportPublicKey(keyID)
+	pubKey, err := gpgExportPublicKey(context.Background(), keyID)
 	require.NoError(t, err)
 
 	// Try to verify with different data - should fail
 	wrongData := []byte("different data")
-	err = gpgVerify(wrongData, sig, pubKey)
+	err = gpgVerify(context.Background(), wrongData, sig, pubKey)
 	assert.Error(t, err)
 }
 
@@ -284,12 +290,12 @@ func TestGPGVerifyBadPublicKey(t *testing.T) {
 	t.Setenv("GNUPGHOME", gpgHome)
 
 	data := []byte("test data")
-	sig, err := gpgSign(data, keyID)
+	sig, err := gpgSign(context.Background(), data, keyID)
 	require.NoError(t, err)
 
 	// Try to verify with invalid public key - should fail
 	badPubKey := []byte("not a valid public key")
-	err = gpgVerify(data, sig, badPubKey)
+	err = gpgVerify(context.Background(), data, sig, badPubKey)
 	assert.Error(t, err)
 }
 
@@ -312,7 +318,7 @@ func TestManifestSignatureVerification(t *testing.T) {
 	// Build the manifest
 	var buf bytes.Buffer
 
-	err = b.Build(&buf)
+	err = b.Build(context.Background(), &buf)
 	require.NoError(t, err)
 
 	// Parse the manifest - signature should be verified during load
@@ -341,7 +347,7 @@ func TestManifestTamperedSignatureFails(t *testing.T) {
 
 	var buf bytes.Buffer
 
-	err = b.Build(&buf)
+	err = b.Build(context.Background(), &buf)
 	require.NoError(t, err)
 
 	// Tamper with the signature by replacing some bytes
@@ -375,7 +381,7 @@ func TestBuilderWithoutSigning(t *testing.T) {
 	// Build the manifest
 	var buf bytes.Buffer
 
-	err = b.Build(&buf)
+	err = b.Build(context.Background(), &buf)
 	require.NoError(t, err)
 
 	// Parse the manifest and verify signature fields are empty
@@ -390,3 +396,35 @@ func TestBuilderWithoutSigning(t *testing.T) {
 	assert.Empty(t, manifest.pbOuter.GetSigningPubKey(),
 		"signing public key should be empty when not signing")
 }
+
+// TestGPGTimeoutKillsGPG puts a fake gpg that never finishes first on
+// PATH and checks that a run past its deadline is killed and reported as
+// a timeout of the named operation, instead of hanging.
+func TestGPGTimeoutKillsGPG(t *testing.T) {
+	binDir := t.TempDir()
+	fakeGPG := []byte("#!/bin/sh\nexec sleep 10\n")
+	//nolint:gosec // G306: the fake gpg has to be executable
+	require.NoError(t, os.WriteFile(filepath.Join(binDir, "gpg"), fakeGPG, 0o700))
+	t.Setenv("PATH", binDir+string(os.PathListSeparator)+os.Getenv("PATH"))
+
+	ctx, cancel := context.WithTimeout(context.Background(), 100*time.Millisecond)
+	defer cancel()
+
+	_, err := gpgSign(ctx, []byte("data"), GPGKeyID("any"))
+	require.ErrorIs(t, err, context.DeadlineExceeded)
+	assert.Contains(t, err.Error(), "gpg sign failed: gpg timed out")
+}
+
+// TestBuildPassesContextToSigning checks that a caller can cancel the gpg
+// runs that sign a manifest through the context given to Build.
+func TestBuildPassesContextToSigning(t *testing.T) {
+	t.Parallel()
+
+	b := NewBuilder()
+	b.SetSigningOptions(&SigningOptions{KeyID: "any"})
+
+	ctx, cancel := context.WithCancel(context.Background())
+	cancel()
+
+	require.ErrorIs(t, b.Build(ctx, io.Discard), context.Canceled)
+}

mfer/scanner.go

@@ -283,8 +283,7 @@ func (s *Scanner) ToManifest(
 	}
 
 	// Build and write manifest
-	//nolint:contextcheck // Build's GPG signing exec is not cancellable by design
+	return builder.Build(ctx, w)
-	return builder.Build(w)
 }
 
 // configureBuilder constructs a manifest builder configured from the

mfer/serialize.go

@@ -2,6 +2,7 @@ package mfer
 
 import (
 	"bytes"
+	"context"
 	"crypto/sha256"
 	"errors"
 	"fmt"
@@ -50,13 +51,13 @@ func newTimestampFromTime(t time.Time) *Timestamp {
 	}
 }
 
-func (m *manifest) generate() error {
+func (m *manifest) generate(ctx context.Context) error {
 	if m.pbInner == nil {
 		return errInnerNotSet
 	}
 
 	if m.pbOuter == nil {
-		e := m.generateOuter()
+		e := m.generateOuter(ctx)
 		if e != nil {
 			return e
 		}
@@ -77,7 +78,7 @@ func (m *manifest) generate() error {
 	return nil
 }
 
-func (m *manifest) generateOuter() error {
+func (m *manifest) generateOuter(ctx context.Context) error {
 	if m.pbInner == nil {
 		return errInternal
 	}
@@ -135,7 +136,7 @@ func (m *manifest) generateOuter() error {
 
 	// Sign the manifest if signing options are provided
 	if m.signingOptions != nil && m.signingOptions.KeyID != "" {
-		return m.signOuter()
+		return m.signOuter(ctx)
 	}
 
 	return nil
@@ -143,27 +144,27 @@ func (m *manifest) generateOuter() error {
 
 // signOuter signs the outer message with the configured GPG key and
 // embeds the signature, signer fingerprint, and public key.
-func (m *manifest) signOuter() error {
+func (m *manifest) signOuter(ctx context.Context) error {
 	sigString, err := m.signatureString()
 	if err != nil {
 		return fmt.Errorf("failed to generate signature string: %w", err)
 	}
 
-	sig, err := gpgSign([]byte(sigString), m.signingOptions.KeyID)
+	sig, err := gpgSign(ctx, []byte(sigString), m.signingOptions.KeyID)
 	if err != nil {
 		return fmt.Errorf("failed to sign manifest: %w", err)
 	}
 
 	m.pbOuter.Signature = sig
 
-	fingerprint, err := gpgGetKeyFingerprint(m.signingOptions.KeyID)
+	fingerprint, err := gpgGetKeyFingerprint(ctx, m.signingOptions.KeyID)
 	if err != nil {
 		return fmt.Errorf("failed to get key fingerprint: %w", err)
 	}
 
 	m.pbOuter.Signer = fingerprint
 
-	pubKey, err := gpgExportPublicKey(m.signingOptions.KeyID)
+	pubKey, err := gpgExportPublicKey(ctx, m.signingOptions.KeyID)
 	if err != nil {
 		return fmt.Errorf("failed to export public key: %w", err)
 	}

script/docker

@@ -1,7 +1,8 @@
 #!/bin/sh
 # script/docker: build the Docker image tagged with the project name.
 # Identical in all repos; the tag comes from script/projectname.
-# Generic: needs no adaptation.
+# --no-cache because the gate phases the final stage depends on are RUN
+# steps, and a cached one is a check that did not run.
 set -eu
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd -P)"
@@ -9,7 +10,15 @@ ROOT="$(cd "$SCRIPT_DIR/.." && pwd -P)"
 
 main() {
     cd "$ROOT"
-    docker build -t "$("$SCRIPT_DIR/projectname")" .
+    # Own line: a failing command substitution inside an argument does
+    # not trip `set -e`, so the inline form degrades silently to an
+    # empty constant. The VERSION build argument takes precedence over
+    # the version a build stage derives from the .git in the context.
+    version="$(git describe --tags --always --dirty 2>/dev/null || true)"
+    [ -n "$version" ] || version="unknown"
+    docker build --no-cache \
+        --build-arg VERSION="$version" \
+        -t "$("$SCRIPT_DIR/projectname")" .
 }
 
 main "$@"

script/test

@@ -17,7 +17,12 @@ ensure_pb() {
 main() {
     cd "$ROOT"
     ensure_pb
-    go test -v --timeout 10s ./...
+    go test -timeout 30s -race -cover ./... ||
+        {
+            echo "--- Rerunning with -v for details ---"
+            go test -timeout 30s -race -v ./...
+            exit 1
+        }
 }
 
 main "$@"