Return the context's error when it ends during a fetch request (closes #221)

retryingClient.get checked its context right after each request and
returned that request's error, so a deadline that passed while a 503 was
on its way came back as the 503. TestGetStopsWaitingWhenCanceled failed
on that now and then on a loaded host. When the context ends before a
retry, during the request or during the wait, get now returns an error
wrapping both the context's error and the last try's error.

A new test covers the context ending during the request, and
TestGetStopsWaitingWhenCanceled now covers it ending during the wait.
Both answer through a transport rather than a server, so neither depends
on how fast the 503 arrives.

Model: opus-5-5

README.md

@@ -9,13 +9,23 @@ downloading, streaming, and mirroring. It was first published in 2022. The
 manifest files' data is serialized with Google's
 [protobuf serialization format](https://developers.google.com/protocol-buffers).
 The structure of these files can be found
-[in the format specification](https://git.eeqj.de/sneak/mfer/src/branch/main/mfer/mf.proto)
+[in the format specification](docs/FORMAT.md), which refers to the protobuf
-which is included in the [project repository](https://git.eeqj.de/sneak/mfer).
+schema `mfer/mf.proto` for exact field numbers and types. Both are included in
+the [project repository](https://git.eeqj.de/sneak/mfer).
 
 The current version is pre-1.0 and while the repo was published in 2022, there
 has not yet been any versioned release. [SemVer](https://semver.org) will be
 used for releases.
 
+A version is a git tag, and no file in the tree records a version number.
+`mfer version` prints the revision the build stamped into the binary, which for
+`make build` and the Docker image is the output of `git describe` on the
+checkout they build. A binary built without that stamp, as
+`go install sneak.berlin/go/mfer/cmd/mfer@<tag>` builds it, prints the module
+version Go records in it instead. A program that imports the `mfer` package
+finds the version it was built against in its own build information
+(`runtime/debug.ReadBuildInfo`).
+
 This project was started by [@sneak](https://sneak.berlin) to scratch an itch in
 2022 and is currently a one-person effort, though the goal is for this to emerge
 as a de-facto standard and be incorporated into other software. A compatible
@@ -256,8 +266,9 @@ are now tracked only in the [issues](https://git.eeqj.de/sneak/mfer/issues).
 
 - Should the manifest signature format be GnuPG signatures, or those from
   OpenBSD's signify (of which there is a good
-  [golang implementation](https://github.com/frankbraun/gosignify))? Still open,
+  [golang implementation](https://github.com/frankbraun/gosignify))? Settled
-  as question 10 on [issue 82](https://git.eeqj.de/sneak/mfer/issues/82).
+  under question 10 on [issue 82](https://git.eeqj.de/sneak/mfer/issues/82):
+  OpenPGP signatures, which mfer makes and checks itself without running `gpg`.
 
 - Should the on-disk serialization format be proto3 or json? Settled: it is
   proto3, see `docs/FORMAT.md` and `mfer/mf.proto`.
@@ -266,15 +277,55 @@ are now tracked only in the [issues](https://git.eeqj.de/sneak/mfer/issues).
 
 - `mfer gen` / `mfer gen .`
     - recurses under current directory and writes out an `index.mf`
+    - lists regular files only, and skips a named pipe, socket or device, which
+      it names with `-v`
     - records every file's mode as `0000` unless given `--include-permissions`,
       which records each file's permission bits (`0777` at most)
+- `mfer gen /media/drive`
+    - writes `/media/drive/index.mf`, listing each file by its path under
+      `/media/drive`, so `mfer check /media/drive` verifies it. Given a file,
+      gen writes `index.mf` beside it and lists the file by its name; given
+      several paths, it writes `index.mf` in the current directory
+    - `--output` names another file to write instead. What gen lists depends
+      only on the paths it is given and the files under them, so with the same
+      `--seed` and an unchanged tree it writes the same bytes wherever the
+      manifest goes. The file it writes to is never listed
 - `mfer check` / `mfer check .`
     - verifies checksums of all files in manifest, displaying error and exiting
       nonzero if any files are missing or corrupted, or have permission bits
       other than the mode the manifest records, unless that is `0000`
-    - warns about each file under the base directory that the manifest does not
+    - looks for those files under the base directory: the one `--base` names, or
-      list, hidden files included; with `--no-extra-files` each one is a failure
+      else the directory holding the manifest, or the current directory for a
-      instead
+      manifest given by URL. So `mfer check /media/drive` checks a drive against
+      the `index.mf` at its root, from any directory
+    - warns about each regular file under the base directory that the manifest
+      does not list, hidden files included, and each symlink there to a regular
+      file, which gen lists only with `--follow-symlinks`; with
+      `--no-extra-files` each one is a failure instead. A named pipe, socket or
+      device, a symlink to a directory and a broken symlink are never reported,
+      since gen cannot list them
+- `mfer freshen` / `mfer freshen .`
+    - rewrites `index.mf` to list the files now under the directory holding it,
+      or under the one `--base` names, hashing only the files that are new or
+      changed
+    - lists regular files only, as gen does
+    - leaves out hidden files unless given `--include-dotfiles`, and symlinks
+      unless given `--follow-symlinks`, which lists each symlink to a regular
+      file under its own name with the contents of the file it points to
+    - refuses a signed manifest, leaving it as it was and naming the fingerprint
+      of the key that signed it, unless `--sign-key` or `MFER_SIGN_KEY` names a
+      key to sign the new one with
+- `mfer gen --sign-key key.asc` / `mfer freshen --sign-key key.asc`
+    - signs the manifest with the OpenPGP secret key in `key.asc`, armored or
+      binary, as `gpg --export-secret-keys` writes it; `MFER_SIGN_KEY` names the
+      file too. mfer signs it itself and does not need `gpg`. A file holding
+      more than one key is refused, and a key held only on a smartcard cannot
+      sign. The key must be a version 4 key, whose 40-character fingerprint is
+      what `--require-signature` takes, and not a DSA key. A key that cannot
+      sign, because it has expired or been revoked or its passphrase is wrong,
+      stops `gen` and `freshen` before they read any file
+    - takes a protected key's passphrase from `MFER_SIGN_KEY_PASSPHRASE`, or
+      else asks for it at the terminal
 - `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

cmd/mfer/main.go

@@ -10,14 +10,12 @@ import (
 // Appname is the name of this program.
 const Appname = "mfer"
 
-// Version and Gitrev are injected at build time via -ldflags.
+// Gitrev is the revision `mfer version` prints, injected at build time via
+// -ldflags.
 //
 //nolint:gochecknoglobals // set via ldflags at build time
-var (
+var Gitrev string
-	Version string
-	Gitrev  string
-)
 
 func main() {
-	os.Exit(cli.Run(Appname, Version, Gitrev))
+	os.Exit(cli.Run(Appname, Gitrev))
 }

cmd/mfer/main_test.go

@@ -15,11 +15,10 @@ func TestAppname(t *testing.T) {
 	assert.Equal(t, "mfer", Appname)
 }
 
-// TestVersionDefaults documents that Version and Gitrev are empty unless
+// TestGitrevDefault documents that Gitrev is empty unless injected at build
-// injected at build time via -ldflags.
+// time via -ldflags.
-func TestVersionDefaults(t *testing.T) {
+func TestGitrevDefault(t *testing.T) {
 	t.Parallel()
 
-	assert.Empty(t, Version)
 	assert.Empty(t, Gitrev)
 }

docs/FORMAT.md

@@ -6,7 +6,7 @@ Version 1.0
 
 An `.mf` file is a binary manifest that describes a directory tree of files,
 including their paths, sizes, and cryptographic checksums. It supports optional
-GPG signatures for integrity verification and optional timestamps and file
+OpenPGP signatures for integrity verification and optional timestamps and file
 permissions for metadata preservation.
 
 Nothing goes in the 1.0 manifest that 1.0 does not read or write: no field is
@@ -20,9 +20,14 @@ An `.mf` file consists of two parts, concatenated:
 2. **Outer message**: a Protocol Buffers serialized `MFFileOuter` message
 
 There is no length prefix or version byte between the magic and the protobuf
-message. The protobuf message extends to the end of the file.
+message. The protobuf message extends to the end of the file, so a `.mf` is
+always a whole file; a different framing, such as one with a length prefix,
+would need a different magic. The format's version is the outer message's
+`version` field.
 
 See [`mfer/mf.proto`](../mfer/mf.proto) for exact field numbers and types.
+Readers ignore any field they do not know, in any message, so a later version
+can add a field without breaking 1.0 readers.
 
 ## Outer Message (`MFFileOuter`)
 
@@ -34,11 +39,11 @@ The outer message contains:
 | `compressionType` | 102    | enum             | Compression of `innerMessage`; must be `COMPRESSION_ZSTD` (1)            |
 | `size`            | 103    | int64            | Uncompressed size of `innerMessage` (corruption detection)               |
 | `sha256`          | 104    | bytes            | SHA-256 hash of the **compressed** `innerMessage` (corruption detection) |
-| `uuid`            | 105    | bytes            | Random v4 UUID; must match the inner message UUID                        |
+| `uuid`            | 105    | bytes            | 16-byte UUID; must match the inner message UUID                          |
 | `innerMessage`    | 199    | bytes            | Zstd-compressed serialized `MFFile` message                              |
-| `signature`       | 201    | bytes (optional) | GPG signature (ASCII-armored or binary)                                  |
+| `signature`       | 201    | bytes (optional) | One OpenPGP signature over the canonical string, armored or binary       |
-| `signer`          | 202    | bytes (optional) | Full GPG key ID of the signer                                            |
+| `signer`          | 202    | bytes (optional) | Fingerprint of the signing primary key, in upper-case hex                |
-| `signingPubKey`   | 203    | bytes (optional) | Full GPG signing public key                                              |
+| `signingPubKey`   | 203    | bytes (optional) | Full OpenPGP public key of the signing key (ASCII-armored or binary)     |
 
 ### SHA-256 Hash
 
@@ -64,26 +69,26 @@ for the signature, the signing key and the other outer fields.
 After decompressing `innerMessage`, the result is a serialized `MFFile`
 (referred to as the manifest):
 
-| Field       | Number | Type                  | Description                           |
+| Field       | Number | Type                  | Description                         |
-| ----------- | ------ | --------------------- | ------------------------------------- |
+| ----------- | ------ | --------------------- | ----------------------------------- |
-| `version`   | 100    | enum                  | Must be `VERSION_ONE` (1)             |
+| `version`   | 100    | enum                  | Must be `VERSION_ONE` (1)           |
-| `files`     | 101    | repeated `MFFilePath` | List of files in the manifest         |
+| `files`     | 101    | repeated `MFFilePath` | List of files in the manifest       |
-| `uuid`      | 102    | bytes                 | Random v4 UUID; must match outer UUID |
+| `uuid`      | 102    | bytes                 | 16-byte UUID; must match outer UUID |
-| `createdAt` | 201    | Timestamp (optional)  | When the manifest was created         |
+| `createdAt` | 201    | Timestamp (optional)  | When the manifest was created       |
 
 ## File Entries (`MFFilePath`)
 
 Each file entry contains:
 
-| Field      | Number | Type                      | Description                         |
+| Field      | Number | Type                      | Description                                                   |
-| ---------- | ------ | ------------------------- | ----------------------------------- |
+| ---------- | ------ | ------------------------- | ------------------------------------------------------------- |
-| `path`     | 1      | string                    | Relative file path (see Path Rules) |
+| `path`     | 1      | string                    | Relative file path (see Path Rules)                           |
-| `size`     | 2      | int64                     | File size in bytes                  |
+| `size`     | 2      | int64                     | File size in bytes                                            |
-| `hashes`   | 3      | repeated `MFFileChecksum` | At least one hash required          |
+| `hashes`   | 3      | repeated `MFFileChecksum` | At least one hash required; readers reject an entry with none |
-| `mimeType` | 301    | string (optional)         | MIME type                           |
+| `mimeType` | 301    | string (optional)         | MIME type                                                     |
-| `mtime`    | 302    | Timestamp (optional)      | Modification time                   |
+| `mtime`    | 302    | Timestamp (optional)      | Modification time                                             |
-| `ctime`    | 303    | Timestamp (optional)      | Change time (inode metadata change) |
+| `ctime`    | 303    | Timestamp (optional)      | Change time (inode metadata change)                           |
-| `mode`     | 304    | uint32                    | Permission bits (see File Mode)     |
+| `mode`     | 304    | uint32                    | Permission bits (see File Mode)                               |
 
 ## File Mode
 
@@ -107,11 +112,19 @@ All `path` values must satisfy these invariants:
 - **Forward slashes**: use `/` as the path separator (never `\`)
 - **Relative only**: no leading `/`
 - **No parent traversal**: no `..` path segments
+- **No current-directory segments**: no `.` path segments
 - **No empty segments**: no `//` sequences
 - **No trailing slash**: paths refer to files, not directories
+- **Listed once**: each path appears at most once in a manifest, compared byte
+  for byte, so `A.txt` and `a.txt` are two paths
 
 Implementations must validate these invariants when reading and writing
-manifests. Paths that violate these rules must be rejected.
+manifests. Paths that violate these rules must be rejected, and a reader must
+reject a manifest that lists a path more than once.
+
+A path holds each name exactly as the file system gives it, with no Unicode
+normalization, and readers compare paths byte for byte. So `é` stored as one
+code point and `é` stored as `e` followed by a combining accent are two paths.
 
 ## Hash Format (`MFFileChecksum`)
 
@@ -125,34 +138,243 @@ Implementations must be able to verify SHA-256 multihashes at minimum.
 
 ## Signature Scheme
 
-Signing is optional. When present, the signature covers a canonical string
+Signing is optional. A signature is stored only in the outer message's
-constructed as:
+`signature` field, never in a separate file. It is one OpenPGP signature over
+the canonical string below, armored or binary, and does not contain the string,
+which a verifier builds again from the outer message.
+
+The canonical string is three parts separated by hyphens (`-`):
 
 ```
 ZNAVSRFG-<UUID>-<SHA256>
 ```
 
-Where:
+- `ZNAVSRFG` is the magic, in ASCII.
+- `<UUID>` is the 16 bytes of the outer message's `uuid` as 32 lower-case hex
+  digits, with no hyphens.
+- `<SHA256>` is the lower-case hex of the outer message's `sha256` encoded as a
+  SHA-256 multihash (see Hash Format). That multihash is the algorithm code
+  `0x12`, the digest length `0x20` and the 32 bytes of the hash, so this part is
+  68 hex digits starting `1220`.
 
-- `ZNAVSRFG` is the magic bytes string (literal ASCII)
+The signature covers exactly the 110 ASCII characters of the string, with no
-- `<UUID>` is the hex-encoded UUID from the outer message
+line ending. For example, the UUID `b0fb6918-6298-443b-ada2-1b162f4dc0b3` and a
-- `<SHA256>` is the hex-encoded SHA-256 hash from the outer message (covering
+`sha256` of `e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855`
-  compressed data)
+in hex give this canonical string:
 
-Components are separated by hyphens. The signature is produced by GPG over this
+```
-canonical string and stored in the `signature` field of the outer message.
+ZNAVSRFG-b0fb69186298443bada21b162f4dc0b3-1220e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855
+```
+
+The signature covers `innerMessage` only through `sha256`, so a verifier checks
+`sha256` against `innerMessage` (see SHA-256 Hash) as well as the signature.
+
+The signing key's public key goes in `signingPubKey` and the fingerprint of its
+primary key, in upper-case hex, in `signer`. The reference implementation signs
+only with version 4 keys, whose fingerprints are 40 hex digits, and writes both
+the signature and the public key armored.
+
+A verifier accepts a signed manifest only if `signingPubKey` holds exactly one
+primary key, `signature` is one good signature over the canonical string made by
+that key (or one of its subkeys), and `signer` is that primary key's
+fingerprint, compared without regard to case. The reference implementation
+refuses to load a manifest that fails these checks; `check` and `fetch` given
+`--require-signature` then compare the required fingerprint with `signer`. It
+also refuses a manifest whose `signingPubKey` holds a DSA key or subkey, or any
+secret key or subkey, since checking the self-signatures of a DSA key or the
+numbers of a secret key can take hours when those numbers are very large.
+
+A signature is good only if the primary key, and the subkey that made the
+signature, were valid at the signature's creation time under the key validity
+rules of RFC 9580. The key is judged by its current self-signatures and binding
+signatures: for a version 4 key the newest self-signature on its primary user
+ID, for a version 6 key its newest direct-key signature, and for a subkey its
+newest binding signature with the signature embedded in it. So a signature made
+before the newest of those is not good, even if an older one made the key valid
+at that time. The reference implementation checks this by verifying the
+signature a second time with its clock set to the signature's creation time. A
+key that has expired since does not make the signature bad, because a manifest
+outlives its key. A signature past its own expiry time is not good, whether or
+not the key has expired too.
 
 ## Deterministic Serialization
 
-By default, manifests are generated deterministically:
+The reference implementation writes the same inner message for the same files,
+UUID and options, unless the options include `--include-timestamps`. It
+compresses the same inner message to the same bytes:
 
-- File entries are sorted by `path` in **lexicographic byte order**
+- File entries are sorted by `path` in byte order, so `B.txt` comes before
-- `createdAt` is omitted unless explicitly requested
+  `a.txt`.
-- `mode` is `0000` unless explicitly requested
+- Each message is encoded by the Go protobuf library with deterministic
+  marshaling, which writes fields in field-number order and leaves out the
+  fields that are not set. A field not declared `optional` counts as not set
+  when it holds its default value, zero or empty.
+- Each entry holds only `path`, `size`, `hashes` with exactly one hash, `mtime`
+  and `mode`. The hash is the SHA-256 multihash of the file's content, except
+  that `freshen` reads only the files that are new or whose size, `mtime` or
+  `mode` changed, and for every other file carries the first hash of its
+  existing entry over unchanged. `mtime` is the file's modification time as the
+  file system gives it, to the nanosecond, and `mode` is `0000` unless `gen` or
+  `freshen` is given `--include-permissions`.
+- `createdAt` is left out unless `gen` or `freshen` is given
+  `--include-timestamps`. Then it holds the time the run started building the
+  manifest, to the nanosecond, so it differs on every run.
+- A time, in `mtime` or `createdAt`, is written as `seconds`, the whole seconds
+  since 1970-01-01 00:00:00 UTC rounded down, and `nanos`, the rest, from 0
+  to 999999999. So a time before 1970 has negative `seconds` and `nanos` of 0 or
+  more.
+- The inner message is compressed into one zstd frame, with a checksum of its
+  content, by the encoder of the Go library `github.com/klauspost/compress` at
+  its `SpeedBestCompression` level and otherwise its default settings. That
+  encoder gives the same bytes for the same input only within one version of the
+  library. Another zstd encoder gives other bytes for the same inner message,
+  and so another `sha256`.
+- `gen` and `freshen` choose a new random version 4 UUID on every run, except
+  that `gen` given `--seed` takes the first 16 bytes of the SHA-256 of the seed
+  string instead. Those bytes are not a version 4 UUID; readers accept any 16
+  bytes.
 
-This ensures that two independent runs over the same directory tree produce
+So two runs of `gen` over an unchanged tree write byte-identical files only when
-byte-identical `.mf` files (assuming file contents and metadata have not
+both are given the same `--seed`, neither is given `--include-timestamps`, and
-changed).
+neither signs the manifest: a signature records the time it was made, and the
+OpenPGP library adds a random salt to each one.
+
+## Test Vector
+
+[`mfer/testdata/test-vector.mf`](../mfer/testdata/test-vector.mf) is a signed
+manifest the reference implementation made once, with the UUID
+`92197fd5-32bc-4090-8aa9-f86e5518b56c` and an Ed25519 key that the OpenPGP
+library made for this file and nothing else; its secret key was not kept.
+`TestFormatTestVector` in `mfer/deserialize_test.go` checks that the file's
+SHA-256, its canonical string and `signer` are the ones shown here, and verifies
+its signature.
+
+A reader should load the file and accept its signature. A writer given the same
+files and UUID should give the same inner message; its compressed bytes, and so
+its `sha256` and signature, depend on its zstd encoder (see Deterministic
+Serialization).
+
+The manifest has no `createdAt` and lists two files, each with mode `0000` and
+the modification time 2026-10-13 12:00:00.5 UTC (`seconds` 1791892800, `nanos`
+500000000):
+
+| `path`          | `size` | Content                 |
+| --------------- | ------ | ----------------------- |
+| `dir/world.txt` | 6      | `world` and a line feed |
+| `hello.txt`     | 6      | `hello` and a line feed |
+
+The inner message, 164 bytes before compression:
+
+```
+00000000  a0 06 01 aa 06 46 0a 0d  64 69 72 2f 77 6f 72 6c  |.....F..dir/worl|
+00000010  64 2e 74 78 74 10 06 1a  24 0a 22 12 20 e2 58 d2  |d.txt...$.". .X.|
+00000020  48 fd a9 4c 63 75 36 07  f7 c4 49 4e e0 fc be 92  |H..Lcu6...IN....|
+00000030  f1 a7 6b fd ac 79 5c 9d  84 10 1e b3 17 f2 12 0c  |..k..y\.........|
+00000040  08 c0 ba b8 d6 06 10 80  ca b5 ee 01 aa 06 42 0a  |..............B.|
+00000050  09 68 65 6c 6c 6f 2e 74  78 74 10 06 1a 24 0a 22  |.hello.txt...$."|
+00000060  12 20 58 91 b5 b5 22 d5  df 08 6d 0f f0 b1 10 fb  |. X..."...m.....|
+00000070  d9 d2 1b b4 fc 71 63 af  34 d0 82 86 a2 e8 46 f6  |.....qc.4.....F.|
+00000080  be 03 f2 12 0c 08 c0 ba  b8 d6 06 10 80 ca b5 ee  |................|
+00000090  01 b2 06 10 92 19 7f d5  32 bc 40 90 8a a9 f8 6e  |........2.@....n|
+000000a0  55 18 b5 6c                                       |U..l|
+```
+
+Its compressed form is hashed into `sha256`:
+
+```
+2353553205f036a88cefee3d0d9049ccd8e68bb24011a0b462b5867f1fcc6352
+```
+
+So the canonical string is:
+
+```
+ZNAVSRFG-92197fd532bc40908aa9f86e5518b56c-12202353553205f036a88cefee3d0d9049ccd8e68bb24011a0b462b5867f1fcc6352
+```
+
+`signer` is `5E962A37590D855B467D20294947A60319611E6F`, and `signature` holds:
+
+```
+-----BEGIN PGP SIGNATURE-----
+
+wqsEABYIAF0FgmrOejEJEElHpgMZYR5vNRQAAAAAABwAEHNhbHRAbm90YXRpb25z
+Lm9wZW5wZ3Bqcy5vcmddxfykLLTqmTD7G/jHGzY+FiEEXpYqN1kNhVtGfSApSUem
+AxlhHm8AAH0hAQDI6oGxvk1sGqIcu3Abvs7DM/7EalxkND614N75FCg+ywEApP6L
+oIvrZUgEw8DUb9JeK7TChOi6PUAHUFY75Fp6hAE=
+=nfX5
+-----END PGP SIGNATURE-----
+```
+
+The whole file, 1056 bytes, whose SHA-256 is
+`5864187d671b2a55f8e015f858248f92c51956b549cf548b6bb54477c2407fd4`:
+
+```
+00000000  5a 4e 41 56 53 52 46 47  a8 06 01 b0 06 01 b8 06  |ZNAVSRFG........|
+00000010  a4 01 c2 06 20 23 53 55  32 05 f0 36 a8 8c ef ee  |.... #SU2..6....|
+00000020  3d 0d 90 49 cc d8 e6 8b  b2 40 11 a0 b4 62 b5 86  |=..I.....@...b..|
+00000030  7f 1f cc 63 52 ca 06 10  92 19 7f d5 32 bc 40 90  |...cR.......2.@.|
+00000040  8a a9 f8 6e 55 18 b5 6c  ba 0c a1 01 28 b5 2f fd  |...nU..l....(./.|
+00000050  04 00 a5 04 00 94 08 a0  06 01 aa 06 46 0a 0d 64  |............F..d|
+00000060  69 72 2f 77 6f 72 6c 64  2e 74 78 74 10 06 1a 24  |ir/world.txt...$|
+00000070  0a 22 12 20 e2 58 d2 48  fd a9 4c 63 75 36 07 f7  |.". .X.H..Lcu6..|
+00000080  c4 49 4e e0 fc be 92 f1  a7 6b fd ac 79 5c 9d 84  |.IN......k..y\..|
+00000090  10 1e b3 17 f2 12 0c 08  c0 ba b8 d6 06 10 80 ca  |................|
+000000a0  b5 ee 01 aa 06 42 0a 09  68 65 6c 6c 6f 58 91 b5  |.....B..helloX..|
+000000b0  b5 22 d5 df 08 6d 0f f0  b1 10 fb d9 d2 1b b4 fc  |."...m..........|
+000000c0  71 63 af 34 d0 82 86 a2  e8 46 f6 be 03 b2 06 10  |qc.4.....F......|
+000000d0  92 19 7f d5 32 bc 40 90  8a a9 f8 6e 55 18 b5 6c  |....2.@....nU..l|
+000000e0  02 10 06 40 ba b7 10 ce  0c f8 c2 24 13 ca 0c ac  |...@.......$....|
+000000f0  02 2d 2d 2d 2d 2d 42 45  47 49 4e 20 50 47 50 20  |.-----BEGIN PGP |
+00000100  53 49 47 4e 41 54 55 52  45 2d 2d 2d 2d 2d 0a 0a  |SIGNATURE-----..|
+00000110  77 71 73 45 41 42 59 49  41 46 30 46 67 6d 72 4f  |wqsEABYIAF0FgmrO|
+00000120  65 6a 45 4a 45 45 6c 48  70 67 4d 5a 59 52 35 76  |ejEJEElHpgMZYR5v|
+00000130  4e 52 51 41 41 41 41 41  41 42 77 41 45 48 4e 68  |NRQAAAAAABwAEHNh|
+00000140  62 48 52 41 62 6d 39 30  59 58 52 70 62 32 35 7a  |bHRAbm90YXRpb25z|
+00000150  0a 4c 6d 39 77 5a 57 35  77 5a 33 42 71 63 79 35  |.Lm9wZW5wZ3Bqcy5|
+00000160  76 63 6d 64 64 78 66 79  6b 4c 4c 54 71 6d 54 44  |vcmddxfykLLTqmTD|
+00000170  37 47 2f 6a 48 47 7a 59  2b 46 69 45 45 58 70 59  |7G/jHGzY+FiEEXpY|
+00000180  71 4e 31 6b 4e 68 56 74  47 66 53 41 70 53 55 65  |qN1kNhVtGfSApSUe|
+00000190  6d 0a 41 78 6c 68 48 6d  38 41 41 48 30 68 41 51  |m.AxlhHm8AAH0hAQ|
+000001a0  44 49 36 6f 47 78 76 6b  31 73 47 71 49 63 75 33  |DI6oGxvk1sGqIcu3|
+000001b0  41 62 76 73 37 44 4d 2f  37 45 61 6c 78 6b 4e 44  |Abvs7DM/7EalxkND|
+000001c0  36 31 34 4e 37 35 46 43  67 2b 79 77 45 41 70 50  |614N75FCg+ywEApP|
+000001d0  36 4c 0a 6f 49 76 72 5a  55 67 45 77 38 44 55 62  |6L.oIvrZUgEw8DUb|
+000001e0  39 4a 65 4b 37 54 43 68  4f 69 36 50 55 41 48 55  |9JeK7TChOi6PUAHU|
+000001f0  46 59 37 35 46 70 36 68  41 45 3d 0a 3d 6e 66 58  |FY75Fp6hAE=.=nfX|
+00000200  35 0a 2d 2d 2d 2d 2d 45  4e 44 20 50 47 50 20 53  |5.-----END PGP S|
+00000210  49 47 4e 41 54 55 52 45  2d 2d 2d 2d 2d d2 0c 28  |IGNATURE-----..(|
+00000220  35 45 39 36 32 41 33 37  35 39 30 44 38 35 35 42  |5E962A37590D855B|
+00000230  34 36 37 44 32 30 32 39  34 39 34 37 41 36 30 33  |467D20294947A603|
+00000240  31 39 36 31 31 45 36 46  da 0c d4 03 2d 2d 2d 2d  |19611E6F....----|
+00000250  2d 42 45 47 49 4e 20 50  47 50 20 50 55 42 4c 49  |-BEGIN PGP PUBLI|
+00000260  43 20 4b 45 59 20 42 4c  4f 43 4b 2d 2d 2d 2d 2d  |C KEY BLOCK-----|
+00000270  0a 0a 78 6a 4d 45 61 73  31 30 67 42 59 4a 4b 77  |..xjMEas10gBYJKw|
+00000280  59 42 42 41 48 61 52 77  38 42 41 51 64 41 70 71  |YBBAHaRw8BAQdApq|
+00000290  33 32 53 79 4f 72 4e 75  76 31 4d 71 53 55 66 45  |32SyOrNuv1MqSUfE|
+000002a0  44 67 74 42 7a 6e 4b 59  32 39 38 2f 30 47 46 55  |DgtBznKY298/0GFU|
+000002b0  76 6b 0a 6c 6f 42 71 35  69 6e 4e 4b 47 31 6d 5a  |vk.loBq5inNKG1mZ|
+000002c0  58 49 67 64 47 56 7a 64  43 42 32 5a 57 4e 30 62  |XIgdGVzdCB2ZWN0b|
+000002d0  33 49 67 50 48 52 6c 63  33 51 74 64 6d 56 6a 64  |3IgPHRlc3QtdmVjd|
+000002e0  47 39 79 51 47 31 6d 5a  58 49 75 64 47 56 7a 64  |G9yQG1mZXIudGVzd|
+000002f0  44 37 43 0a 76 51 51 54  46 67 67 41 62 77 57 43  |D7C.vQQTFggAbwWC|
+00000300  61 73 31 30 67 41 49 4c  42 77 6b 51 53 55 65 6d  |as10gAILBwkQSUem|
+00000310  41 78 6c 68 48 6d 38 31  46 41 41 41 41 41 41 41  |AxlhHm81FAAAAAAA|
+00000320  48 41 41 51 63 32 46 73  64 45 42 75 62 33 52 68  |HAAQc2FsdEBub3Rh|
+00000330  64 47 6c 76 0a 62 6e 4d  75 62 33 42 6c 62 6e 42  |dGlv.bnMub3BlbnB|
+00000340  6e 63 47 70 7a 4c 6d 39  79 5a 30 79 62 6c 73 34  |ncGpzLm9yZ0ybls4|
+00000350  71 53 43 6d 77 4a 64 45  49 45 6d 4c 72 54 55 45  |qSCmwJdEIEmLrTUE|
+00000360  43 46 51 67 43 46 67 41  43 47 51 45 43 6d 77 4d  |CFQgCFgACGQECmwM|
+00000370  43 48 67 45 57 0a 49 51  52 65 6c 69 6f 33 57 51  |CHgEW.IQRelio3WQ|
+00000380  32 46 57 30 5a 39 49 43  6c 4a 52 36 59 44 47 57  |2FW0Z9IClJR6YDGW|
+00000390  45 65 62 77 41 41 31 67  73 41 2f 32 61 2f 50 58  |EebwAA1gsA/2a/PX|
+000003a0  68 6c 44 49 4b 78 67 32  79 4e 30 4c 58 39 48 68  |hlDIKxg2yN0LX9Hh|
+000003b0  49 44 43 54 7a 69 0a 49  32 43 53 71 44 74 2b 34  |IDCTzi.I2CSqDt+4|
+000003c0  62 2f 73 7a 6d 59 64 41  51 43 66 2b 63 6a 6b 4f  |b/szmYdAQCf+cjkO|
+000003d0  71 6c 34 4c 47 5a 41 43  6c 2f 73 2f 2f 6d 31 71  |ql4LGZACl/s//m1q|
+000003e0  62 74 6e 2f 4a 31 46 45  53 52 56 73 4e 68 65 2f  |btn/J1FESRVsNhe/|
+000003f0  76 6d 69 41 67 3d 3d 0a  3d 56 6b 4f 33 0a 2d 2d  |vmiAg==.=VkO3.--|
+00000400  2d 2d 2d 45 4e 44 20 50  47 50 20 50 55 42 4c 49  |---END PGP PUBLI|
+00000410  43 20 4b 45 59 20 42 4c  4f 43 4b 2d 2d 2d 2d 2d  |C KEY BLOCK-----|
+```
 
 ## MIME Type
 

go.mod

@@ -3,6 +3,8 @@ module sneak.berlin/go/mfer
 go 1.27.1
 
 require (
+	github.com/ProtonMail/go-crypto v1.5.2
+	github.com/creack/pty v1.1.25-0.20260601142114-9246436fffe8
 	github.com/davecgh/go-spew v1.1.1
 	github.com/dustin/go-humanize v1.1.0
 	github.com/klauspost/compress v1.20.1
@@ -15,6 +17,7 @@ require (
 )
 
 require (
+	github.com/cloudflare/circl v1.6.3 // indirect
 	github.com/klauspost/cpuid/v2 v2.4.0 // indirect
 	github.com/minio/sha256-simd v1.0.1 // indirect
 	github.com/mr-tron/base58 v1.3.0 // indirect

go.sum

@@ -1,3 +1,9 @@
+github.com/ProtonMail/go-crypto v1.5.2 h1:cucYnvqcY7UOXVD//mSyjeaPY0SSN3v5cDkYPxumINk=
+github.com/ProtonMail/go-crypto v1.5.2/go.mod h1:/RaSu30DaKO4RY+XdV/ACcCcZkGr7AhUIduq5sjzzCo=
+github.com/cloudflare/circl v1.6.3 h1:9GPOhQGF9MCYUeXyMYlqTR6a5gTrgR/fBLXvUgtVcg8=
+github.com/cloudflare/circl v1.6.3/go.mod h1:2eXP6Qfat4O/Yhh8BznvKnJ+uzEoTQ6jVKJRn81BiS4=
+github.com/creack/pty v1.1.25-0.20260601142114-9246436fffe8 h1:CY3gjC7naqYGLMiywvj3suPfa1i0p/QEr7o8ujxL/2M=
+github.com/creack/pty v1.1.25-0.20260601142114-9246436fffe8/go.mod h1:08sCNb52WyoAwi2QDyzUCTgcvVFhUzewun7wtTfvcwE=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/dustin/go-humanize v1.1.0 h1:dbKTrvD0klcbBV/h4AWJdMuZogJACoMlvWIWZ5b2xWg=

internal/cli/check.go

@@ -21,8 +21,8 @@ import (
 	"sneak.berlin/go/mfer/mfer"
 )
 
-// fingerprintHexLen is the length of a full GPG key fingerprint in hex
+// fingerprintHexLen is the length in hex characters of the fingerprint of
-// characters.
+// an OpenPGP version 4 key, the only version mfer signs with.
 const fingerprintHexLen = 40
 
 var (
@@ -108,7 +108,7 @@ func (mfa *CLIApp) fetchManifestToTemp(
 	if tmpErr != nil {
 		_ = rc.Close()
 
-		return "", fmt.Errorf("failed to create temp file: %w", tmpErr)
+		return "", tmpErr
 	}
 
 	tmpPath := tmpFile.Name()
@@ -126,17 +126,15 @@ func (mfa *CLIApp) fetchManifestToTemp(
 	if cpErr != nil {
 		_ = mfa.Fs.Remove(tmpPath)
 
-		return "", fmt.Errorf("failed to download manifest: %w", cpErr)
+		return "", fmt.Errorf("download manifest: %w", cpErr)
 	}
 
 	return tmpPath, nil
 }
 
 // verifyRequiredSigner enforces the --require-signature fingerprint
-// against the manifest's embedded signing key.
+// against the key that made the manifest's signature.
-func verifyRequiredSigner(
+func verifyRequiredSigner(chk *mfer.Checker, requiredSigner string) error {
-	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))
@@ -144,7 +142,7 @@ func verifyRequiredSigner(
 
 	_, err := hex.DecodeString(requiredSigner)
 	if err != nil {
-		return fmt.Errorf("invalid fingerprint: must be valid hex: %w", err)
+		return fmt.Errorf("invalid fingerprint: %w", err)
 	}
 
 	if !chk.IsSigned() {
@@ -152,22 +150,17 @@ func verifyRequiredSigner(
 			errManifestNotSigned, requiredSigner)
 	}
 
-	// Extract fingerprint from the embedded public key (not from the
+	// Loading the manifest checked that the signer is the fingerprint of
-	// signer field). This validates the key is importable and gets its
+	// the key that made the signature.
-	// actual fingerprint.
+	signer := string(chk.Signer())
-	embeddedFP, err := chk.ExtractEmbeddedSigningKeyFP(ctx)
-	if err != nil {
-		return fmt.Errorf(
-			"failed to extract fingerprint from embedded signing key: %w", err)
-	}
 
 	// Compare fingerprints - must be exact match (case-insensitive)
-	if !strings.EqualFold(embeddedFP, requiredSigner) {
+	if !strings.EqualFold(signer, requiredSigner) {
 		return fmt.Errorf("embedded signing key fingerprint %s %w %s",
-			embeddedFP, errSignerMismatch, requiredSigner)
+			signer, errSignerMismatch, requiredSigner)
 	}
 
-	log.Infof("manifest signature verified (signer: %s)", embeddedFP)
+	log.Infof("manifest signature verified (signer: %s)", signer)
 
 	return nil
 }
@@ -196,8 +189,8 @@ func reportCheckProgress(progress <-chan mfer.CheckStatus, wg *sync.WaitGroup) {
 	log.ProgressDone()
 }
 
-// countCheckFailures consumes check results, counting and logging
+// countCheckFailures consumes check results, counting failures and logging
-// failures, then closes done.
+// each at error level so that --quiet still shows them, then closes done.
 func countCheckFailures(
 	results <-chan mfer.Result, failures *int64, done chan<- struct{},
 ) {
@@ -205,7 +198,7 @@ func countCheckFailures(
 		if result.Status != mfer.StatusOK {
 			*failures++
 
-			log.Infof("%s: %s (%s)", result.Status, result.Path, result.Message)
+			log.Errorf("%s: %s (%s)", result.Status, result.Path, result.Message)
 		} else {
 			log.Verbosef("%s: %s", result.Status, result.Path)
 		}
@@ -215,8 +208,8 @@ func countCheckFailures(
 }
 
 // findExtraFiles reports files present on disk but absent from the
-// manifest, and anything the search cannot read: each is a failure under
+// manifest, and anything the search cannot read: each is a failure, logged
-// --no-extra-files, otherwise a warning.
+// at error level, under --no-extra-files, otherwise a warning.
 func findExtraFiles(
 	ctx context.Context, cmd *cli.Command, chk *mfer.Checker, failures *int64,
 ) error {
@@ -228,7 +221,7 @@ func findExtraFiles(
 			if cmd.Bool("no-extra-files") {
 				*failures++
 
-				log.Infof("%s: %s (%s)", result.Status, result.Path, result.Message)
+				log.Errorf("%s: %s (%s)", result.Status, result.Path, result.Message)
 			} else {
 				log.Warnf("%s: %s (%s)", result.Status, result.Path, result.Message)
 			}
@@ -239,7 +232,7 @@ func findExtraFiles(
 
 	err := chk.FindExtraFiles(ctx, extraResults)
 	if err != nil {
-		return fmt.Errorf("failed to check for extra files: %w", err)
+		return fmt.Errorf("find extra files: %w", err)
 	}
 
 	<-extraDone
@@ -282,7 +275,7 @@ func runCheck(
 	progressWg.Wait()
 
 	if err != nil {
-		return 0, fmt.Errorf("check failed: %w", err)
+		return 0, fmt.Errorf("check files: %w", err)
 	}
 
 	// Wait for results processing to complete
@@ -303,14 +296,18 @@ func (mfa *CLIApp) checkManifestOperation(
 
 	manifestPath, err := mfa.resolveManifestArg(cmd)
 	if err != nil {
-		return fmt.Errorf("check: %w", err)
+		return err
 	}
 
+	// Done before a URL is swapped for the temp file it is downloaded to,
+	// whose directory is not the base.
+	basePath := resolveBasePath(cmd, manifestPath)
+
 	// URL manifests need to be downloaded to a temp file for the checker
 	if isHTTPURL(manifestPath) {
 		tmpPath, tmpErr := mfa.fetchManifestToTemp(ctx, manifestPath)
 		if tmpErr != nil {
-			return fmt.Errorf("check: %w", tmpErr)
+			return tmpErr
 		}
 
 		defer func() { _ = mfa.Fs.Remove(tmpPath) }()
@@ -318,26 +315,24 @@ func (mfa *CLIApp) checkManifestOperation(
 		manifestPath = tmpPath
 	}
 
-	basePath := cmd.String("base")
 	showProgress := cmd.Bool("progress")
 
 	log.Infof("checking manifest %s with base %s", manifestPath, basePath)
 
 	// Create checker
-	//nolint:contextcheck // mfer loads a manifest without a context
 	chk, err := mfer.NewChecker(&mfer.CheckerOptions{
 		ManifestPath: manifestPath,
 		BasePath:     basePath,
 		Fs:           mfa.Fs,
 	})
 	if err != nil {
-		return fmt.Errorf("failed to load manifest: %w", err)
+		return fmt.Errorf("load manifest: %w", err)
 	}
 
-	// Check signature requirement
+	// Check signature requirement. An empty fingerprint is checked too,
-	requiredSigner := cmd.String(flagRequireSignature)
+	// and refused as one of the wrong length.
-	if requiredSigner != "" {
+	if cmd.IsSet(flagRequireSignature) {
-		err = verifyRequiredSigner(ctx, chk, requiredSigner)
+		err = verifyRequiredSigner(chk, cmd.String(flagRequireSignature))
 		if err != nil {
 			return err
 		}

internal/cli/entry.go

@@ -26,8 +26,7 @@ func noColorEnvSet() bool {
 // Use DefaultRunOptions for standard CLI execution, or construct manually for testing.
 type RunOptions struct {
 	Appname string    // Application name displayed in help and version output
-	Version string    // Version string (typically set at build time)
+	Gitrev  string    // Revision stamped in at build time, or empty
-	Gitrev  string    // Git revision hash (typically set at build time)
 	Args    []string  // Command-line arguments (typically os.Args)
 	Stdin   io.Reader // Standard input stream
 	Stdout  io.Writer // Standard output stream
@@ -36,10 +35,9 @@ type RunOptions struct {
 }
 
 // DefaultRunOptions returns RunOptions configured for normal CLI execution.
-func DefaultRunOptions(appname, version, gitrev string) *RunOptions {
+func DefaultRunOptions(appname, gitrev string) *RunOptions {
 	return &RunOptions{
 		Appname: appname,
-		Version: version,
 		Gitrev:  gitrev,
 		Args:    os.Args,
 		Stdin:   os.Stdin,
@@ -50,15 +48,14 @@ func DefaultRunOptions(appname, version, gitrev string) *RunOptions {
 }
 
 // Run creates and runs the CLI application with default options.
-func Run(appname, version, gitrev string) int {
+func Run(appname, gitrev string) int {
-	return RunWithOptions(DefaultRunOptions(appname, version, gitrev))
+	return RunWithOptions(DefaultRunOptions(appname, gitrev))
 }
 
 // RunWithOptions creates and runs the CLI application with the given options.
 func RunWithOptions(opts *RunOptions) int {
 	m := &CLIApp{
 		appname:         opts.Appname,
-		version:         opts.Version,
 		gitrev:          opts.Gitrev,
 		exitCode:        0,
 		maxManifestSize: mfer.MaxManifestSize,

internal/cli/entry_test.go

@@ -8,8 +8,10 @@ import (
 	"fmt"
 	"io"
 	"math/rand"
+	"net/http/httptest"
 	"os"
 	"path/filepath"
+	"runtime/debug"
 	"slices"
 	"strings"
 	"sync"
@@ -26,6 +28,7 @@ import (
 
 const (
 	testApp         = "mfer"
+	testGitrev      = "abc123"
 	testDir         = "/testdir"
 	testFile1       = "/testdir/file1.txt"
 	testMF          = "/testdir/test.mf"
@@ -35,6 +38,8 @@ const (
 	testFlagNoExtra = "--no-extra-files"
 	testFlagVersion = "--version"
 	testFlagVerbose = "--verbose"
+	testFlagHelp    = "--help"
+	testCmdHelp     = "help"
 )
 
 var errSimulatedWrite = errors.New("simulated write failure")
@@ -57,9 +62,10 @@ func runCLI(opts *RunOptions) int {
 // runCLIWithLevel is runCLI that also returns the log level the run left
 // set, read while runMu still keeps other runs from changing it. Each run
 // starts at the default level, as a new process does. Before releasing the
-// lock it points the process-global logger at io.Discard: other tests log
+// lock it points the process-global logger at io.Discard: test helpers also
-// outside the lock (manifest loads, scans), and those lines must not land in
+// log under runMu outside any run (manifest loads, scans), and those lines
-// this run's buffers once it has returned and its test is reading them.
+// must not land in this run's buffers once it has returned and its test is
+// reading them.
 func runCLIWithLevel(opts *RunOptions) (int, log.Level) {
 	runMu.Lock()
 	defer runMu.Unlock()
@@ -92,8 +98,7 @@ func TestBuild(t *testing.T) {
 func testOpts(args []string, fs afero.Fs) *RunOptions {
 	return &RunOptions{
 		Appname: testApp,
-		Version: "1.0.0",
+		Gitrev:  testGitrev,
-		Gitrev:  "abc123",
 		Args:    args,
 		Stdin:   &bytes.Buffer{},
 		Stdout:  &bytes.Buffer{},
@@ -135,10 +140,35 @@ func TestVersionCommand(t *testing.T) {
 	exitCode := runCLI(opts)
 
 	assert.Equal(t, 0, exitCode)
+	assert.Equal(t, "mfer version "+testGitrev+"\n", testStdout(t, opts))
+}
 
-	stdout := testStdout(t, opts)
+// TestVersionFromBuildInfo covers a binary whose build stamped no Gitrev,
-	assert.Contains(t, stdout, mfer.Version)
+// as `go install` builds it: mfer version prints the main module's version
-	assert.Contains(t, stdout, "abc123")
+// from the build information instead.
+func TestVersionFromBuildInfo(t *testing.T) {
+	t.Parallel()
+
+	info, ok := debug.ReadBuildInfo()
+	require.True(t, ok)
+	require.NotEmpty(t, info.Main.Version)
+
+	opts := testOpts([]string{testApp, cmdVersion}, afero.NewMemMapFs())
+	opts.Gitrev = ""
+
+	require.Equal(t, 0, runCLI(opts))
+	assert.Equal(t, "mfer version "+info.Main.Version+"\n", testStdout(t, opts))
+}
+
+// TestModuleVersionEmpty covers build information that holds no module
+// version, as in a build with GO111MODULE=off, and a binary with no build
+// information at all. Both report "unknown": an empty version would print
+// nothing after "mfer version" and drop the --version flag.
+func TestModuleVersionEmpty(t *testing.T) {
+	t.Parallel()
+
+	assert.Equal(t, "unknown", moduleVersion(&debug.BuildInfo{}, true))
+	assert.Equal(t, "unknown", moduleVersion(nil, false))
 }
 
 // TestVFlagCollision covers the -v/--verbose vs --version flag interaction
@@ -164,7 +194,7 @@ func TestVFlagCollision(t *testing.T) {
 			exitCode := runCLI(opts)
 
 			assert.Equal(t, 0, exitCode, "stderr: %s", testStderr(t, opts))
-			assert.Contains(t, testStdout(t, opts), mfer.Version)
+			assert.Contains(t, testStdout(t, opts), testGitrev)
 			assert.NotContains(t, testStderr(t, opts), "two forms of the same flag")
 		})
 	}
@@ -205,13 +235,13 @@ func TestVersionFlagAndCommandMatch(t *testing.T) {
 
 // TestRootVerbosityFlags asserts that -q and -v given before any subcommand
 // name take effect: in the root itself, and in the fetch and export
-// subcommands (issue #64). It does not run in parallel: other tests log
+// subcommands (issue #64).
-// outside runMu (manifest loads, scans), and a line logged while one of these
-// runs is in progress lands in its output.
-//
-//nolint:paralleltest // see above
 func TestRootVerbosityFlags(t *testing.T) {
+	t.Parallel()
+
 	t.Run("quiet with no subcommand hides the banner", func(t *testing.T) {
+		t.Parallel()
+
 		loud := testOpts([]string{testApp}, afero.NewMemMapFs())
 		require.Equal(t, 0, runCLI(loud))
 		assert.Contains(t, testStdout(t, loud), banner)
@@ -223,6 +253,8 @@ func TestRootVerbosityFlags(t *testing.T) {
 	})
 
 	t.Run("quiet before fetch hides the banner", func(t *testing.T) {
+		t.Parallel()
+
 		opts := testOpts([]string{testApp, "-q", cmdFetch}, afero.NewMemMapFs())
 
 		assert.Equal(t, 1, runCLI(opts))
@@ -231,6 +263,8 @@ func TestRootVerbosityFlags(t *testing.T) {
 	})
 
 	t.Run("verbose twice before fetch enables debug logging", func(t *testing.T) {
+		t.Parallel()
+
 		opts := testOpts([]string{testApp, "-v", "-v", cmdFetch}, afero.NewMemMapFs())
 
 		assert.Equal(t, 1, runCLI(opts))
@@ -238,6 +272,8 @@ func TestRootVerbosityFlags(t *testing.T) {
 	})
 
 	t.Run("quiet before export hides the manifest summary", func(t *testing.T) {
+		t.Parallel()
+
 		fs := afero.NewMemMapFs()
 		manifest := buildTestManifest(t, map[string][]byte{"a.txt": []byte("a")})
 		require.NoError(t, afero.WriteFile(fs, testManifest, manifest, 0o644))
@@ -320,7 +356,7 @@ func TestHelpCommand(t *testing.T) {
 	t.Parallel()
 
 	fs := afero.NewMemMapFs()
-	opts := testOpts([]string{testApp, "--help"}, fs)
+	opts := testOpts([]string{testApp, testFlagHelp}, fs)
 
 	exitCode := runCLI(opts)
 
@@ -354,6 +390,44 @@ func TestGenerateCommand(t *testing.T) {
 	assert.True(t, exists)
 }
 
+// TestGenerateRefusesTwoFilesAtOnePath runs gen on arguments whose files
+// would share a path in the manifest: two directories that each hold a.txt,
+// and one directory given twice. gen must fail while it lists the files,
+// before it hashes any, naming the path, and write no manifest.
+func TestGenerateRefusesTwoFilesAtOnePath(t *testing.T) {
+	t.Parallel()
+
+	for _, tc := range []struct {
+		name          string
+		first, second string
+	}{
+		{"two directories", testDir, "/other"},
+		{"one directory twice", testDir, testDir},
+	} {
+		t.Run(tc.name, func(t *testing.T) {
+			t.Parallel()
+
+			fs := afero.NewMemMapFs()
+			require.NoError(t, fs.MkdirAll(testDir, 0o755))
+			require.NoError(t, fs.MkdirAll("/other", 0o755))
+			writeTestFile(t, fs, "/testdir/a.txt", "first")
+			writeTestFile(t, fs, "/other/a.txt", "second")
+
+			opts := testOpts([]string{
+				testApp, cmdGenerate, "-q", "-o", testOutput, tc.first, tc.second,
+			}, fs)
+			assert.Equal(t, 1, runCLI(opts))
+			assert.Contains(t, testStderr(t, opts),
+				`enumerate files: duplicate path "a.txt": `+
+					tc.first+"/a.txt and "+tc.second+"/a.txt")
+
+			exists, err := afero.Exists(fs, testOutput)
+			require.NoError(t, err)
+			assert.False(t, exists)
+		})
+	}
+}
+
 // TestGenerateSeededManifestBytes pins the exact bytes `gen --seed` writes
 // for a fixed tree, so that a Go or dependency update that changes what
 // mfer writes fails here. testdata/seeded.mf was written by an mfer built
@@ -613,6 +687,32 @@ func runCheckAfterRewrite(t *testing.T, rewritten, msg string) {
 	assert.Equal(t, 1, exitCode, msg)
 }
 
+// TestCheckRequireSignatureRefusesOtherSigningKey runs check
+// --require-signature on a manifest signed by another key whose embedded
+// public key block also holds the required key. check must refuse it.
+func TestCheckRequireSignatureRefusesOtherSigningKey(t *testing.T) {
+	t.Parallel()
+
+	content := []byte("signed file")
+	manifest, required := manifestSignedByAnotherKey(t,
+		map[string][]byte{testFileTxt: content})
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll(testDir, 0o755))
+	require.NoError(t, afero.WriteFile(fs,
+		filepath.Join(testDir, testFileTxt), content, 0o644))
+	require.NoError(t, afero.WriteFile(fs, testManifest, manifest, 0o644))
+
+	opts := testOpts([]string{
+		testApp, cmdCheck, "-q", testFlagBase, testDir,
+		"--" + flagRequireSignature, required, testManifest,
+	}, fs)
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts),
+		"load manifest: "+
+			"embedded public key block must hold exactly one key, found 2")
+}
+
 func TestCheckCommandWithCorruptedFile(t *testing.T) {
 	t.Parallel()
 
@@ -629,6 +729,33 @@ func TestCheckCommandWithSizeMismatch(t *testing.T) {
 		"check should have failed for size mismatch")
 }
 
+// TestCheckQuietShowsFailedFiles asserts that check -q prints nothing for a
+// tree that passes and still names each file that fails: --quiet hides
+// everything except errors, and a failed file is an error.
+func TestCheckQuietShowsFailedFiles(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll(testDir, 0o755))
+	writeTestFile(t, fs, testFile1, "hello world")
+
+	opts := testOpts([]string{testApp, cmdGenerate, "-q", "-o", testManifest, testDir}, fs)
+	require.Equal(t, 0, runCLI(opts), "generate failed: %s", testStderr(t, opts))
+
+	args := []string{testApp, cmdCheck, "-q", testFlagBase, testDir, testManifest}
+
+	opts = testOpts(args, fs)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+	assert.Empty(t, testStdout(t, opts))
+	assert.Empty(t, testStderr(t, opts))
+
+	writeTestFile(t, fs, testFile1, "HELLO WORLD")
+
+	opts = testOpts(args, fs)
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts), "HASH_MISMATCH: file1.txt")
+}
+
 func TestBannerOutput(t *testing.T) {
 	t.Parallel()
 
@@ -647,6 +774,9 @@ func TestBannerOutput(t *testing.T) {
 	stdout := testStdout(t, opts)
 	assert.Contains(t, stdout, "___")
 	assert.Contains(t, stdout, "\\")
+
+	// The banner shows the version mfer version prints, and nothing after it.
+	assert.Contains(t, stdout, "mfer by @sneak: "+testGitrev+"\n")
 }
 
 func TestUnknownCommand(t *testing.T) {
@@ -679,13 +809,9 @@ func TestGenerateExcludesDotfilesByDefault(t *testing.T) {
 	assert.True(t, exists)
 
 	// Verify manifest only has 1 file (the non-dotfile)
-	manifest, err := mfer.NewManifestFromFile(&mfer.ManifestFromFileOptions{
+	paths := manifestPaths(t, fs, testMF)
-		Path: testMF,
+	require.Len(t, paths, 1)
-		Fs:   fs,
+	assert.Equal(t, "file1.txt", paths[0])
-	})
-	require.NoError(t, err)
-	assert.Len(t, manifest.Files(), 1)
-	assert.Equal(t, "file1.txt", manifest.Files()[0].GetPath())
 }
 
 func TestGenerateWithIncludeDotfiles(t *testing.T) {
@@ -706,12 +832,7 @@ func TestGenerateWithIncludeDotfiles(t *testing.T) {
 	require.Equal(t, 0, exitCode)
 
 	// Verify manifest has 2 files (including dotfile)
-	manifest, err := mfer.NewManifestFromFile(&mfer.ManifestFromFileOptions{
+	assert.Len(t, manifestPaths(t, fs, testMF), 2)
-		Path: testMF,
-		Fs:   fs,
-	})
-	require.NoError(t, err)
-	assert.Len(t, manifest.Files(), 2)
 }
 
 func TestMultipleInputPaths(t *testing.T) {
@@ -861,8 +982,56 @@ func TestCheckWarnsAboutUnlistedFiles(t *testing.T) {
 			assert.Equal(t, 1, exitCode, "stderr: %s", stderr)
 			assert.Contains(t, stderr, unlisted)
 
-			exitCode, _ = check("-q", testFlagNoExtra)
+			exitCode, stderr = check("-q", testFlagNoExtra)
 			assert.Equal(t, 1, exitCode)
+			assert.Contains(t, stderr, unlisted)
+		})
+	}
+}
+
+// TestCheckReportsUnlistedSymlinkToFileOnly makes a tree holding a symlink
+// to a directory, one to a file and a broken one. gen lists the symlink to
+// the file only with --follow-symlinks, and never lists the other two, so
+// check --no-extra-files passes on the manifest gen --follow-symlinks writes
+// and fails only on the symlink to the file on the one plain gen writes.
+func TestCheckReportsUnlistedSymlinkToFileOnly(t *testing.T) {
+	t.Parallel()
+
+	for name, tc := range map[string]struct {
+		genFlags []string
+		exitCode int
+		extras   []string // what check reports as not in the manifest
+	}{
+		"gen --follow-symlinks": {[]string{"--follow-symlinks"}, 0, nil},
+		"plain gen":             {nil, 1, []string{"filelink"}},
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			dir := t.TempDir()
+			fs := afero.NewOsFs()
+			writeTestTree(t, fs, dir)
+			require.NoError(t, os.Symlink(testSubdir, filepath.Join(dir, "dirlink")))
+			require.NoError(t, os.Symlink(testFileTxt, filepath.Join(dir, "filelink")))
+			require.NoError(t,
+				os.Symlink("nowhere", filepath.Join(dir, "brokenlink")))
+
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdGenerate, "-q"}, tc.genFlags, []string{dir},
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			opts = testOpts([]string{testApp, cmdCheck, testFlagNoExtra, dir}, fs)
+			exitCode := runCLI(opts)
+			stderr := testStderr(t, opts)
+
+			assert.Equal(t, tc.exitCode, exitCode, "stderr: %s", stderr)
+			assert.Equal(t, len(tc.extras),
+				strings.Count(stderr, "not in manifest"), stderr)
+
+			for _, extra := range tc.extras {
+				assert.Contains(t, stderr, "EXTRA: "+extra)
+			}
 		})
 	}
 }
@@ -914,6 +1083,90 @@ func TestCheckNeverReportsManifest(t *testing.T) {
 	}
 }
 
+// The directory setupManifestInSubdir makes and the manifest it writes there,
+// relative to the working directory it sets.
+const (
+	testSubdir         = "sub"
+	testSubdirManifest = testSubdir + "/" + defaultManifestName
+)
+
+// setupManifestInSubdir makes a temp dir holding file.txt and sub/b.txt,
+// where sub/index.mf is the manifest gen writes for sub, and makes it the
+// working directory, so a test calling it cannot run in parallel. It returns
+// the temp dir.
+func setupManifestInSubdir(t *testing.T) string {
+	t.Helper()
+
+	root := t.TempDir()
+	sub := filepath.Join(root, testSubdir)
+
+	fs := afero.NewOsFs()
+	require.NoError(t, fs.MkdirAll(sub, 0o750))
+	writeTestFile(t, fs, filepath.Join(root, testFileTxt), "not in the manifest")
+	writeTestFile(t, fs, filepath.Join(sub, "b.txt"), "in the manifest")
+
+	opts := testOpts([]string{
+		testApp, cmdGenerate, "-q", "-o", filepath.Join(sub, defaultManifestName), sub,
+	}, fs)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	t.Chdir(root)
+
+	return root
+}
+
+// TestCheckResolvesEntriesAgainstManifestDirectory runs check from the
+// directory above sub, on the manifest in sub. Without --base, the
+// manifest's entries are looked for in sub, whether check is given the
+// manifest or sub, and the files above sub are not reported. --base names
+// the directory to look in instead, the current one included.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestCheckResolvesEntriesAgainstManifestDirectory(t *testing.T) {
+	root := setupManifestInSubdir(t)
+
+	for _, tc := range []struct {
+		args     []string
+		exitCode int
+		failure  string // a line check must print, if any
+	}{
+		{[]string{testSubdir}, 0, ""},
+		{[]string{testSubdirManifest}, 0, ""},
+		{[]string{filepath.Join(root, testSubdir)}, 0, ""},
+		{[]string{testFlagBase, testSubdir, testSubdirManifest}, 0, ""},
+		{[]string{testFlagBase, ".", testSubdirManifest}, 1, "MISSING: b.txt"},
+	} {
+		t.Run(strings.Join(tc.args, " "), func(t *testing.T) {
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdCheck, testFlagNoExtra}, tc.args,
+			), afero.NewOsFs())
+			assert.Equal(t, tc.exitCode, runCLI(opts), "stderr: %s", testStderr(t, opts))
+			assert.Contains(t, testStderr(t, opts), tc.failure)
+		})
+	}
+}
+
+// TestCheckURLManifestResolvesEntriesAgainstCurrentDirectory runs check on
+// a manifest given by URL, from a directory holding the file it lists: the
+// file is looked for there.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestCheckURLManifestResolvesEntriesAgainstCurrentDirectory(t *testing.T) {
+	files := map[string][]byte{testFileTxt: []byte("hello")}
+
+	server := httptest.NewServer(fetchTestHandler(manifestOf(t, files), files))
+	defer server.Close()
+
+	cwd := chdirTemp(t)
+	require.NoError(t,
+		os.WriteFile(filepath.Join(cwd, testFileTxt), files[testFileTxt], 0o600))
+
+	opts := testOpts([]string{
+		testApp, cmdCheck, testFlagNoExtra, server.URL + "/" + defaultManifestName,
+	}, afero.NewOsFs())
+	assert.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+}
+
 // unlistableDirFs is a filesystem on which one directory cannot be listed.
 type unlistableDirFs struct {
 	afero.Fs
@@ -1047,6 +1300,11 @@ func TestGenerateFailsWithoutForceWhenOutputExists(t *testing.T) {
 func manifestPaths(t *testing.T, fs afero.Fs, path string) []string {
 	t.Helper()
 
+	// Loading a manifest logs to the process-global logger, so serialize
+	// with the CLI runs.
+	runMu.Lock()
+	defer runMu.Unlock()
+
 	manifest, err := mfer.NewManifestFromFile(&mfer.ManifestFromFileOptions{
 		Path: path,
 		Fs:   fs,
@@ -1139,6 +1397,225 @@ func TestGenerateLeavesLeftoverTempFileOutOfListing(t *testing.T) {
 	assert.Equal(t, []string{testFileTxt}, manifestPaths(t, fs, output))
 }
 
+// writeTestTree writes file.txt and sub/nested.txt under dir.
+func writeTestTree(t *testing.T, fs afero.Fs, dir string) {
+	t.Helper()
+
+	require.NoError(t, fs.MkdirAll(filepath.Join(dir, testSubdir), 0o750))
+	writeTestFile(t, fs, filepath.Join(dir, testFileTxt), "hello")
+	writeTestFile(t, fs, filepath.Join(dir, testSubdir, "nested.txt"), "in sub")
+}
+
+// TestGenerateDefaultOutput runs gen without --output on one directory or
+// one file: it writes index.mf in that directory, or beside that file,
+// listing each file by its path under the directory index.mf is in, and
+// check given that directory passes.
+func TestGenerateDefaultOutput(t *testing.T) {
+	t.Parallel()
+
+	// Paths are relative to a temp dir holding file.txt and sub/nested.txt.
+	for name, tc := range map[string]struct {
+		input, output string
+		listed        []string
+	}{
+		"directory": {
+			".", defaultManifestName, []string{testFileTxt, "sub/nested.txt"},
+		},
+		"subdirectory": {testSubdir, testSubdirManifest, []string{"nested.txt"}},
+		"file":         {testFileTxt, defaultManifestName, []string{testFileTxt}},
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			root := t.TempDir()
+			fs := afero.NewOsFs()
+			writeTestTree(t, fs, root)
+
+			opts := testOpts([]string{
+				testApp, cmdGenerate, "-q", filepath.Join(root, tc.input),
+			}, fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			output := filepath.Join(root, tc.output)
+			assert.ElementsMatch(t, tc.listed, manifestPaths(t, fs, output))
+
+			opts = testOpts([]string{
+				testApp, cmdCheck, "-q", filepath.Dir(output),
+			}, fs)
+			assert.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+		})
+	}
+}
+
+// TestGenerateSeveralPathsDefaultOutput runs gen without --output on two
+// directories: it writes index.mf in the current directory, listing both
+// directories' files, and writes no index.mf in either directory.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestGenerateSeveralPathsDefaultOutput(t *testing.T) {
+	root := t.TempDir()
+	fs := afero.NewOsFs()
+	dirs := []string{"first", "second"}
+
+	for _, dir := range dirs {
+		require.NoError(t, fs.MkdirAll(filepath.Join(root, dir), 0o750))
+		writeTestFile(t, fs, filepath.Join(root, dir, dir+".txt"), dir)
+	}
+
+	t.Chdir(root)
+
+	opts := testOpts(append([]string{testApp, cmdGenerate, "-q"}, dirs...), fs)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	assert.ElementsMatch(t, []string{"first.txt", "second.txt"},
+		manifestPaths(t, fs, filepath.Join(root, defaultManifestName)))
+
+	for _, dir := range dirs {
+		exists, err := afero.Exists(fs, filepath.Join(root, dir, defaultManifestName))
+		require.NoError(t, err)
+		assert.False(t, exists, "index.mf written in %s", dir)
+	}
+}
+
+// testLink is the name of the symlink to a tree that the
+// DirectoryNamedThroughSymlink tests make in a temp dir.
+const testLink = "link"
+
+// TestGenerateDirectoryNamedThroughSymlink runs gen on a directory named
+// through a symlink, given as the argument or as the working directory: the
+// manifest lists the files in the directory the symlink points to, and
+// leaves out a symlink inside it, as gen does without --follow-symlinks.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestGenerateDirectoryNamedThroughSymlink(t *testing.T) {
+	// Paths are relative to a temp dir holding data and link, a symlink to
+	// data.
+	for name, tc := range map[string]struct {
+		workDir string
+		args    []string
+	}{
+		"argument":          {".", []string{testLink}},
+		"working directory": {testLink, nil},
+	} {
+		t.Run(name, func(t *testing.T) {
+			root := t.TempDir()
+			data := filepath.Join(root, "data")
+
+			fs := afero.NewOsFs()
+			writeTestTree(t, fs, data)
+			require.NoError(t,
+				os.Symlink(testFileTxt, filepath.Join(data, "alias.txt")))
+			require.NoError(t, os.Symlink(data, filepath.Join(root, testLink)))
+
+			// t.Chdir sets PWD to the path it is given, as a shell does, and
+			// os.Getwd returns PWD when it names the working directory.
+			t.Chdir(filepath.Join(root, tc.workDir))
+
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdGenerate, "-q"}, tc.args,
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			assert.ElementsMatch(t, []string{testFileTxt, "sub/nested.txt"},
+				manifestPaths(t, fs, filepath.Join(data, defaultManifestName)))
+		})
+	}
+}
+
+// TestGenerateBytesDoNotDependOnOutput runs gen --seed on one tree, each
+// time writing to another file, over a file already there and beside an
+// earlier run's temp file: neither is listed, and what is listed depends
+// only on the tree, so every manifest has the same bytes.
+func TestGenerateBytesDoNotDependOnOutput(t *testing.T) {
+	t.Parallel()
+
+	root := t.TempDir()
+	tree := filepath.Join(root, "tree")
+	defaultOutput := filepath.Join(tree, defaultManifestName)
+
+	fs := afero.NewOsFs()
+	writeTestTree(t, fs, tree)
+
+	var first []byte
+
+	for _, output := range []string{
+		defaultOutput,
+		filepath.Join(tree, "listing.mf"),
+		filepath.Join(tree, testSubdir, "listing.mf"),
+		filepath.Join(root, "outside.mf"),
+	} {
+		writeTestFile(t, fs, output, "previous manifest")
+		writeTestFile(t, fs, manifestTempPath(output), "part of a manifest")
+
+		args := []string{testApp, cmdGenerate, "-q", "-f", "--seed", "mfer"}
+		if output != defaultOutput {
+			args = append(args, "-o", output)
+		}
+
+		args = append(args, tree)
+
+		opts := testOpts(args, fs)
+		require.Equal(t, 0, runCLI(opts),
+			"output %s, stderr: %s", output, testStderr(t, opts))
+
+		got, err := afero.ReadFile(fs, output)
+		require.NoError(t, err)
+		require.NoError(t, fs.Remove(output))
+
+		if first == nil {
+			first = got
+		}
+
+		assert.Equal(t, first, got, "output %s", output)
+	}
+}
+
+// TestGenerateRefusesExistingDefaultOutput runs gen without --output or
+// --force on a directory already holding index.mf: gen fails, naming that
+// file, and leaves it as it was.
+func TestGenerateRefusesExistingDefaultOutput(t *testing.T) {
+	t.Parallel()
+
+	output := filepath.Join(testDir, defaultManifestName)
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll(testDir, 0o755))
+	writeTestFile(t, fs, testFile1, "hello")
+	writeTestFile(t, fs, output, "previous manifest")
+
+	opts := testOpts([]string{testApp, cmdGenerate, "-q", testDir}, fs)
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts),
+		"output file "+output+" already exists (use --force to overwrite)")
+
+	content, err := afero.ReadFile(fs, output)
+	require.NoError(t, err)
+	assert.Equal(t, "previous manifest", string(content))
+}
+
+// TestGenerateRefusesEmptyOutput runs gen with --force and an --output
+// given an empty value, as an unset shell variable gives it, on a
+// directory already holding index.mf: gen fails and leaves that file as it
+// was.
+func TestGenerateRefusesEmptyOutput(t *testing.T) {
+	t.Parallel()
+
+	output := filepath.Join(testDir, defaultManifestName)
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll(testDir, 0o755))
+	writeTestFile(t, fs, testFile1, "hello")
+	writeTestFile(t, fs, output, "previous manifest")
+
+	opts := testOpts([]string{testApp, cmdGenerate, "-q", "-f", "-o", "", testDir}, fs)
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts), errEmptyOutput.Error())
+
+	content, err := afero.ReadFile(fs, output)
+	require.NoError(t, err)
+	assert.Equal(t, "previous manifest", string(content))
+}
+
 func TestGenerateAtomicWriteUsesTemp(t *testing.T) {
 	t.Parallel()
 
@@ -1296,20 +1773,200 @@ func TestGenerateValidatesInputPaths(t *testing.T) {
 	})
 }
 
-// TestFlagAfterArgumentIsArgument asserts that flags are read only before a
+// generateTestDir writes testFile1 and runs gen on testDir, which writes
-// command's first argument: after it, -v is a path, not the verbose flag.
+// the manifest to testDir/index.mf.
-func TestFlagAfterArgumentIsArgument(t *testing.T) {
+func generateTestDir(t *testing.T, fs afero.Fs) {
-	t.Parallel()
+	t.Helper()
 
-	fs := afero.NewMemMapFs()
 	require.NoError(t, fs.MkdirAll(testDir, 0o755))
 	writeTestFile(t, fs, testFile1, "content")
 
-	opts := testOpts([]string{testApp, cmdGenerate, testDir, "-v"}, fs)
+	opts := testOpts([]string{testApp, cmdGenerate, "-q", testDir}, fs)
-	exitCode := runCLI(opts)
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+}
 
-	assert.Equal(t, 1, exitCode)
+// TestCheckReadsOptionAfterPath runs check on an unsigned manifest with
-	assert.Contains(t, testStderr(t, opts), "path does not exist: -v")
+// --require-signature after the directory. check must refuse the manifest.
+func TestCheckReadsOptionAfterPath(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewMemMapFs()
+	generateTestDir(t, fs)
+
+	opts := testOpts([]string{
+		testApp, cmdCheck, "-q", testDir, "--" + flagRequireSignature, msgFpA,
+	}, fs)
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts), "manifest is not signed")
+}
+
+// TestFreshenReadsOptionAfterPath runs freshen with --include-permissions
+// after the directory. freshen must record the file's mode.
+func TestFreshenReadsOptionAfterPath(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewOsFs()
+	root, manifestPath := setupFreshenDir(t, fs,
+		map[string]string{testFileTxt: "a file"})
+	require.NoError(t, fs.Chmod(filepath.Join(root, testFileTxt), 0o640))
+
+	opts := testOpts([]string{
+		testApp, cmdFreshen, "-q", root, "--" + flagIncludePermissions,
+	}, fs)
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+	files := manifestFiles(t, fs, manifestPath)
+	require.Len(t, files, 1)
+	assert.Equal(t, uint32(0o640), files[0].GetMode())
+}
+
+// TestFetchReadsOptionAfterURL runs fetch with --dest after the URL. The
+// file and the manifest must land in that directory and nothing in the
+// current one.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestFetchReadsOptionAfterURL(t *testing.T) {
+	content := []byte("fetched")
+	manifest := manifestOf(t, map[string][]byte{testFileTxt: content})
+
+	server := httptest.NewServer(fetchTestHandler(manifest,
+		map[string][]byte{testFileTxt: content}))
+	defer server.Close()
+
+	cwd := chdirTemp(t)
+	dest := t.TempDir()
+
+	opts := testOpts([]string{
+		testApp, cmdFetch, "-q", server.URL, "--" + flagDest, dest,
+	}, afero.NewOsFs())
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+	assert.Equal(t,
+		map[string][]byte{testFileTxt: content, defaultManifestName: manifest},
+		filesUnder(t, dest))
+	assert.Empty(t, filesUnder(t, cwd), "fetch wrote outside --dest")
+}
+
+// TestOneArgumentCommandsRefuseSecond runs each command that takes one
+// argument with two. It must fail naming the second.
+func TestOneArgumentCommandsRefuseSecond(t *testing.T) {
+	t.Parallel()
+
+	for _, command := range []string{
+		cmdCheck, cmdFreshen, cmdList, cmdExport, cmdFetch,
+	} {
+		t.Run(command, func(t *testing.T) {
+			t.Parallel()
+
+			fs := afero.NewMemMapFs()
+			generateTestDir(t, fs)
+
+			opts := testOpts([]string{testApp, command, testDir, "/second"}, fs)
+			assert.Equal(t, 1, runCLI(opts))
+			assert.Contains(t, testStderr(t, opts),
+				`unexpected argument "/second"`)
+		})
+	}
+}
+
+// TestGenerateReadsPathAfterDoubleDash runs gen -- -x where -x is a
+// directory. -x must be read as the path to list, not as an option.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestGenerateReadsPathAfterDoubleDash(t *testing.T) {
+	chdirTemp(t)
+
+	fs := afero.NewOsFs()
+	require.NoError(t, fs.Mkdir("-x", 0o755))
+	writeTestFile(t, fs, filepath.Join("-x", testFileTxt), "content")
+
+	opts := testOpts([]string{testApp, cmdGenerate, "-q", "--", "-x"}, fs)
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+	files := manifestFiles(t, fs, filepath.Join("-x", defaultManifestName))
+	require.Len(t, files, 1)
+	assert.Equal(t, testFileTxt, files[0].GetPath())
+}
+
+// TestPathNamedHelp runs gen, then check with --require-signature, on a
+// directory named help and on one named h, the two names of urfave/cli's
+// help command. gen must write the manifest into the directory, and check
+// must refuse it as unsigned.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestPathNamedHelp(t *testing.T) {
+	for _, name := range []string{testCmdHelp, "h"} {
+		t.Run(name, func(t *testing.T) {
+			chdirTemp(t)
+
+			fs := afero.NewOsFs()
+			require.NoError(t, fs.Mkdir(name, 0o755))
+			writeTestFile(t, fs, filepath.Join(name, testFileTxt), "content")
+
+			opts := testOpts([]string{testApp, cmdGenerate, "-q", name}, fs)
+			require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+			files := manifestFiles(t, fs, filepath.Join(name, defaultManifestName))
+			require.Len(t, files, 1)
+
+			opts = testOpts([]string{
+				testApp, cmdCheck, "-q", name, "--" + flagRequireSignature, msgFpA,
+			}, fs)
+			assert.Equal(t, 1, runCLI(opts))
+			assert.Contains(t, testStderr(t, opts), "manifest is not signed")
+		})
+	}
+}
+
+// TestCommandsReadHelpAsArgument runs each command that takes a path or URL
+// on help and on h where nothing by that name exists. Each must fail on the
+// missing path or bad URL instead of printing its help.
+func TestCommandsReadHelpAsArgument(t *testing.T) {
+	t.Parallel()
+
+	for _, command := range []string{
+		cmdGenerate, cmdCheck, cmdFreshen, cmdList, cmdExport, cmdFetch,
+	} {
+		for _, name := range []string{testCmdHelp, "h"} {
+			t.Run(command+" "+name, func(t *testing.T) {
+				t.Parallel()
+
+				opts := testOpts([]string{testApp, command, name}, afero.NewMemMapFs())
+				assert.Equal(t, 1, runCLI(opts))
+				assert.NotContains(t, testStdout(t, opts), "USAGE:")
+			})
+		}
+	}
+}
+
+// TestHelpBesideArgument runs each command that takes a path or URL with
+// --help or -h before and after a directory, and runs help on that command.
+// Each must print what the command's own --help prints.
+func TestHelpBesideArgument(t *testing.T) {
+	t.Parallel()
+
+	for _, command := range []string{
+		cmdGenerate, cmdCheck, cmdFreshen, cmdList, cmdExport, cmdFetch,
+	} {
+		want := testOpts([]string{testApp, command, testFlagHelp}, afero.NewMemMapFs())
+		require.Equal(t, 0, runCLI(want))
+		require.Contains(t, testStdout(t, want), testApp+" "+command)
+
+		for _, args := range [][]string{
+			{command, testDir, testFlagHelp},
+			{command, testFlagHelp, testDir},
+			{command, testDir, "-h"},
+			{testCmdHelp, command},
+		} {
+			t.Run(strings.Join(args, " "), func(t *testing.T) {
+				t.Parallel()
+
+				opts := testOpts(slices.Concat([]string{testApp}, args), afero.NewMemMapFs())
+				assert.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+				assert.Equal(t, testStdout(t, want), testStdout(t, opts))
+			})
+		}
+	}
 }
 
 func TestCheckDetectsManifestCorruption(t *testing.T) {

internal/cli/errmsg_test.go

@@ -4,17 +4,23 @@ package cli
 import (
 	"bytes"
 	"context"
+	"encoding/hex"
+	"io"
 	"net/http"
 	"net/http/httptest"
 	"os"
-	"os/exec"
 	"path/filepath"
+	"strings"
 	"testing"
 
+	"github.com/ProtonMail/go-crypto/openpgp"
+	"github.com/ProtonMail/go-crypto/openpgp/armor"
+	"github.com/ProtonMail/go-crypto/openpgp/packet"
 	"github.com/spf13/afero"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 	urfcli "github.com/urfave/cli/v3"
+	"google.golang.org/protobuf/proto"
 	"sneak.berlin/go/mfer/mfer"
 )
 
@@ -48,6 +54,11 @@ func runLocked(fn func() error) error {
 func unsignedChecker(t *testing.T) *mfer.Checker {
 	t.Helper()
 
+	// The scan and the manifest load log to the process-global logger, so
+	// serialize with the CLI runs.
+	runMu.Lock()
+	defer runMu.Unlock()
+
 	fs := afero.NewMemMapFs()
 	require.NoError(t, fs.MkdirAll("/d", 0o755))
 	require.NoError(t, afero.WriteFile(fs, "/d/f.txt", []byte("hi"), 0o644))
@@ -86,8 +97,7 @@ func TestVerifyRequiredSignerMessages(t *testing.T) {
 	t.Run("invalid fingerprint length", func(t *testing.T) {
 		t.Parallel()
 
-		err := verifyRequiredSigner(context.Background(),
+		err := verifyRequiredSigner(unsignedChecker(t), "12345678")
-			unsignedChecker(t), "12345678")
 		require.ErrorIs(t, err, errInvalidFingerprint)
 		assert.EqualError(t, err,
 			"invalid fingerprint: must be exactly 40 hex characters, got 8")
@@ -96,8 +106,7 @@ func TestVerifyRequiredSignerMessages(t *testing.T) {
 	t.Run("manifest not signed", func(t *testing.T) {
 		t.Parallel()
 
-		err := verifyRequiredSigner(context.Background(),
+		err := verifyRequiredSigner(unsignedChecker(t), msgFpA)
-			unsignedChecker(t), msgFpA)
 		require.ErrorIs(t, err, errManifestNotSigned)
 		assert.EqualError(t, err,
 			"manifest is not signed, but signature from "+msgFpA+" is required")
@@ -105,63 +114,65 @@ func TestVerifyRequiredSignerMessages(t *testing.T) {
 }
 
 // TestSignerMismatchMessage drives verifyRequiredSigner against a real signed
-// manifest. The embedded fingerprint is whatever the generated key produced,
+// manifest. The signing key's fingerprint is whatever the generated key
-// so it is read back from the checker and substituted into the expected
+// produced, so it is read back from the checker and substituted into the
-// string; the required signer is a fixed value that cannot match it. Requires
+// expected string; the required signer is a fixed value that cannot match
-// gpg and is skipped where it is absent, as the other signing tests are.
+// it.
-//
-//nolint:paralleltest // signedManifest calls t.Setenv, which bars t.Parallel
 func TestSignerMismatchMessage(t *testing.T) {
+	t.Parallel()
+
 	chk := signedChecker(t,
 		signedManifest(t, map[string][]byte{"f.txt": []byte("signed file")}))
 
-	embeddedFP, err := chk.ExtractEmbeddedSigningKeyFP(context.Background())
+	err := verifyRequiredSigner(chk, msgFpB)
-	require.NoError(t, err)
-
-	err = verifyRequiredSigner(context.Background(), chk, msgFpB)
 	require.ErrorIs(t, err, errSignerMismatch)
 	assert.EqualError(t, err,
-		"embedded signing key fingerprint "+embeddedFP+
+		"embedded signing key fingerprint "+string(chk.Signer())+
 			" does not match required "+msgFpB)
 }
 
-// signedManifest returns a manifest of files signed by a throwaway GPG key
+// testSecretKey returns a new OpenPGP key with its secret key, armored, as
-// generated in a temporary GNUPGHOME, which it leaves set for the rest of
+// gpg --export-secret-keys --armor writes it, and the key's fingerprint.
-// the test.
+// The key is protected by passphrase unless that is nil. config sets how
+// the key is made; without one it is an Ed25519 key, which is quick to
+// make.
+func testSecretKey(
+	t *testing.T, passphrase []byte, config *packet.Config,
+) ([]byte, string) {
+	t.Helper()
+
+	if config == nil {
+		config = &packet.Config{Algorithm: packet.PubKeyAlgoEdDSA}
+	}
+
+	key, err := openpgp.NewEntity("MFER Test Key", "", "test@mfer.test", config)
+	require.NoError(t, err)
+
+	if passphrase != nil {
+		require.NoError(t, key.EncryptPrivateKeys(passphrase, nil))
+	}
+
+	var buf bytes.Buffer
+
+	w, err := armor.Encode(&buf, openpgp.PrivateKeyType, nil)
+	require.NoError(t, err)
+	require.NoError(t, key.SerializePrivateWithoutSigning(w, nil))
+	require.NoError(t, w.Close())
+
+	return buf.Bytes(), strings.ToUpper(hex.EncodeToString(key.PrimaryKey.Fingerprint))
+}
+
+// signedManifest returns a manifest of files signed by a new OpenPGP key.
 func signedManifest(t *testing.T, files map[string][]byte) []byte {
 	t.Helper()
 
-	_, err := exec.LookPath("gpg")
+	secretKey, _ := testSecretKey(t, nil, nil)
-	if err != nil {
-		t.Skip("gpg not installed, skipping signing test")
-	}
-
-	gpgHome := t.TempDir()
-	params := "%no-protection\n" +
-		"Key-Type: RSA\nKey-Length: 2048\n" +
-		"Name-Real: MFER Test Key\nName-Email: test@mfer.test\n" +
-		"Expire-Date: 0\n%commit\n"
-	paramsFile := filepath.Join(gpgHome, "key-params")
-	require.NoError(t, os.WriteFile(paramsFile, []byte(params), 0o600))
-
-	//nolint:gosec // paramsFile is a test-controlled path inside t.TempDir()
-	cmd := exec.CommandContext(context.Background(), "gpg",
-		"--batch", "--gen-key", paramsFile)
-
-	cmd.Env = append(os.Environ(), "GNUPGHOME="+gpgHome)
-
-	out, err := cmd.CombinedOutput()
-	if err != nil {
-		t.Skipf("failed to generate test GPG key: %v: %s", err, out)
-	}
-
-	t.Setenv("GNUPGHOME", gpgHome)
 
 	b := mfer.NewBuilder()
-	b.SetSigningOptions(&mfer.SigningOptions{KeyID: mfer.GPGKeyID("test@mfer.test")})
+	b.SetSigningOptions(&mfer.SigningOptions{SecretKey: secretKey})
 
 	for path, content := range files {
-		_, err = b.AddFile(mfer.RelFilePath(path), mfer.FileSize(len(content)),
+		_, err := b.AddFile(mfer.RelFilePath(path), mfer.FileSize(len(content)),
 			mfer.ModTime{}, 0, bytes.NewReader(content), nil)
 		require.NoError(t, err)
 	}
@@ -177,6 +188,11 @@ func signedManifest(t *testing.T, files map[string][]byte) []byte {
 func signedChecker(t *testing.T, manifest []byte) *mfer.Checker {
 	t.Helper()
 
+	// Loading a manifest logs to the process-global logger, so serialize
+	// with the CLI runs.
+	runMu.Lock()
+	defer runMu.Unlock()
+
 	fs := afero.NewMemMapFs()
 	require.NoError(t, afero.WriteFile(fs, "/index.mf", manifest, 0o644))
 
@@ -191,6 +207,52 @@ func signedChecker(t *testing.T, manifest []byte) *mfer.Checker {
 	return chk
 }
 
+// manifestSignedByAnotherKey returns a manifest of files and the
+// fingerprint of a new key, the required key, that did not sign it.
+// The manifest is signed by a second new key; its embedded public key
+// block holds the required key followed by the second key, and its signer
+// field names the required key.
+func manifestSignedByAnotherKey(
+	t *testing.T, files map[string][]byte,
+) ([]byte, string) {
+	t.Helper()
+
+	required := new(mfer.MFFileOuter)
+	require.NoError(t, proto.Unmarshal(
+		signedManifest(t, files)[len(mfer.MAGIC):], required))
+
+	outer := new(mfer.MFFileOuter)
+	require.NoError(t, proto.Unmarshal(
+		signedManifest(t, files)[len(mfer.MAGIC):], outer))
+
+	// One armored block holding both keys, as gpg --export --armor writes
+	// two keys.
+	var block bytes.Buffer
+
+	w, err := armor.Encode(&block, openpgp.PublicKeyType, nil)
+	require.NoError(t, err)
+
+	for _, key := range [][]byte{
+		required.GetSigningPubKey(), outer.GetSigningPubKey(),
+	} {
+		decoded, err := armor.Decode(bytes.NewReader(key))
+		require.NoError(t, err)
+
+		_, err = io.Copy(w, decoded.Body)
+		require.NoError(t, err)
+	}
+
+	require.NoError(t, w.Close())
+
+	outer.SigningPubKey = block.Bytes()
+	outer.Signer = required.GetSigner()
+
+	data, err := proto.Marshal(outer)
+	require.NoError(t, err)
+
+	return append([]byte(mfer.MAGIC), data...), string(required.GetSigner())
+}
+
 func TestPathDoesNotExistMessage(t *testing.T) {
 	t.Parallel()
 
@@ -277,7 +339,7 @@ func TestManifestLoaderHTTPStatusMessage(t *testing.T) {
 	_, err := mfa.openManifestReader(context.Background(), server.URL+"/foo.mf")
 	require.ErrorIs(t, err, errHTTPStatus)
 	assert.EqualError(t, err,
-		"failed to fetch "+server.URL+"/foo.mf: HTTP 404")
+		"download manifest "+server.URL+"/foo.mf: unexpected HTTP status 404")
 }
 
 func TestFetchManifestHTTPStatusMessage(t *testing.T) {
@@ -299,7 +361,7 @@ func TestFetchManifestHTTPStatusMessage(t *testing.T) {
 		return cmd.Run(context.Background(), []string{cmdFetch, server.URL})
 	})
 	require.ErrorIs(t, err, errHTTPStatus)
-	assert.EqualError(t, err, "failed to fetch manifest: HTTP 404")
+	assert.EqualError(t, err, "download manifest: unexpected HTTP status 404")
 }
 
 func TestFetchFileHTTPStatusMessage(t *testing.T) {
@@ -317,7 +379,151 @@ func TestFetchFileHTTPStatusMessage(t *testing.T) {
 			&mfer.MFFilePath{}, nil)
 	})
 	require.ErrorIs(t, err, errHTTPStatus)
-	assert.EqualError(t, err, "HTTP 500")
+	assert.EqualError(t, err, "unexpected HTTP status 500")
+}
+
+// TestCheckCorruptManifestMessage runs check on a file that is not a
+// manifest.
+func TestCheckCorruptManifestMessage(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, afero.WriteFile(fs, "/bad.mf", []byte("not a manifest"), 0o644))
+
+	mfa := &CLIApp{Fs: fs}
+	cmd := mfa.checkCommand()
+	cmd.Action = mfa.checkManifestOperation
+
+	// checkManifestOperation logs to the process-global logger.
+	err := runLocked(func() error {
+		return cmd.Run(context.Background(), []string{cmdCheck, "/bad.mf"})
+	})
+	assert.EqualError(t, err, "load manifest: invalid file format")
+}
+
+// TestListMissingManifestMessage runs list on a manifest file that does not
+// exist.
+func TestListMissingManifestMessage(t *testing.T) {
+	t.Parallel()
+
+	mfa := &CLIApp{Fs: afero.NewMemMapFs()}
+	cmd := mfa.listCommand()
+
+	// listManifestOperation sets the process-global log level.
+	err := runLocked(func() error {
+		return cmd.Run(context.Background(), []string{cmdList, "/nope.mf"})
+	})
+	require.ErrorIs(t, err, os.ErrNotExist)
+	assert.EqualError(t, err, "open /nope.mf: file does not exist")
+}
+
+// TestFetchHashMismatchMessage runs fetch against a server that sends a
+// listed file with other content of the same size.
+func TestFetchHashMismatchMessage(t *testing.T) {
+	t.Parallel()
+
+	manifest := builtManifest(t, map[string][]byte{testFileTxt: []byte("listed")})
+
+	server := httptest.NewServer(fetchTestHandler(manifest,
+		map[string][]byte{testFileTxt: []byte("served")}))
+	defer server.Close()
+
+	mfa := &CLIApp{Fs: afero.NewMemMapFs(), maxManifestSize: mfer.MaxManifestSize}
+	cmd := mfa.fetchCommand()
+	cmd.Action = mfa.fetchManifestOperation
+
+	// fetchManifestOperation logs to the process-global logger.
+	err := runLocked(func() error {
+		return cmd.Run(context.Background(),
+			[]string{cmdFetch, "--" + flagDest, t.TempDir(), server.URL})
+	})
+	require.ErrorIs(t, err, errHashMismatch)
+	assert.EqualError(t, err, "download "+testFileTxt+": hash mismatch")
+}
+
+// TestFreshenBackslashPathMessage runs freshen on a tree that has gained a
+// file whose name holds a backslash, which a manifest path may not contain.
+func TestFreshenBackslashPathMessage(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewOsFs()
+	root, manifestPath := setupFreshenDir(t, fs,
+		map[string]string{testFileTxt: "content"})
+	writeTestFile(t, fs, filepath.Join(root, `a\b.txt`), "new")
+
+	mfa := &CLIApp{Fs: fs}
+	cmd := mfa.freshenCommand()
+	cmd.Action = mfa.freshenManifestOperation
+
+	// freshenManifestOperation logs to the process-global logger.
+	err := runLocked(func() error {
+		return cmd.Run(context.Background(),
+			[]string{cmdFreshen, testFlagBase, root, manifestPath})
+	})
+	assert.EqualError(t, err,
+		`path "a\\b.txt" contains backslash; use forward slashes only`)
+}
+
+// TestFreshenReadErrorMessage has freshen hash a directory as though it
+// were a file, so reading it fails.
+func TestFreshenReadErrorMessage(t *testing.T) {
+	t.Parallel()
+
+	root := t.TempDir()
+	require.NoError(t, os.Mkdir(filepath.Join(root, "sub"), 0o750))
+
+	hasher := &freshenHasher{
+		fs:      afero.NewOsFs(),
+		absBase: root,
+		builder: mfer.NewBuilder(),
+	}
+
+	err := hasher.processEntry(&freshenEntry{path: "sub", needsHash: true})
+	assert.EqualError(t, err,
+		"read "+filepath.Join(root, "sub")+": is a directory")
+}
+
+// TestFreshenSizeChangedMessage has freshen hash a file that has grown or
+// shrunk since the scan recorded its size.
+func TestFreshenSizeChangedMessage(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewMemMapFs()
+	writeTestFile(t, fs, "/d/log.txt", "hello")
+
+	t.Run("grown", func(t *testing.T) {
+		t.Parallel()
+
+		hasher := &freshenHasher{
+			fs:      fs,
+			absBase: "/d",
+			builder: mfer.NewBuilder(),
+		}
+
+		err := hasher.processEntry(
+			&freshenEntry{path: "log.txt", size: 3, needsHash: true})
+		require.ErrorIs(t, err, errSizeMismatch)
+		assert.EqualError(t, err, `size mismatch for "log.txt": `+
+			`3 bytes when scanned but 5 bytes when read; `+
+			`the file changed while freshen ran`)
+	})
+
+	t.Run("shrunk", func(t *testing.T) {
+		t.Parallel()
+
+		hasher := &freshenHasher{
+			fs:      fs,
+			absBase: "/d",
+			builder: mfer.NewBuilder(),
+		}
+
+		err := hasher.processEntry(
+			&freshenEntry{path: "log.txt", size: 8, needsHash: true})
+		require.ErrorIs(t, err, errSizeMismatch)
+		assert.EqualError(t, err, `size mismatch for "log.txt": `+
+			`8 bytes when scanned but 5 bytes when read; `+
+			`the file changed while freshen ran`)
+	})
 }
 
 func TestURLRequiredMessage(t *testing.T) {

internal/cli/export.go

@@ -26,20 +26,19 @@ func (mfa *CLIApp) exportManifestOperation(
 ) error {
 	pathOrURL, err := mfa.resolveManifestArg(cmd)
 	if err != nil {
-		return fmt.Errorf("export: %w", err)
+		return err
 	}
 
 	rc, err := mfa.openManifestReader(ctx, pathOrURL)
 	if err != nil {
-		return fmt.Errorf("export: %w", err)
+		return err
 	}
 
 	defer func() { _ = rc.Close() }()
 
-	//nolint:contextcheck // mfer loads a manifest without a context
 	manifest, err := mfer.NewManifestFromReader(rc)
 	if err != nil {
-		return fmt.Errorf("export: failed to parse manifest: %w", err)
+		return fmt.Errorf("parse manifest: %w", err)
 	}
 
 	files := manifest.Files()
@@ -76,7 +75,7 @@ func (mfa *CLIApp) exportManifestOperation(
 
 	err = enc.Encode(entries)
 	if err != nil {
-		return fmt.Errorf("export: failed to encode JSON: %w", err)
+		return fmt.Errorf("encode JSON: %w", err)
 	}
 
 	return nil

internal/cli/export_test.go

@@ -20,6 +20,11 @@ const testCmdExport = "export"
 func buildTestManifest(t *testing.T, files map[string][]byte) []byte {
 	t.Helper()
 
+	// The scan logs to the process-global logger, so serialize with the
+	// CLI runs.
+	runMu.Lock()
+	defer runMu.Unlock()
+
 	sourceFs := afero.NewMemMapFs()
 	for path, content := range files {
 		require.NoError(t, sourceFs.MkdirAll("/", 0o755))

internal/cli/fetch.go

@@ -86,7 +86,8 @@ var (
 	// 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.
+	// size, or a file freshen read at a size other than the one its scan
+	// recorded.
 	errSizeMismatch = errors.New("size mismatch")
 	// errHashMismatch indicates a downloaded file whose hash matches no
 	// manifest hash.
@@ -125,8 +126,9 @@ type retryingClient struct {
 // to a limit that doubles each time, unless the server's Retry-After
 // header says how long to wait. Any other failure, an error from use
 // included, is returned at once and unwrapped; a non-OK status is
-// returned as errHTTPStatus. use must start over each time it is called,
+// returned as errHTTPStatus. If ctx ends before a retry, the error wraps
-// since a retry calls it again with a new response.
+// both ctx's error and the last try's error. use must start over each
+// time it is called, since a retry calls it again with a new response.
 func (c retryingClient) get(
 	ctx context.Context, rawURL string, use func(*http.Response) error,
 ) error {
@@ -168,15 +170,19 @@ func (c retryingClient) get(
 			}
 		}
 
-		if !retry || attempt == fetchAttempts || ctx.Err() != nil {
+		if !retry || attempt == fetchAttempts {
 			return err
 		}
 
+		if ctx.Err() != nil {
+			return fmt.Errorf("%w: %w", ctx.Err(), err)
+		}
+
 		log.Warnf("%s: %s, retrying in %s", rawURL, err, wait.Round(time.Millisecond))
 
 		select {
 		case <-ctx.Done():
-			return ctx.Err()
+			return fmt.Errorf("%w: %w", ctx.Err(), err)
 		case <-time.After(wait):
 		}
 
@@ -239,7 +245,7 @@ func reportDownloadProgress(progress <-chan DownloadProgress, done chan<- struct
 func manifestBaseURL(manifestURL string) (*url.URL, error) {
 	parsed, err := url.Parse(manifestURL)
 	if err != nil {
-		return nil, fmt.Errorf("fetch: invalid manifest URL: %w", err)
+		return nil, fmt.Errorf("invalid manifest URL: %w", err)
 	}
 
 	// JoinPath cleans the path it builds, so ".." drops the manifest's
@@ -268,7 +274,7 @@ func downloadManifestFiles(
 		// Sanitize the path to prevent path traversal attacks
 		localPath, err := sanitizePath(f.GetPath())
 		if err != nil {
-			return 0, 0, fmt.Errorf("invalid path in manifest: %w", err)
+			return 0, 0, fmt.Errorf("invalid file entry: %w", err)
 		}
 
 		if alreadyPresent(dest, localPath, f) {
@@ -284,7 +290,7 @@ func downloadManifestFiles(
 
 		err = downloadFile(ctx, client, fileURL, dest, localPath, f, progress)
 		if err != nil {
-			return 0, 0, fmt.Errorf("failed to download %s: %w", f.GetPath(), err)
+			return 0, 0, fmt.Errorf("download %s: %w", f.GetPath(), err)
 		}
 
 		downloaded++
@@ -376,7 +382,7 @@ func (mfa *CLIApp) fetchManifestOperation(
 
 	err = os.MkdirAll(dest, dirPerms)
 	if err != nil {
-		return fmt.Errorf("failed to create destination directory %s: %w", dest, err)
+		return err
 	}
 
 	// Create progress channel and start progress reporter goroutine
@@ -403,7 +409,7 @@ func (mfa *CLIApp) fetchManifestOperation(
 	// "mfer check" can verify the tree later.
 	err = saveManifest(dest, manifestData)
 	if err != nil {
-		return fmt.Errorf("failed to save manifest: %w", err)
+		return fmt.Errorf("save manifest: %w", err)
 	}
 
 	// Print summary
@@ -429,6 +435,14 @@ func (mfa *CLIApp) fetchManifestOperation(
 func (mfa *CLIApp) fetchManifest(
 	ctx context.Context, cmd *cli.Command, client retryingClient, manifestURL string,
 ) ([]byte, []*mfer.MFFilePath, error) {
+	// An empty fingerprint is refused before anything is requested, with
+	// the message check gives for it; any other is checked against the
+	// manifest once it is downloaded.
+	requiredSigner := cmd.String(flagRequireSignature)
+	if cmd.IsSet(flagRequireSignature) && requiredSigner == "" {
+		return nil, nil, fmt.Errorf("%w, got 0", errInvalidFingerprint)
+	}
+
 	log.Infof("fetching manifest from %s", manifestURL)
 
 	// Read the whole manifest before parsing it, so that a connection
@@ -446,24 +460,22 @@ func (mfa *CLIApp) fetchManifest(
 		return readErr
 	})
 	if err != nil {
-		return nil, nil, fmt.Errorf("failed to fetch manifest: %w", err)
+		return nil, nil, fmt.Errorf("download manifest: %w", err)
 	}
 
 	if int64(len(manifestData)) > mfa.maxManifestSize {
-		return nil, nil, fmt.Errorf("failed to fetch manifest: %w of %d bytes",
+		return nil, nil, fmt.Errorf("download manifest: %w of %d bytes",
 			errManifestTooLarge, mfa.maxManifestSize)
 	}
 
 	// Parse manifest
-	//nolint:contextcheck // mfer loads a manifest without a context
 	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(manifestData))
 	if err != nil {
-		return nil, nil, fmt.Errorf("failed to parse manifest: %w", err)
+		return nil, nil, fmt.Errorf("parse manifest: %w", err)
 	}
 
-	requiredSigner := cmd.String(flagRequireSignature)
 	if requiredSigner != "" {
-		err = verifyFetchedSigner(ctx, manifestData, requiredSigner)
+		err = verifyFetchedSigner(manifestData, requiredSigner)
 		if err != nil {
 			return nil, nil, err
 		}
@@ -545,9 +557,7 @@ func checkNoNameClash(files []*mfer.MFFilePath) error {
 // 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
 // memory.
-func verifyFetchedSigner(
+func verifyFetchedSigner(manifestData []byte, requiredSigner string) error {
-	ctx context.Context, manifestData []byte, requiredSigner string,
-) error {
 	memFs := afero.NewMemMapFs()
 	manifestPath := "/" + defaultManifestName
 
@@ -556,17 +566,16 @@ func verifyFetchedSigner(
 		return err
 	}
 
-	//nolint:contextcheck // mfer loads a manifest without a context
 	chk, err := mfer.NewChecker(&mfer.CheckerOptions{
 		ManifestPath: manifestPath,
 		BasePath:     "/",
 		Fs:           memFs,
 	})
 	if err != nil {
-		return fmt.Errorf("failed to load manifest: %w", err)
+		return fmt.Errorf("load manifest: %w", err)
 	}
 
-	return verifyRequiredSigner(ctx, chk, requiredSigner)
+	return verifyRequiredSigner(chk, requiredSigner)
 }
 
 // saveManifest writes the fetched manifest into dest under the default
@@ -655,7 +664,7 @@ func checkNoSymlinks(dest, p string) error {
 		}
 
 		if err != nil {
-			return fmt.Errorf("failed to check %s for a symlink: %w", current, err)
+			return err
 		}
 
 		if info.Mode()&os.ModeSymlink != 0 {
@@ -683,21 +692,26 @@ func resolveManifestURL(inputURL string) (string, error) {
 	return parsed.JoinPath(defaultManifestName).String(), nil
 }
 
-// progressWriter wraps an io.Writer and reports progress to a channel.
+// progressWriter wraps an io.Writer and reports progress to a channel,
+// at most once per second and once more when the last byte is written.
 type progressWriter struct {
-	w         io.Writer
+	w            io.Writer
-	path      string
+	path         string
-	total     int64
+	total        int64
-	written   int64
+	written      int64
-	startTime time.Time
+	startTime    time.Time
-	progress  chan<- DownloadProgress
+	lastProgress time.Time
+	progress     chan<- DownloadProgress
 }
 
 func (pw *progressWriter) Write(p []byte) (int, error) {
 	n, err := pw.w.Write(p)
 
 	pw.written += int64(n)
-	if pw.progress != nil {
+
+	isLast := pw.written == pw.total
+	if pw.progress != nil &&
+		(isLast || time.Since(pw.lastProgress) >= time.Second) {
 		var (
 			bytesPerSec float64
 			eta         time.Duration
@@ -719,6 +733,8 @@ func (pw *progressWriter) Write(p []byte) (int, error) {
 			BytesPerSec: bytesPerSec,
 			ETA:         eta,
 		})
+
+		pw.lastProgress = time.Now()
 	}
 
 	return n, err
@@ -772,7 +788,7 @@ func tempPathFor(localPath string) string {
 func verifyDownloadedHash(digest []byte, entry *mfer.MFFilePath) error {
 	computed, err := multihash.Encode(digest, multihash.SHA2_256)
 	if err != nil {
-		return fmt.Errorf("failed to encode hash: %w", err)
+		return fmt.Errorf("encode hash: %w", err)
 	}
 
 	for _, hash := range entry.GetHashes() {
@@ -799,7 +815,7 @@ func downloadFile(
 	// so every entry point to downloadFile gets the same treatment.
 	localPath, err := sanitizePath(localPath)
 	if err != nil {
-		return fmt.Errorf("invalid path: %w", err)
+		return fmt.Errorf("invalid file entry: %w", err)
 	}
 
 	// Create parent directories if needed
@@ -814,7 +830,7 @@ func downloadFile(
 
 		err = os.MkdirAll(dir, dirPerms)
 		if err != nil {
-			return fmt.Errorf("failed to create directory %s: %w", dir, err)
+			return err
 		}
 	}
 
@@ -848,7 +864,7 @@ func createTempFile(dest, tmpPath string) (*os.File, error) {
 	out, err := os.OpenFile( //nolint:gosec // G304: see comment above
 		path, os.O_RDWR|os.O_CREATE|os.O_EXCL, filePerms)
 	if err != nil {
-		return nil, fmt.Errorf("failed to create temp file: %w", err)
+		return nil, err
 	}
 
 	return out, nil
@@ -861,12 +877,7 @@ func moveIntoPlace(dest, tmpPath, localPath string) error {
 		return err
 	}
 
-	err = os.Rename(filepath.Join(dest, tmpPath), filepath.Join(dest, localPath))
+	return os.Rename(filepath.Join(dest, tmpPath), filepath.Join(dest, localPath))
-	if err != nil {
-		return fmt.Errorf("failed to rename temp file: %w", err)
-	}
-
-	return nil
 }
 
 // saveResponse writes resp's body to tmpPath, verifies it against entry,
@@ -901,20 +912,23 @@ func saveResponse(
 			_ = out.Close()
 			_ = os.Remove(filepath.Join(dest, tmpPath))
 
-			return fmt.Errorf("failed to set mode: %w", err)
+			return err
 		}
 	}
 
 	// Set up hash computation
 	h := sha256.New()
 
-	// Create progress-reporting writer that also computes hash
+	// Create progress-reporting writer that also computes hash. The first
+	// update waits a second, as gen's and check's do.
+	start := time.Now()
 	pw := &progressWriter{
-		w:         io.MultiWriter(out, h),
+		w:            io.MultiWriter(out, h),
-		path:      localPath,
+		path:         localPath,
-		total:     totalBytes,
+		total:        totalBytes,
-		startTime: time.Now(),
+		startTime:    start,
-		progress:  progress,
+		lastProgress: start,
+		progress:     progress,
 	}
 
 	// Copy content while hashing and reporting progress. One byte past

internal/cli/fetch_test.go

@@ -171,6 +171,11 @@ func TestResolveManifestURL(t *testing.T) {
 func scanToManifest(t *testing.T, sourceFs afero.Fs) []byte {
 	t.Helper()
 
+	// The scan logs to the process-global logger, so serialize with the
+	// CLI runs.
+	runMu.Lock()
+	defer runMu.Unlock()
+
 	s := mfer.NewScannerWithOptions(&mfer.ScannerOptions{Fs: sourceFs})
 	require.NoError(t, s.EnumerateFS(sourceFs, "/", nil))
 
@@ -314,8 +319,11 @@ func TestFetchFromHTTP(t *testing.T) {
 	// Change to a fresh destination directory for the test
 	destDir := chdirTemp(t)
 
-	// Parse the manifest to get file entries
+	// Parse the manifest to get file entries. Loading a manifest logs to
+	// the process-global logger.
+	runMu.Lock()
 	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(manifestData))
+	runMu.Unlock()
 	require.NoError(t, err)
 
 	files := manifest.Files()
@@ -365,7 +373,10 @@ func TestFetchHashMismatch(t *testing.T) {
 	// Generate and parse manifest
 	manifestData := scanToManifest(t, sourceFs)
 
+	// Loading a manifest logs to the process-global logger.
+	runMu.Lock()
 	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(manifestData))
+	runMu.Unlock()
 	require.NoError(t, err)
 
 	files := manifest.Files()
@@ -411,7 +422,10 @@ func TestFetchSizeMismatch(t *testing.T) {
 	// Generate and parse manifest
 	manifestData := scanToManifest(t, sourceFs)
 
+	// Loading a manifest logs to the process-global logger.
+	runMu.Lock()
 	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(manifestData))
+	runMu.Unlock()
 	require.NoError(t, err)
 
 	files := manifest.Files()
@@ -502,8 +516,9 @@ func TestManifestDownloadStopsAtLimit(t *testing.T) {
 				[]string{cmd.Name, server.URL + "/index.mf"})
 		})
 		require.ErrorIs(t, err, errManifestTooLarge, cmd.Name)
-		require.ErrorContains(t, err,
+		require.EqualError(t, err,
-			"maximum allowed size of 65536 bytes", cmd.Name)
+			"download manifest: file exceeds maximum allowed size of 65536 bytes",
+			cmd.Name)
 	}
 
 	leftover, err := os.ReadDir(tmpDir)
@@ -515,14 +530,17 @@ func TestManifestDownloadStopsAtLimit(t *testing.T) {
 func TestFetchProgress(t *testing.T) {
 	// Create source filesystem with a larger test file
 	sourceFs := afero.NewMemMapFs()
-	// Create content large enough to trigger multiple progress updates
+	// Content large enough that io.Copy writes it in at least four chunks
 	content := bytes.Repeat([]byte("x"), 100*1024) // 100KB
 	require.NoError(t, afero.WriteFile(sourceFs, "/large.txt", content, 0o644))
 
 	// Generate and parse manifest
 	manifestData := scanToManifest(t, sourceFs)
 
+	// Loading a manifest logs to the process-global logger.
+	runMu.Lock()
 	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(manifestData))
+	runMu.Unlock()
 	require.NoError(t, err)
 
 	files := manifest.Files()
@@ -558,8 +576,11 @@ func TestFetchProgress(t *testing.T) {
 	}()
 
 	// Download
+	start := time.Now()
 	err = downloadFile(context.Background(), testClient(),
 		server.URL+"/large.txt", ".", "large.txt", files[0], progress)
+	elapsed := time.Since(start)
+
 	close(progress)
 	<-done
 
@@ -568,6 +589,12 @@ func TestFetchProgress(t *testing.T) {
 	// Verify we got progress updates
 	assert.NotEmpty(t, progressUpdates, "should have received progress updates")
 
+	// At most one update per second, plus the one reporting the file
+	// complete: a download that takes under a second sends two at most,
+	// however many chunks it writes.
+	assert.LessOrEqual(t, len(progressUpdates), 2+int(elapsed/time.Second),
+		"one progress update per second at most, plus the last")
+
 	// Verify final progress shows complete
 	if len(progressUpdates) > 0 {
 		last := progressUpdates[len(progressUpdates)-1]
@@ -605,27 +632,27 @@ func TestFetchRefusesSymlinks(t *testing.T) {
 	}{
 		{
 			"parent directory", "sub/deeper/file.txt", "sub", ".",
-			"failed to download sub/deeper/file.txt",
+			"download sub/deeper/file.txt",
 		},
 		{
 			"directory inside a plain directory", "docs/data/passwd", "docs/data", ".",
-			"failed to download docs/data/passwd",
+			"download docs/data/passwd",
 		},
 		{
 			"temp file", testFileTxt, ".file.txt.tmp", newFile,
-			"failed to download " + testFileTxt,
+			"download " + testFileTxt,
 		},
 		{
 			"file", testFileTxt, testFileTxt, newFile,
-			"failed to download " + testFileTxt,
+			"download " + testFileTxt,
 		},
 		{
 			"manifest temp file", testFileTxt, tempPathFor(defaultManifestName), newFile,
-			"failed to save manifest",
+			"save manifest",
 		},
 		{
 			"manifest", testFileTxt, defaultManifestName, newFile,
-			"failed to save manifest",
+			"save manifest",
 		},
 	}
 
@@ -692,7 +719,7 @@ func TestFetchDoesNotSkipThroughSymlink(t *testing.T) {
 	}, 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)
+		"download sub/"+testFileTxt+": symlink in path not allowed: "+link)
 	assert.Equal(t, map[string][]byte{testFileTxt: content}, filesUnder(t, outside))
 }
 
@@ -762,7 +789,8 @@ func TestGetRetriesTransientStatusesOnly(t *testing.T) {
 
 			err := getNothing(testClient(), server.URL, 10*time.Second)
 			require.ErrorIs(t, err, errHTTPStatus)
-			require.EqualError(t, err, fmt.Sprintf("HTTP %d", tt.status))
+			require.EqualError(t, err,
+				fmt.Sprintf("unexpected HTTP status %d", tt.status))
 			assert.Equal(t, tt.requests, requests.Load())
 		})
 	}
@@ -869,23 +897,59 @@ func TestGetHonorsRetryAfter(t *testing.T) {
 	}
 }
 
-// TestGetStopsWaitingWhenCanceled gives get a server that always answers
+// instant503Transport answers every request with a 503 at once, so the
-// 503 and an hour's wait before each retry, then lets the context expire
+// 503 is in hand before any deadline can pass.
-// during that wait. get returning at all shows it stopped waiting.
+type instant503Transport struct{}
+
+func (instant503Transport) RoundTrip(*http.Request) (*http.Response, error) {
+	return &http.Response{
+		StatusCode: http.StatusServiceUnavailable,
+		Body:       http.NoBody,
+	}, nil
+}
+
+// TestGetStopsWaitingWhenCanceled answers every request with a 503 and
+// sets an hour's wait before each retry, then lets the context expire
+// during that wait. get returning at all shows it stopped waiting; it must
+// return the deadline error and keep the 503 with it.
 func TestGetStopsWaitingWhenCanceled(t *testing.T) {
 	t.Parallel()
 
-	server := httptest.NewServer(
-		http.HandlerFunc(func(w http.ResponseWriter, _ *http.Request) {
-			w.WriteHeader(http.StatusServiceUnavailable)
-		}))
-	defer server.Close()
-
 	client := testClient()
+	client.client.Transport = instant503Transport{}
 	client.firstDelay = time.Hour
 
-	err := getNothing(client, server.URL, 50*time.Millisecond)
+	err := getNothing(client, "http://example.invalid/", 50*time.Millisecond)
 	require.ErrorIs(t, err, context.DeadlineExceeded)
+	require.ErrorIs(t, err, errHTTPStatus)
+}
+
+// late503Transport answers every request with a 503, but only once the
+// request's context has ended. A real server cannot stand in for it: the
+// client drops a response still on its way when the context ends.
+type late503Transport struct{}
+
+func (late503Transport) RoundTrip(req *http.Request) (*http.Response, error) {
+	<-req.Context().Done()
+
+	return &http.Response{
+		StatusCode: http.StatusServiceUnavailable,
+		Body:       http.NoBody,
+	}, nil
+}
+
+// TestGetStopsWhenContextEndsDuringRequest lets the context expire while
+// the first request is still waiting for its 503. get must return the
+// deadline error and keep the 503 with it.
+func TestGetStopsWhenContextEndsDuringRequest(t *testing.T) {
+	t.Parallel()
+
+	client := testClient()
+	client.client.Transport = late503Transport{}
+
+	err := getNothing(client, "http://example.invalid/", 50*time.Millisecond)
+	require.ErrorIs(t, err, context.DeadlineExceeded)
+	require.ErrorIs(t, err, errHTTPStatus)
 }
 
 // TestDownloadFileRetriesToSuccess serves a file that fails twice before
@@ -895,9 +959,12 @@ func TestGetStopsWaitingWhenCanceled(t *testing.T) {
 //nolint:paralleltest // changes the process-global working directory
 func TestDownloadFileRetriesToSuccess(t *testing.T) {
 	content := []byte("the whole file, every byte of it")
+	manifestData := manifestOf(t, map[string][]byte{testFileTxt: content})
 
-	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(
+	// Loading a manifest logs to the process-global logger.
-		manifestOf(t, map[string][]byte{testFileTxt: content})))
+	runMu.Lock()
+	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(manifestData))
+	runMu.Unlock()
 	require.NoError(t, err)
 
 	var requests atomic.Int32
@@ -920,8 +987,11 @@ func TestDownloadFileRetriesToSuccess(t *testing.T) {
 
 	chdirTemp(t)
 
-	err = downloadFile(context.Background(), testClient(),
+	// downloadFile logs each retry to the process-global logger.
-		server.URL+"/"+testFileTxt, ".", testFileTxt, manifest.Files()[0], nil)
+	err = runLocked(func() error {
+		return downloadFile(context.Background(), testClient(),
+			server.URL+"/"+testFileTxt, ".", testFileTxt, manifest.Files()[0], nil)
+	})
 	require.NoError(t, err)
 	assert.Equal(t, int32(3), requests.Load())
 
@@ -1187,25 +1257,28 @@ func TestFetchIntoDest(t *testing.T) {
 // TestFetchRequireSignature runs fetch with --require-signature. A
 // manifest that is unsigned, or signed by another key, must stop fetch
 // with check's message before it downloads or writes anything; the
-// required key lets it through. The signed cases need gpg and are skipped
+// required key lets it through. A manifest signed by another key whose
-// without it, as the other signing tests are.
+// embedded public key block also holds the required key must stop fetch
-//
+// too.
-//nolint:paralleltest // signedManifest calls t.Setenv, which bars t.Parallel
 func TestFetchRequireSignature(t *testing.T) {
+	t.Parallel()
+
 	files := map[string][]byte{testFileTxt: []byte("signed file")}
 
 	t.Run("unsigned", func(t *testing.T) {
+		t.Parallel()
+
 		assertFetchRefused(t, manifestOf(t, files), files,
 			"manifest is not signed, but signature from "+msgFpA+" is required",
 			"--"+flagRequireSignature, msgFpA)
 	})
 
 	t.Run("signed", func(t *testing.T) {
+		t.Parallel()
+
 		manifest := signedManifest(t, files)
 
-		signer, err := signedChecker(t, manifest).
+		signer := string(signedChecker(t, manifest).Signer())
-			ExtractEmbeddedSigningKeyFP(context.Background())
-		require.NoError(t, err)
 
 		assertFetchRefused(t, manifest, files,
 			"embedded signing key fingerprint "+signer+" does not match required "+msgFpB,
@@ -1223,14 +1296,25 @@ func TestFetchRequireSignature(t *testing.T) {
 		require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
 		assert.Equal(t, files[testFileTxt], filesUnder(t, dest)[testFileTxt])
 	})
+
+	t.Run("signed by another key embedded after the required one", func(t *testing.T) {
+		t.Parallel()
+
+		manifest, required := manifestSignedByAnotherKey(t, files)
+
+		assertFetchRefused(t, manifest, files,
+			"parse manifest: "+
+				"embedded public key block must hold exactly one key, found 2",
+			"--"+flagRequireSignature, required)
+	})
 }
 
 // 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
+// temp file: as a file, as a directory and in capitals. Saving the
-// "./". Saving the manifest would replace or remove what is listed there,
+// manifest would replace or remove what is listed there, so fetch must
-// so fetch must refuse the manifest before it creates the destination or
+// refuse the manifest before it creates the destination or requests any
-// requests any file.
+// file.
 func TestFetchRefusesListedManifestName(t *testing.T) {
 	t.Parallel()
 
@@ -1239,7 +1323,6 @@ func TestFetchRefusesListedManifestName(t *testing.T) {
 		tempPathFor(defaultManifestName),
 		defaultManifestName + "/" + testFileTxt,
 		"INDEX.MF",
-		"./" + defaultManifestName,
 	} {
 		t.Run(listed, func(t *testing.T) {
 			t.Parallel()
@@ -1315,9 +1398,9 @@ func TestFetchRefusesListedTempName(t *testing.T) {
 // directory, one of them under a spelling the manifest does not list,
 // and check reports that file as not in the manifest. So fetch must
 // refuse each on every filesystem before it creates the destination or
-// requests any file. A file and a directory with the same name, and a
+// requests any file. A file and a directory with the same name are
-// file listed twice, are refused the same way. A manifest whose names
+// refused the same way. A manifest whose names differ in more than
-// differ in more than letter case is fetched in full.
+// letter case is fetched in full.
 func TestFetchRefusesNamesEqualIgnoringCase(t *testing.T) {
 	t.Parallel()
 
@@ -1327,7 +1410,6 @@ func TestFetchRefusesNamesEqualIgnoringCase(t *testing.T) {
 		{"Dir", "dir/x", "dir/x (the file Dir)"},
 		{"Dir/a.txt", "dir/b.txt", "dir/b.txt (the directory Dir)"},
 		{"dir", "dir/x", "dir/x (the file dir)"},
-		{"./x.txt", "x.txt", "x.txt (the file ./x.txt)"},
 	} {
 		t.Run(tc.first+" and "+tc.second, func(t *testing.T) {
 			t.Parallel()
@@ -1388,14 +1470,18 @@ func TestFetchSetsRecordedMode(t *testing.T) {
 		require.NoError(t, afero.WriteFile(sourceFs, "/"+p, content, modes[p]))
 	}
 
-	scanner := mfer.NewScannerWithOptions(&mfer.ScannerOptions{
-		Fs:                 sourceFs,
-		IncludePermissions: true,
-	})
-	require.NoError(t, scanner.EnumerateFS(sourceFs, "/", nil))
-
 	var manifest bytes.Buffer
-	require.NoError(t, scanner.ToManifest(context.Background(), &manifest, nil))
+
+	// The scan logs to the process-global logger.
+	require.NoError(t, runLocked(func() error {
+		scanner := mfer.NewScannerWithOptions(&mfer.ScannerOptions{
+			Fs:                 sourceFs,
+			IncludePermissions: true,
+		})
+		require.NoError(t, scanner.EnumerateFS(sourceFs, "/", nil))
+
+		return scanner.ToManifest(context.Background(), &manifest, nil)
+	}))
 
 	tree := fetchTestHandler(manifest.Bytes(), files)
 
@@ -1557,8 +1643,7 @@ func manifestWithMode(t *testing.T, path string, content []byte, mode uint32) []
 }
 
 // builtManifest returns a manifest of files, built directly rather than
-// scanned, since a scan lists no hidden files and never a path starting
+// scanned, since a scan lists no hidden files.
-// with "./".
 func builtManifest(t *testing.T, files map[string][]byte) []byte {
 	t.Helper()
 

internal/cli/freshen.go

@@ -28,9 +28,19 @@ const (
 	scanProgressInterval = 100
 )
 
-// errEntryMissingMtime indicates a manifest entry that carries no
+var (
-// modification time where one is required to carry it forward unchanged.
+	// errEntryMissingMtime indicates a manifest entry that carries no
-var errEntryMissingMtime = errors.New("manifest entry has no mtime")
+	// modification time where one is required to carry it forward unchanged.
+	errEntryMissingMtime = errors.New("manifest entry has no mtime")
+
+	// errEntryMissingHash indicates a manifest entry that carries no hash
+	// to carry forward.
+	errEntryMissingHash = errors.New("manifest entry has no hash")
+)
+
+// errSignKeyNeeded indicates a signed manifest given to freshen with no
+// key to sign the rewritten one.
+var errSignKeyNeeded = errors.New("give --sign-key to keep it signed")
 
 // FreshenStatus contains progress information for the freshen operation.
 type FreshenStatus struct {
@@ -165,8 +175,7 @@ func (s *freshenScanner) walk(path string, info fs.FileInfo, walkErr error) erro
 	// Get relative path
 	relPath, err := filepath.Rel(s.absBase, path)
 	if err != nil {
-		return fmt.Errorf(
+		return err
-			"freshen: failed to compute relative path for %s: %w", path, err)
 	}
 
 	// Handle dotfiles
@@ -193,6 +202,13 @@ func (s *freshenScanner) walk(path string, info fs.FileInfo, walkErr error) erro
 		info = realInfo
 	}
 
+	// Opening a named pipe can block, and reading a device may never end.
+	if !info.Mode().IsRegular() {
+		log.Verbosef("skipping %s: not a regular file", relPath)
+
+		return nil
+	}
+
 	for _, excluded := range s.excluded {
 		if os.SameFile(info, excluded) {
 			return nil
@@ -280,13 +296,8 @@ func (h *freshenHasher) reportProgress(n int64) {
 // processEntry hashes the entry if needed and adds it to the builder.
 func (h *freshenHasher) processEntry(e *freshenEntry) error {
 	if !e.needsHash {
-		// Use existing entry
+		// Use existing entry; the error names the entry
-		err := addExistingToBuilder(h.builder, e.existing)
+		return addExistingToBuilder(h.builder, e.existing)
-		if err != nil {
-			return fmt.Errorf("failed to add %s: %w", e.path, err)
-		}
-
-		return nil
 	}
 
 	// Need to read and hash the file
@@ -294,26 +305,31 @@ func (h *freshenHasher) processEntry(e *freshenEntry) error {
 
 	f, err := h.fs.Open(absPath)
 	if err != nil {
-		return fmt.Errorf("failed to open %s: %w", e.path, err)
+		return err
 	}
 
 	hash, bytesRead, err := hashFile(f, h.reportProgress)
 	_ = f.Close()
 
 	if err != nil {
-		return fmt.Errorf("failed to hash %s: %w", e.path, err)
+		return err
+	}
+
+	// The scan recorded the size; a file that grew or shrank since would
+	// get an entry whose size and hash describe different contents.
+	if bytesRead != e.size {
+		return fmt.Errorf(
+			"%w for %q: %d bytes when scanned but %d bytes when read; "+
+				"the file changed while freshen ran",
+			errSizeMismatch, e.path, e.size, bytesRead,
+		)
 	}
 
 	h.hashedBytes += bytesRead
 	h.hashedFiles++
 
-	// Add to builder with computed hash
+	// Add to builder with computed hash; a refused path is named in the error
-	err = addFileToBuilder(h.builder, e.path, e.size, e.mtime, e.mode, hash)
+	return addFileToBuilder(h.builder, e.path, e.size, e.mtime, e.mode, hash)
-	if err != nil {
-		return fmt.Errorf("failed to add %s: %w", e.path, err)
-	}
-
-	return nil
 }
 
 // writeFreshenedManifest writes the manifest atomically (write to a
@@ -325,7 +341,7 @@ func writeFreshenedManifest(
 
 	outFile, err := afs.Create(tmpPath)
 	if err != nil {
-		return fmt.Errorf("failed to create temp file: %w", err)
+		return err
 	}
 
 	err = builder.Build(ctx, outFile)
@@ -334,7 +350,7 @@ func writeFreshenedManifest(
 	if err != nil {
 		_ = afs.Remove(tmpPath)
 
-		return fmt.Errorf("failed to write manifest: %w", err)
+		return fmt.Errorf("build manifest: %w", err)
 	}
 
 	// Rename temp to final
@@ -342,29 +358,46 @@ func writeFreshenedManifest(
 	if err != nil {
 		_ = afs.Remove(tmpPath)
 
-		return fmt.Errorf("failed to rename manifest: %w", err)
+		return err
 	}
 
 	return nil
 }
 
 // newFreshenBuilder constructs the manifest builder configured from CLI
-// flags.
+// flags, and returns the fingerprint of the --sign-key key, or "" when
-func newFreshenBuilder(cmd *cli.Command) *mfer.Builder {
+// none is given. A --sign-key given with an empty value is refused.
+func (mfa *CLIApp) newFreshenBuilder(
+	cmd *cli.Command,
+) (*mfer.Builder, string, error) {
 	builder := mfer.NewBuilder()
 	if cmd.Bool("include-timestamps") {
 		builder.SetIncludeTimestamps(true)
 	}
 
+	var signKeyFingerprint string
+
 	// Set up signing options if sign-key is provided
-	if signKey := cmd.String("sign-key"); signKey != "" {
+	if cmd.IsSet("sign-key") {
-		builder.SetSigningOptions(&mfer.SigningOptions{
+		signKey := cmd.String("sign-key")
-			KeyID: mfer.GPGKeyID(signKey),
+		if signKey == "" {
-		})
+			return nil, "", errEmptySignKey
-		log.Infof("signing manifest with GPG key: %s", signKey)
+		}
+
+		signing, err := mfa.signingOptions(signKey)
+		if err != nil {
+			return nil, "", err
+		}
+
+		signKeyFingerprint, err = mfer.SecretKeyFingerprint(signing.SecretKey)
+		if err != nil {
+			return nil, "", fmt.Errorf("%s: %w", signKey, err)
+		}
+
+		builder.SetSigningOptions(signing)
 	}
 
-	return builder
+	return builder, signKeyFingerprint, nil
 }
 
 // freshenScan runs the scan phase against the loaded manifest entries
@@ -390,6 +423,14 @@ func (mfa *CLIApp) freshenScan(
 		}
 	}
 
+	// The walk does not follow a symlink at its top, so a base directory
+	// named through one is resolved first. If that fails, the base is
+	// walked as named and the walk reports the problem.
+	resolved, err := filepath.EvalSymlinks(absBase)
+	if err == nil {
+		absBase = resolved
+	}
+
 	scanner := &freshenScanner{
 		fs:                 mfa.Fs,
 		absBase:            absBase,
@@ -401,14 +442,14 @@ func (mfa *CLIApp) freshenScan(
 		existingByPath:     existingByPath,
 	}
 
-	err := afero.Walk(mfa.Fs, absBase, scanner.walk)
+	err = afero.Walk(mfa.Fs, absBase, scanner.walk)
 
 	if showProgress {
 		log.ProgressDone()
 	}
 
 	if err != nil {
-		return nil, 0, fmt.Errorf("failed to scan filesystem: %w", err)
+		return nil, 0, fmt.Errorf("scan filesystem: %w", err)
 	}
 
 	// Remaining entries in existingByPath are removed files
@@ -444,7 +485,7 @@ func hashTotals(entries []*freshenEntry) (int64, int64) {
 }
 
 // runFreshenHash processes every entry through the hasher, aborting if
-// the context is canceled.
+// the context is canceled, and ends the hasher's progress line.
 func runFreshenHash(
 	ctx context.Context, hasher *freshenHasher, entries []*freshenEntry,
 ) error {
@@ -461,14 +502,26 @@ func runFreshenHash(
 		}
 	}
 
+	if hasher.showProgress && hasher.filesToHash > 0 {
+		log.ProgressDone()
+	}
+
 	return nil
 }
 
-// loadExistingEntries loads the manifest and indexes its file entries
+// existingManifest is what freshen uses of the manifest it rewrites.
-// by path.
+type existingManifest struct {
-func (mfa *CLIApp) loadExistingEntries(
+	entriesByPath map[string]*mfer.MFFilePath
-	manifestPath string,
+	signer        string // fingerprint of the key it is signed with, "" if unsigned
-) (map[string]*mfer.MFFilePath, error) {
+	hasCreatedAt  bool
+}
+
+// loadExistingManifest loads the manifest and indexes its file entries
+// by path. It refuses a signed manifest when no --sign-key is given, as
+// the rewritten manifest would be unsigned.
+func (mfa *CLIApp) loadExistingManifest(
+	cmd *cli.Command, manifestPath string,
+) (*existingManifest, error) {
 	log.Infof("loading manifest from %s", manifestPath)
 
 	// Load existing manifest
@@ -477,7 +530,11 @@ func (mfa *CLIApp) loadExistingEntries(
 		Fs:   mfa.Fs,
 	})
 	if err != nil {
-		return nil, fmt.Errorf("failed to load manifest: %w", err)
+		return nil, fmt.Errorf("load manifest: %w", err)
+	}
+
+	if signer := manifest.Signer(); signer != nil && cmd.String("sign-key") == "" {
+		return nil, fmt.Errorf("manifest is signed by %s: %w", signer, errSignKeyNeeded)
 	}
 
 	existingFiles := manifest.Files()
@@ -489,7 +546,11 @@ func (mfa *CLIApp) loadExistingEntries(
 		existingByPath[f.GetPath()] = f
 	}
 
-	return existingByPath, nil
+	return &existingManifest{
+		entriesByPath: existingByPath,
+		signer:        string(manifest.Signer()),
+		hasCreatedAt:  manifest.CreatedAt() != nil,
+	}, nil
 }
 
 func (mfa *CLIApp) freshenManifestOperation(
@@ -497,29 +558,30 @@ func (mfa *CLIApp) freshenManifestOperation(
 ) error {
 	log.Debug("freshenManifestOperation()")
 
-	basePath := cmd.String("base")
-	showProgress := cmd.Bool("progress")
-
 	// Find manifest file
 	manifestPath, err := mfa.resolveFreshenManifestPath(cmd)
-	if err != nil {
-		return fmt.Errorf("freshen: %w", err)
-	}
-
-	//nolint:contextcheck // mfer loads a manifest without a context
-	existingByPath, err := mfa.loadExistingEntries(manifestPath)
 	if err != nil {
 		return err
 	}
 
-	absBase, err := filepath.Abs(basePath)
+	builder, signKeyFingerprint, err := mfa.newFreshenBuilder(cmd)
 	if err != nil {
-		return fmt.Errorf("freshen: invalid base path: %w", err)
+		return err
+	}
+
+	existing, err := mfa.loadExistingManifest(cmd, manifestPath)
+	if err != nil {
+		return err
+	}
+
+	absBase, err := filepath.Abs(resolveBasePath(cmd, manifestPath))
+	if err != nil {
+		return fmt.Errorf("invalid base path: %w", err)
 	}
 
 	// Phase 1: Scan filesystem
 	scanner, removed, err := mfa.freshenScan(cmd, manifestPath, absBase,
-		existingByPath)
+		existing.entriesByPath)
 	if err != nil {
 		return err
 	}
@@ -536,11 +598,11 @@ func (mfa *CLIApp) freshenManifestOperation(
 	hasher := &freshenHasher{
 		fs:             mfa.Fs,
 		absBase:        absBase,
-		showProgress:   showProgress,
+		showProgress:   cmd.Bool("progress"),
 		totalHashBytes: totalHashBytes,
 		filesToHash:    filesToHash,
 		startHash:      time.Now(),
-		builder:        newFreshenBuilder(cmd),
+		builder:        builder,
 	}
 
 	err = runFreshenHash(ctx, hasher, scanner.entries)
@@ -548,16 +610,18 @@ func (mfa *CLIApp) freshenManifestOperation(
 		return err
 	}
 
-	if showProgress && filesToHash > 0 {
-		log.ProgressDone()
-	}
-
 	// Print summary
 	log.Infof("freshen complete: %d unchanged, %d changed, %d added, %d removed",
 		scanner.unchanged, scanner.changed, scanner.added, removed)
 
-	// Skip writing if nothing changed
+	// Skip writing only when the manifest would come out the same: nothing
-	if scanner.changed == 0 && scanner.added == 0 && removed == 0 {
+	// in the tree changed, and the manifest already holds what --sign-key,
+	// --include-timestamps and --include-permissions ask for. The scan
+	// counts a file whose recorded mode is not what --include-permissions
+	// asks for as changed.
+	if scanner.changed == 0 && scanner.added == 0 && removed == 0 &&
+		existing.signer == signKeyFingerprint &&
+		existing.hasCreatedAt == cmd.Bool("include-timestamps") {
 		log.Infof("manifest unchanged, skipping write")
 
 		return nil
@@ -606,9 +670,7 @@ func hashFile(r io.Reader, progress func(int64)) ([]byte, int64, error) {
 			break
 		}
 
-		// Returned unwrapped: the caller renders this as
+		// Returned unwrapped: a read error already names the file.
-		// "failed to hash <path>: <err>" and adding a second layer here
-		// would change that message.
 		if err != nil {
 			return nil, total, err
 		}
@@ -637,6 +699,8 @@ func addFileToBuilder(
 // Entries reach this path only when recordEntry classified them as
 // unchanged, which requires a recorded mtime, so an absent mtime here is
 // an error rather than something to paper over with the Unix epoch.
+// Loading refuses an entry with no hash; one that got here anyway is an
+// error too, not a file to leave out of the manifest.
 func addExistingToBuilder(b *mfer.Builder, entry *mfer.MFFilePath) error {
 	mtime, ok := entryMtime(entry)
 	if !ok {
@@ -644,7 +708,7 @@ func addExistingToBuilder(b *mfer.Builder, entry *mfer.MFFilePath) error {
 	}
 
 	if len(entry.GetHashes()) == 0 {
-		return nil
+		return fmt.Errorf("%w: %s", errEntryMissingHash, entry.GetPath())
 	}
 
 	err := b.AddFileWithHash(mfer.RelFilePath(entry.GetPath()),

internal/cli/freshen_test.go

@@ -7,6 +7,7 @@ import (
 	"os"
 	"path/filepath"
 	"slices"
+	"strings"
 	"testing"
 	"time"
 
@@ -69,6 +70,11 @@ func runFreshen(t *testing.T, fs afero.Fs, root, manifestPath string) {
 func manifestFiles(t *testing.T, fs afero.Fs, path string) []*mfer.MFFilePath {
 	t.Helper()
 
+	// Loading a manifest logs to the process-global logger, so serialize
+	// with the CLI runs.
+	runMu.Lock()
+	defer runMu.Unlock()
+
 	manifest, err := mfer.NewManifestFromFile(&mfer.ManifestFromFileOptions{
 		Path: path,
 		Fs:   fs,
@@ -78,6 +84,23 @@ func manifestFiles(t *testing.T, fs afero.Fs, path string) []*mfer.MFFilePath {
 	return manifest.Files()
 }
 
+// manifestCreatedAt returns the createdAt timestamp of the manifest at
+// path, or nil if it has none.
+func manifestCreatedAt(t *testing.T, fs afero.Fs, path string) *mfer.Timestamp {
+	t.Helper()
+
+	runMu.Lock()
+	defer runMu.Unlock()
+
+	manifest, err := mfer.NewManifestFromFile(&mfer.ManifestFromFileOptions{
+		Path: path,
+		Fs:   fs,
+	})
+	require.NoError(t, err)
+
+	return manifest.CreatedAt()
+}
+
 // TestFreshenUnchanged freshens a tree that has not changed since gen
 // made its manifest: the manifest must list the same entries as before.
 func TestFreshenUnchanged(t *testing.T) {
@@ -135,6 +158,41 @@ func TestFreshenRecordsModeOnlyWhenAsked(t *testing.T) {
 		recordedModes())
 }
 
+// TestFreshenIncludeTimestampsOnUnchangedTree runs freshen
+// --include-timestamps on a tree that has not changed since gen made its
+// manifest, which has no createdAt timestamp. freshen must rewrite the
+// manifest with one. Run again with the flag it must leave the manifest as
+// it is; run without it, it must rewrite the manifest without one.
+func TestFreshenIncludeTimestampsOnUnchangedTree(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewOsFs()
+	root, manifestPath := setupFreshenDir(t, fs, map[string]string{testFileTxt: "hello"})
+
+	freshenWithTimestamps := func() {
+		opts := testOpts([]string{
+			testApp, cmdFreshen, "-q", "--include-timestamps",
+			testFlagBase, root, manifestPath,
+		}, fs)
+		require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+	}
+
+	freshenWithTimestamps()
+	assert.NotNil(t, manifestCreatedAt(t, fs, manifestPath))
+
+	before, err := afero.ReadFile(fs, manifestPath)
+	require.NoError(t, err)
+
+	freshenWithTimestamps()
+
+	after, err := afero.ReadFile(fs, manifestPath)
+	require.NoError(t, err)
+	assert.Equal(t, before, after, "manifest that has a createdAt was rewritten")
+
+	runFreshen(t, fs, root, manifestPath)
+	assert.Nil(t, manifestCreatedAt(t, fs, manifestPath))
+}
+
 // assertManifestLists asserts that the manifest at manifestPath lists
 // exactly the files in want, each with the size and SHA-256 hash of its
 // content in want and the mtime of the file of that name under root.
@@ -242,6 +300,58 @@ func TestFreshenWithChanges(t *testing.T) {
 	}
 }
 
+// growingFileFs appends to one file each time it is opened, as a program
+// still writing to the file would between freshen's scan and its hash.
+type growingFileFs struct {
+	afero.Fs
+
+	path string
+}
+
+//nolint:ireturn // Open must return afero.File to satisfy afero.Fs.
+func (f growingFileFs) Open(name string) (afero.File, error) {
+	if name == f.path {
+		file, err := f.OpenFile(name, os.O_APPEND|os.O_WRONLY, 0)
+		if err != nil {
+			return nil, err
+		}
+
+		_, err = file.WriteString(" world")
+		_ = file.Close()
+
+		if err != nil {
+			return nil, err
+		}
+	}
+
+	return f.Fs.Open(name)
+}
+
+// TestFreshenFileChangedSinceScan has a new file grow after freshen's scan
+// recorded its size and before freshen hashes it: freshen must fail and
+// leave the manifest as it was.
+func TestFreshenFileChangedSinceScan(t *testing.T) {
+	t.Parallel()
+
+	osFs := afero.NewOsFs()
+	root, manifestPath := setupFreshenDir(t, osFs,
+		map[string]string{testFileTxt: "content"})
+	grown := filepath.Join(root, "log.txt")
+	writeTestFile(t, osFs, grown, "hello")
+
+	before, err := afero.ReadFile(osFs, manifestPath)
+	require.NoError(t, err)
+
+	opts := testOpts([]string{
+		testApp, cmdFreshen, "-q", testFlagBase, root, manifestPath,
+	}, growingFileFs{Fs: osFs, path: grown})
+	assert.Equal(t, 1, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	after, err := afero.ReadFile(osFs, manifestPath)
+	require.NoError(t, err)
+	assert.Equal(t, before, after, "manifest changed")
+}
+
 // TestFreshenLeavesManifestOutOfListing freshens a manifest kept in a
 // subdirectory of the tree it lists: the manifest is not listed, while an
 // ordinary file of the same name at the top of the tree is. The manifest
@@ -300,6 +410,84 @@ func TestFreshenLeavesLeftoverTempFileOutOfListing(t *testing.T) {
 		manifestPaths(t, fs, manifestPath))
 }
 
+// TestFreshenResolvesEntriesAgainstManifestDirectory adds sub/c.txt, then
+// runs freshen from the directory above sub, on the manifest in sub.
+// Without --base, the manifest then lists the files in sub, whether freshen
+// is given the manifest or sub. --base names the directory to list instead,
+// the current one included.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestFreshenResolvesEntriesAgainstManifestDirectory(t *testing.T) {
+	for _, tc := range []struct {
+		args []string
+		want []string // the paths the manifest lists afterwards
+	}{
+		{[]string{testSubdir}, []string{"b.txt", "c.txt"}},
+		{[]string{testSubdirManifest}, []string{"b.txt", "c.txt"}},
+		{
+			[]string{testFlagBase, ".", testSubdirManifest},
+			[]string{testFileTxt, "sub/b.txt", "sub/c.txt"},
+		},
+	} {
+		t.Run(strings.Join(tc.args, " "), func(t *testing.T) {
+			fs := afero.NewOsFs()
+			root := setupManifestInSubdir(t)
+			writeTestFile(t, fs, filepath.Join(root, testSubdir, "c.txt"), "added")
+
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdFreshen, "-q"}, tc.args,
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			assert.ElementsMatch(t, tc.want, manifestPaths(t, fs,
+				filepath.Join(root, testSubdirManifest)))
+		})
+	}
+}
+
+// TestFreshenDirectoryNamedThroughSymlink adds a file to a tree after gen
+// made its manifest, then freshens it with the tree named through a symlink,
+// given as the argument or as the working directory: the manifest lists the
+// files in the tree, and leaves out a symlink inside it, as freshen does
+// without --follow-symlinks.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestFreshenDirectoryNamedThroughSymlink(t *testing.T) {
+	// Paths are relative to a temp dir holding link, a symlink to the tree.
+	for name, tc := range map[string]struct {
+		workDir string
+		args    []string
+	}{
+		"argument":          {".", []string{testLink}},
+		"working directory": {testLink, nil},
+	} {
+		t.Run(name, func(t *testing.T) {
+			fs := afero.NewOsFs()
+			tree, manifestPath := setupFreshenDir(t, fs,
+				map[string]string{testFileTxt: "in the tree"})
+			writeTestFile(t, fs, filepath.Join(tree, "later.txt"), "added later")
+			require.NoError(t,
+				os.Symlink(testFileTxt, filepath.Join(tree, "alias.txt")))
+
+			root := t.TempDir()
+			require.NoError(t, os.Symlink(tree, filepath.Join(root, testLink)))
+
+			// t.Chdir sets PWD to the path it is given, as a shell does, and
+			// os.Getwd returns PWD when it names the working directory.
+			t.Chdir(filepath.Join(root, tc.workDir))
+
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdFreshen, "-q"}, tc.args,
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			assertManifestLists(t, fs, tree, manifestPath, map[string]string{
+				testFileTxt: "in the tree", "later.txt": "added later",
+			})
+		})
+	}
+}
+
 // TestFreshenRecordEntryMtimePresence pins the behavior of recordEntry
 // with respect to MFFilePath.Mtime, which is a message pointer with
 // proto3 field presence and may legitimately be absent.
@@ -357,7 +545,11 @@ func TestFreshenRecordEntryMtimePresence(t *testing.T) {
 			s := &freshenScanner{
 				existingByPath: map[string]*mfer.MFFilePath{relPath: tc.entry},
 			}
+
+			// recordEntry logs to the process-global logger.
+			runMu.Lock()
 			s.recordEntry(relPath, info)
+			runMu.Unlock()
 
 			require.Len(t, s.entries, 1)
 			assert.Equal(t, tc.needsHash, s.entries[0].needsHash)
@@ -392,6 +584,24 @@ func TestFreshenAddExistingRejectsMissingMtime(t *testing.T) {
 	assert.Contains(t, err.Error(), "file1.txt")
 }
 
+// TestFreshenAddExistingRejectsMissingHash pins that an entry with no hash
+// is an error rather than a file left out of the rebuilt manifest.
+func TestFreshenAddExistingRejectsMissingHash(t *testing.T) {
+	t.Parallel()
+
+	b := mfer.NewBuilder()
+	entry := &mfer.MFFilePath{
+		Path:  "data.bin",
+		Size:  8,
+		Mtime: &mfer.Timestamp{Seconds: 1_700_000_000},
+	}
+
+	err := addExistingToBuilder(b, entry)
+	require.ErrorIs(t, err, errEntryMissingHash)
+	assert.Contains(t, err.Error(), "data.bin")
+	assert.Zero(t, b.FileCount())
+}
+
 // TestFreshenAddExistingRejectsShortHash pins that an existing manifest
 // entry whose hash the builder refuses is reported as a problem with the
 // manifest, with the command that fixes it.

internal/cli/gen.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"io"
 	"os"
 	"os/signal"
 	"path/filepath"
@@ -26,6 +27,10 @@ var (
 	// rendered message stays exactly as mfer has always printed it.
 	errOutputExists = errors.New(
 		"already exists (use --force to overwrite)")
+	// errEmptyOutput indicates --output given with an empty value.
+	errEmptyOutput = errors.New("--output must not be empty")
+	// errEmptySignKey indicates --sign-key given with an empty value.
+	errEmptySignKey = errors.New("--sign-key must not be empty")
 )
 
 // reportEnumProgress renders enumeration progress until the channel
@@ -74,7 +79,7 @@ func (mfa *CLIApp) collectInputPaths(args cli.Args) ([]string, error) {
 
 		ap, err := filepath.Abs(inputPath)
 		if err != nil {
-			return nil, fmt.Errorf("generate: invalid path %q: %w", inputPath, err)
+			return nil, fmt.Errorf("invalid path %q: %w", inputPath, err)
 		}
 		// Validate path exists before adding to list
 		if exists, _ := afero.Exists(mfa.Fs, ap); !exists {
@@ -88,9 +93,41 @@ func (mfa *CLIApp) collectInputPaths(args cli.Args) ([]string, error) {
 	return paths, nil
 }
 
-// buildScannerOptions constructs scanner options from the CLI flags.
+// outputPath returns the file gen writes the manifest to: the one --output
-func (mfa *CLIApp) buildScannerOptions(cmd *cli.Command) *mfer.ScannerOptions {
+// names, or else index.mf in the directory the only argument names, or
-	output := cmd.String("output")
+// beside the file it names, or else in the current directory. An --output
+// given with an empty value is refused.
+func (mfa *CLIApp) outputPath(cmd *cli.Command) (string, error) {
+	if cmd.IsSet("output") {
+		output := cmd.String("output")
+		if output == "" {
+			return "", errEmptyOutput
+		}
+
+		return output, nil
+	}
+
+	if cmd.Args().Len() != 1 {
+		return defaultManifestName, nil
+	}
+
+	arg := cmd.Args().First()
+
+	// A path that does not exist is refused when it is enumerated.
+	info, err := mfa.Fs.Stat(arg)
+	if err == nil && !info.IsDir() {
+		return filepath.Join(filepath.Dir(arg), defaultManifestName), nil
+	}
+
+	return filepath.Join(arg, defaultManifestName), nil
+}
+
+// buildScannerOptions constructs scanner options from the CLI flags and
+// the path the manifest is written to. A --sign-key given with an empty
+// value is refused.
+func (mfa *CLIApp) buildScannerOptions(
+	cmd *cli.Command, output string,
+) (*mfer.ScannerOptions, error) {
 	opts := &mfer.ScannerOptions{
 		IncludeDotfiles:    cmd.Bool("include-dotfiles"),
 		FollowSymLinks:     cmd.Bool("follow-symlinks"),
@@ -110,14 +147,21 @@ func (mfa *CLIApp) buildScannerOptions(cmd *cli.Command) *mfer.ScannerOptions {
 	}
 
 	// Set up signing options if sign-key is provided
-	if signKey := cmd.String("sign-key"); signKey != "" {
+	if cmd.IsSet("sign-key") {
-		opts.SigningOptions = &mfer.SigningOptions{
+		signKey := cmd.String("sign-key")
-			KeyID: mfer.GPGKeyID(signKey),
+		if signKey == "" {
+			return nil, errEmptySignKey
 		}
-		log.Infof("signing manifest with GPG key: %s", signKey)
+
+		signing, err := mfa.signingOptions(signKey)
+		if err != nil {
+			return nil, err
+		}
+
+		opts.SigningOptions = signing
 	}
 
-	return opts
+	return opts, nil
 }
 
 // enumerateInputs runs the enumeration phase over the argument paths,
@@ -129,8 +173,7 @@ func (mfa *CLIApp) enumerateInputs(
 		// Default to current directory
 		err := s.EnumeratePath(".", enumProgress)
 		if err != nil {
-			return fmt.Errorf(
+			return fmt.Errorf("enumerate current directory: %w", err)
-				"generate: failed to enumerate current directory: %w", err)
 		}
 
 		return nil
@@ -144,7 +187,7 @@ func (mfa *CLIApp) enumerateInputs(
 
 	err = s.EnumeratePaths(enumProgress, paths...)
 	if err != nil {
-		return fmt.Errorf("generate: failed to enumerate paths: %w", err)
+		return fmt.Errorf("enumerate files: %w", err)
 	}
 
 	return nil
@@ -203,23 +246,59 @@ func (mfa *CLIApp) runEnumeratePhase(cmd *cli.Command, s *mfer.Scanner) error {
 	return nil
 }
 
+// runScanPhase reads the enumerated files and writes the manifest to out,
+// with optional progress reporting.
+func (mfa *CLIApp) runScanPhase(
+	ctx context.Context, cmd *cli.Command, s *mfer.Scanner, out io.Writer,
+) error {
+	var (
+		scanProgress chan mfer.ScanStatus
+		scanWg       sync.WaitGroup
+	)
+
+	if cmd.Bool("progress") {
+		scanProgress = make(chan mfer.ScanStatus, 1)
+
+		scanWg.Add(1)
+
+		go reportScanProgress(scanProgress, &scanWg)
+	}
+
+	err := s.ToManifest(ctx, out, scanProgress)
+
+	scanWg.Wait()
+
+	if err != nil {
+		return fmt.Errorf("generate manifest: %w", err)
+	}
+
+	return nil
+}
+
 func (mfa *CLIApp) generateManifestOperation(
 	ctx context.Context, cmd *cli.Command,
 ) error {
 	log.Debug("generateManifestOperation()")
 
-	s := mfer.NewScannerWithOptions(mfa.buildScannerOptions(cmd))
+	outputPath, err := mfa.outputPath(cmd)
-
-	// Phase 1: Enumeration - collect paths and stat files
-	err := mfa.runEnumeratePhase(cmd, s)
 	if err != nil {
 		return err
 	}
 
-	showProgress := cmd.Bool("progress")
+	opts, err := mfa.buildScannerOptions(cmd, outputPath)
+	if err != nil {
+		return err
+	}
+
+	s := mfer.NewScannerWithOptions(opts)
+
+	// Phase 1: Enumeration - collect paths and stat files
+	err = mfa.runEnumeratePhase(cmd, s)
+	if err != nil {
+		return err
+	}
 
 	// Check if output file exists
-	outputPath := cmd.String("output")
 	if exists, _ := afero.Exists(mfa.Fs, outputPath); exists && !cmd.Bool("force") {
 		return fmt.Errorf("output file %s %w", outputPath, errOutputExists)
 	}
@@ -229,7 +308,7 @@ func (mfa *CLIApp) generateManifestOperation(
 
 	outFile, err := mfa.Fs.Create(tmpPath)
 	if err != nil {
-		return fmt.Errorf("failed to create temp file: %w", err)
+		return err
 	}
 
 	// Set up signal handler to clean up temp file on Ctrl-C
@@ -250,37 +329,21 @@ func (mfa *CLIApp) generateManifestOperation(
 	}()
 
 	// Phase 2: Scan - read file contents and generate manifest
-	var (
+	err = mfa.runScanPhase(ctx, cmd, s, outFile)
-		scanProgress chan mfer.ScanStatus
-		scanWg       sync.WaitGroup
-	)
-
-	if showProgress {
-		scanProgress = make(chan mfer.ScanStatus, 1)
-
-		scanWg.Add(1)
-
-		go reportScanProgress(scanProgress, &scanWg)
-	}
-
-	err = s.ToManifest(ctx, outFile, scanProgress)
-
-	scanWg.Wait()
-
 	if err != nil {
-		return fmt.Errorf("failed to generate manifest: %w", err)
+		return err
 	}
 
 	// Close file before rename to ensure all data is flushed
 	err = outFile.Close()
 	if err != nil {
-		return fmt.Errorf("failed to close temp file: %w", err)
+		return err
 	}
 
 	// Atomic rename
 	err = mfa.Fs.Rename(tmpPath, outputPath)
 	if err != nil {
-		return fmt.Errorf("failed to rename temp file: %w", err)
+		return err
 	}
 
 	success = true

internal/cli/list.go

@@ -19,20 +19,19 @@ func (mfa *CLIApp) listManifestOperation(ctx context.Context, cmd *cli.Command)
 
 	pathOrURL, err := mfa.resolveManifestArg(cmd)
 	if err != nil {
-		return fmt.Errorf("list: %w", err)
+		return err
 	}
 
 	rc, err := mfa.openManifestReader(ctx, pathOrURL)
 	if err != nil {
-		return fmt.Errorf("list: %w", err)
+		return err
 	}
 
 	defer func() { _ = rc.Close() }()
 
-	//nolint:contextcheck // mfer loads a manifest without a context
 	manifest, err := mfer.NewManifestFromReader(rc)
 	if err != nil {
-		return fmt.Errorf("list: failed to parse manifest: %w", err)
+		return fmt.Errorf("parse manifest: %w", err)
 	}
 
 	files := manifest.Files()

internal/cli/manifest_loader.go

@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"io"
 	"net/http"
+	"path/filepath"
 	"strings"
 	"time"
 
@@ -15,17 +16,13 @@ import (
 // manifestFetchTimeout bounds HTTP requests made to fetch a manifest.
 const manifestFetchTimeout = 30 * time.Second
 
-// errHTTPStatus indicates an HTTP response with a non-OK status code.
+// errHTTPStatus indicates an HTTP response with a non-OK status code. It is
-//
+// followed by the code, as in "unexpected HTTP status 404".
-// Its text is the literal "HTTP" prefix of the rendered "HTTP <code>"
+var errHTTPStatus = errors.New("unexpected HTTP status")
-// message that mfer has always printed, so that wrapping it does not
-// change any user-visible output. Match it with errors.Is; do not read
-// its message.
-var errHTTPStatus = errors.New("HTTP")
 
 // errManifestTooLarge indicates a manifest download that passed
 // CLIApp.maxManifestSize.
-var errManifestTooLarge = errors.New("manifest exceeds maximum allowed size")
+var errManifestTooLarge = errors.New("file exceeds maximum allowed size")
 
 // isHTTPURL returns true if the string starts with http:// or https://.
 func isHTTPURL(s string) bool {
@@ -40,20 +37,22 @@ func (mfa *CLIApp) openManifestReader(
 	if isHTTPURL(pathOrURL) {
 		client := &http.Client{Timeout: manifestFetchTimeout}
 
+		// The *url.Error that NewRequestWithContext and Do return names
+		// the URL.
 		req, err := http.NewRequestWithContext(ctx, http.MethodGet, pathOrURL, nil)
 		if err != nil {
-			return nil, fmt.Errorf("failed to fetch %s: %w", pathOrURL, err)
+			return nil, fmt.Errorf("download manifest: %w", err)
 		}
 
 		resp, err := client.Do(req)
 		if err != nil {
-			return nil, fmt.Errorf("failed to fetch %s: %w", pathOrURL, err)
+			return nil, fmt.Errorf("download manifest: %w", err)
 		}
 
 		if resp.StatusCode != http.StatusOK {
 			_ = resp.Body.Close()
 
-			return nil, fmt.Errorf("failed to fetch %s: %w %d",
+			return nil, fmt.Errorf("download manifest %s: %w %d",
 				pathOrURL, errHTTPStatus, resp.StatusCode)
 		}
 
@@ -88,3 +87,17 @@ func (mfa *CLIApp) resolveManifestArg(cmd *cli.Command) (string, error) {
 
 	return findManifest(mfa.Fs, ".")
 }
+
+// resolveBasePath returns the directory a manifest's paths are resolved
+// against: the one --base names, or else the directory holding the manifest,
+// or the current directory for a manifest URL.
+func resolveBasePath(cmd *cli.Command, manifestPath string) string {
+	switch {
+	case cmd.IsSet(flagBase):
+		return cmd.String(flagBase)
+	case isHTTPURL(manifestPath):
+		return "."
+	default:
+		return filepath.Dir(manifestPath)
+	}
+}

internal/cli/mfer.go

@@ -6,12 +6,12 @@ import (
 	"fmt"
 	"io"
 	"os"
+	"runtime/debug"
 	"time"
 
 	"github.com/spf13/afero"
 	"github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/internal/log"
-	"sneak.berlin/go/mfer/mfer"
 )
 
 // Command and flag names shared across command definitions and tests.
@@ -24,6 +24,7 @@ const (
 	cmdList     = "list"
 	cmdVersion  = "version"
 
+	flagBase               = "base"
 	flagProgress           = "progress"
 	flagTimeout            = "timeout"
 	flagDest               = "dest"
@@ -47,13 +48,16 @@ func manifestTempPath(out string) string {
 // errUnknownCommand indicates an unrecognized command argument.
 var errUnknownCommand = errors.New("unknown command")
 
+// errUnexpectedArgument indicates a second argument to a command that takes
+// one.
+var errUnexpectedArgument = errors.New("unexpected argument")
+
 // CLIApp is the main CLI application container. It holds configuration,
 // I/O streams, and filesystem abstraction to enable testing and flexibility.
 //
 //nolint:revive // established name used throughout the codebase and tests
 type CLIApp struct {
 	appname     string
-	version     string
 	gitrev      string
 	startupTime time.Time
 	exitCode    int
@@ -82,13 +86,26 @@ const banner = `
    \  \:\        \  \:\      \  \::/       \  \:\
     \__\/         \__\/       \__\/         \__\/`
 
-// VersionString returns the version and git revision formatted for display.
+// VersionString returns the version mfer reports: the revision the build
+// stamped into main.Gitrev or, when it stamped none, as with `go install`,
+// the main module's version from the binary's build information.
 func (mfa *CLIApp) VersionString() string {
 	if mfa.gitrev != "" {
-		return fmt.Sprintf("%s (%s)", mfer.Version, mfa.gitrev)
+		return mfa.gitrev
 	}
 
-	return mfer.Version
+	return moduleVersion(debug.ReadBuildInfo())
+}
+
+// moduleVersion returns the main module's version from the binary's build
+// information, or "unknown" when the binary has none or it holds no version,
+// as in a build with GO111MODULE=off.
+func moduleVersion(info *debug.BuildInfo, ok bool) string {
+	if !ok || info.Main.Version == "" {
+		return "unknown"
+	}
+
+	return info.Main.Version
 }
 
 // printVersion writes the version line shared by the --version flag and the
@@ -101,8 +118,7 @@ func (mfa *CLIApp) printBanner() {
 	if log.GetLevel() <= log.InfoLevel {
 		_, _ = fmt.Fprintln(mfa.Stdout, banner)
 		_, _ = fmt.Fprintf(mfa.Stdout,
-			"        mfer by @sneak: v%s released %s\n",
+			"        mfer by @sneak: %s\n", mfa.VersionString())
-			mfer.Version, mfer.ReleaseDate)
 		_, _ = fmt.Fprintln(mfa.Stdout, "            https://sneak.berlin/go/mfer")
 	}
 }
@@ -153,13 +169,25 @@ func commonFlags() []cli.Flag {
 	}
 }
 
-// stopOnFirstArg returns the StopOnNthArg setting every command uses: flags
+// refuseExtraArgs is the ArgValidator of the commands that take one
-// are read only before the command's first argument, and everything after it
+// argument: it refuses a second one, naming it.
-// is an argument, as with urfave/cli v2. So `mfer gen d -v` names a path "-v".
+func refuseExtraArgs(_ context.Context, cmd *cli.Command) error {
-func stopOnFirstArg() *int {
+	if cmd.Args().Len() > 1 {
-	n := 1
+		return fmt.Errorf("%w %q", errUnexpectedArgument, cmd.Args().Get(1))
+	}
 
-	return &n
+	return nil
+}
+
+// showCommandHelp is the CommandNotFound of the commands that take a path or
+// URL. Those commands set HideHelpCommand, so that a path or URL named help or
+// h is an argument rather than urfave/cli's help command; each sets it itself,
+// because on the root it would also remove `mfer help`. With --help,
+// urfave/cli looks the command's first argument up as a help topic, so
+// `check DIR --help` asks for a topic DIR and finds none; this prints the
+// command's own help instead, as `check --help` does.
+func showCommandHelp(ctx context.Context, cmd *cli.Command, _ string) {
+	_ = cli.ShowCommandHelp(ctx, cmd.Root(), cmd.Name)
 }
 
 // requireSignatureFlag returns the --require-signature flag taken by the
@@ -168,7 +196,7 @@ func requireSignatureFlag() *cli.StringFlag {
 	return &cli.StringFlag{
 		Name:    flagRequireSignature,
 		Aliases: []string{"S"},
-		Usage:   "Require manifest to be signed by the specified GPG key ID",
+		Usage:   "Require manifest to be signed by the OpenPGP key with this fingerprint",
 		Sources: cli.EnvVars("MFER_REQUIRE_SIGNATURE"),
 	}
 }
@@ -185,11 +213,12 @@ func includePermissionsFlag() *cli.BoolFlag {
 
 func (mfa *CLIApp) generateCommand() *cli.Command {
 	return &cli.Command{
-		Name:         cmdGenerate,
+		Name:            cmdGenerate,
-		Aliases:      []string{"gen"},
+		Aliases:         []string{"gen"},
-		Usage:        "Generate manifest file",
+		Usage:           "Generate manifest file",
-		ArgsUsage:    "[path ...]",
+		ArgsUsage:       "[path ...]",
-		StopOnNthArg: stopOnFirstArg(),
+		HideHelpCommand: true,
+		CommandNotFound: showCommandHelp,
 		Action: func(ctx context.Context, cmd *cli.Command) error {
 			mfa.setVerbosity(cmd)
 			mfa.printBanner()
@@ -210,9 +239,10 @@ func (mfa *CLIApp) generateCommand() *cli.Command {
 			},
 			&cli.StringFlag{
 				Name:    "output",
-				Value:   defaultManifestName,
 				Aliases: []string{"o"},
-				Usage:   "Specify output filename",
+				Usage: "File to write the manifest to (default: index.mf in " +
+					"the directory given, or beside the file given; with no " +
+					"path or several, index.mf in the current directory)",
 			},
 			&cli.BoolFlag{
 				Name:    "force",
@@ -227,7 +257,7 @@ func (mfa *CLIApp) generateCommand() *cli.Command {
 			&cli.StringFlag{
 				Name:    "sign-key",
 				Aliases: []string{"s"},
-				Usage:   "GPG key ID to sign the manifest with",
+				Usage:   "OpenPGP secret key file to sign the manifest with",
 				Sources: cli.EnvVars("MFER_SIGN_KEY"),
 			},
 			&cli.StringFlag{
@@ -247,10 +277,12 @@ func (mfa *CLIApp) generateCommand() *cli.Command {
 
 func (mfa *CLIApp) checkCommand() *cli.Command {
 	return &cli.Command{
-		Name:         cmdCheck,
+		Name:            cmdCheck,
-		Usage:        "Validate files using manifest file",
+		Usage:           "Validate files using manifest file",
-		ArgsUsage:    manifestArgsUsage,
+		ArgsUsage:       manifestArgsUsage,
-		StopOnNthArg: stopOnFirstArg(),
+		ArgValidator:    refuseExtraArgs,
+		HideHelpCommand: true,
+		CommandNotFound: showCommandHelp,
 		Action: func(ctx context.Context, cmd *cli.Command) error {
 			mfa.setVerbosity(cmd)
 			mfa.printBanner()
@@ -259,10 +291,11 @@ func (mfa *CLIApp) checkCommand() *cli.Command {
 		},
 		Flags: append(commonFlags(),
 			&cli.StringFlag{
-				Name:    "base",
+				Name:    flagBase,
 				Aliases: []string{"b"},
-				Value:   ".",
+				Usage: "Base directory for resolving relative paths from manifest " +
-				Usage:   "Base directory for resolving relative paths from manifest",
+					"(by default the directory holding the manifest, or the " +
+					"current directory for a manifest URL)",
 			},
 			&cli.BoolFlag{
 				Name:    flagProgress,
@@ -280,10 +313,12 @@ func (mfa *CLIApp) checkCommand() *cli.Command {
 
 func (mfa *CLIApp) freshenCommand() *cli.Command {
 	return &cli.Command{
-		Name:         cmdFreshen,
+		Name:            cmdFreshen,
-		Usage:        "Update manifest with changed, new, and removed files",
+		Usage:           "Update manifest with changed, new, and removed files",
-		ArgsUsage:    manifestArgsUsage,
+		ArgsUsage:       manifestArgsUsage,
-		StopOnNthArg: stopOnFirstArg(),
+		ArgValidator:    refuseExtraArgs,
+		HideHelpCommand: true,
+		CommandNotFound: showCommandHelp,
 		Action: func(ctx context.Context, cmd *cli.Command) error {
 			mfa.setVerbosity(cmd)
 			mfa.printBanner()
@@ -292,10 +327,10 @@ func (mfa *CLIApp) freshenCommand() *cli.Command {
 		},
 		Flags: append(commonFlags(),
 			&cli.StringFlag{
-				Name:    "base",
+				Name:    flagBase,
 				Aliases: []string{"b"},
-				Value:   ".",
+				Usage: "Base directory for resolving relative paths " +
-				Usage:   "Base directory for resolving relative paths",
+					"(by default the directory holding the manifest)",
 			},
 			&cli.BoolFlag{
 				Name:    "follow-symlinks",
@@ -316,7 +351,7 @@ func (mfa *CLIApp) freshenCommand() *cli.Command {
 			&cli.StringFlag{
 				Name:    "sign-key",
 				Aliases: []string{"s"},
-				Usage:   "GPG key ID to sign the manifest with",
+				Usage:   "OpenPGP secret key file to sign the manifest with",
 				Sources: cli.EnvVars("MFER_SIGN_KEY"),
 			},
 			&cli.BoolFlag{
@@ -331,10 +366,12 @@ func (mfa *CLIApp) freshenCommand() *cli.Command {
 
 func (mfa *CLIApp) exportCommand() *cli.Command {
 	return &cli.Command{
-		Name:         cmdExport,
+		Name:            cmdExport,
-		Usage:        "Export manifest contents as JSON",
+		Usage:           "Export manifest contents as JSON",
-		ArgsUsage:    "[manifest file or URL]",
+		ArgsUsage:       "[manifest file or URL]",
-		StopOnNthArg: stopOnFirstArg(),
+		ArgValidator:    refuseExtraArgs,
+		HideHelpCommand: true,
+		CommandNotFound: showCommandHelp,
 		Action: func(ctx context.Context, cmd *cli.Command) error {
 			mfa.setVerbosity(cmd)
 
@@ -345,9 +382,8 @@ func (mfa *CLIApp) exportCommand() *cli.Command {
 
 func (mfa *CLIApp) versionCommand() *cli.Command {
 	return &cli.Command{
-		Name:         cmdVersion,
+		Name:  cmdVersion,
-		Usage:        "Show version",
+		Usage: "Show version",
-		StopOnNthArg: stopOnFirstArg(),
 		Action: func(context.Context, *cli.Command) error {
 			mfa.printVersion()
 
@@ -358,12 +394,14 @@ func (mfa *CLIApp) versionCommand() *cli.Command {
 
 func (mfa *CLIApp) listCommand() *cli.Command {
 	return &cli.Command{
-		Name:         cmdList,
+		Name:            cmdList,
-		Aliases:      []string{"ls"},
+		Aliases:         []string{"ls"},
-		Usage:        "List files in manifest",
+		Usage:           "List files in manifest",
-		ArgsUsage:    manifestArgsUsage,
+		ArgsUsage:       manifestArgsUsage,
-		StopOnNthArg: stopOnFirstArg(),
+		ArgValidator:    refuseExtraArgs,
-		Action:       mfa.listManifestOperation,
+		HideHelpCommand: true,
+		CommandNotFound: showCommandHelp,
+		Action:          mfa.listManifestOperation,
 		Flags: []cli.Flag{
 			&cli.BoolFlag{
 				Name:    "long",
@@ -380,10 +418,12 @@ func (mfa *CLIApp) listCommand() *cli.Command {
 
 func (mfa *CLIApp) fetchCommand() *cli.Command {
 	return &cli.Command{
-		Name:         cmdFetch,
+		Name:            cmdFetch,
-		Usage:        "fetch manifest and referenced files",
+		Usage:           "fetch manifest and referenced files",
-		ArgsUsage:    "URL",
+		ArgsUsage:       "URL",
-		StopOnNthArg: stopOnFirstArg(),
+		ArgValidator:    refuseExtraArgs,
+		HideHelpCommand: true,
+		CommandNotFound: showCommandHelp,
 		Action: func(ctx context.Context, cmd *cli.Command) error {
 			mfa.setVerbosity(cmd)
 			mfa.printBanner()
@@ -442,9 +482,8 @@ func (mfa *CLIApp) run(args []string) {
 		Writer:                mfa.Stdout,
 		// v3 writes its "Incorrect Usage" line to ErrWriter; v2 wrote it to
 		// stdout, before the help, so it stays on stdout.
-		ErrWriter:    mfa.Stdout,
+		ErrWriter: mfa.Stdout,
-		Flags:        commonFlags(),
+		Flags:     commonFlags(),
-		StopOnNthArg: stopOnFirstArg(),
 		Action: func(_ context.Context, cmd *cli.Command) error {
 			if cmd.Args().Len() > 0 {
 				return fmt.Errorf("%w %q", errUnknownCommand, cmd.Args().First())

internal/cli/pipe_test.go

@@ -0,0 +1,94 @@
+//go:build unix
+
+//nolint:testpackage // white-box tests exercise unexported internals
+package cli
+
+import (
+	"os"
+	"path/filepath"
+	"syscall"
+	"testing"
+	"time"
+
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+const (
+	// testPipe is the name of the named pipe the pipe tests make in a tree.
+	testPipe = "pipe"
+
+	// pipeDeadline is how long a test lets a run go before it opens the
+	// test's named pipes for writing.
+	pipeDeadline = 5 * time.Second
+)
+
+// makePipe makes a named pipe at path. Opening a named pipe for reading
+// blocks until it is opened for writing, so once pipeDeadline has passed,
+// unless the test has ended, makePipe opens it for writing and closes it
+// again. A run that wrongly reads the pipe then ends, and the test fails on
+// what it reports instead of hanging. That lets one read through, so each
+// path a wrong run would read gets a pipe of its own.
+func makePipe(t *testing.T, path string) {
+	t.Helper()
+
+	require.NoError(t, syscall.Mkfifo(path, 0o600))
+
+	timer := time.AfterFunc(pipeDeadline, func() {
+		f, err := os.OpenFile(path, os.O_WRONLY, 0) //nolint:gosec // test-controlled path
+		if err == nil {
+			_ = f.Close()
+		}
+	})
+
+	t.Cleanup(func() { timer.Stop() })
+}
+
+// TestGenerateSkipsPipe runs gen -v on a tree holding a named pipe: the
+// manifest lists the regular file only, and gen names the pipe it skipped.
+func TestGenerateSkipsPipe(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	fs := afero.NewOsFs()
+	writeTestFile(t, fs, filepath.Join(dir, testFileTxt), "regular")
+	makePipe(t, filepath.Join(dir, testPipe))
+
+	opts := testOpts([]string{testApp, cmdGenerate, "-v", dir}, fs)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	assert.Equal(t, []string{testFileTxt},
+		manifestPaths(t, fs, filepath.Join(dir, defaultManifestName)))
+	assert.Contains(t, testStderr(t, opts), "skipping pipe: not a regular file")
+}
+
+// TestFreshenSkipsPipes adds a named pipe to a tree after gen made its
+// manifest, and a symlink to another pipe. freshen -v --follow-symlinks
+// leaves the manifest listing the regular file only, and names both entries
+// it skipped.
+func TestFreshenSkipsPipes(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewOsFs()
+	root, manifestPath := setupFreshenDir(t, fs,
+		map[string]string{testFileTxt: "regular"})
+	makePipe(t, filepath.Join(root, testPipe))
+
+	// The symlink points outside the tree, so no pipe is read twice.
+	target := filepath.Join(t.TempDir(), testPipe)
+	makePipe(t, target)
+	require.NoError(t, os.Symlink(target, filepath.Join(root, testLink)))
+
+	opts := testOpts([]string{
+		testApp, cmdFreshen, "-v", "--follow-symlinks",
+		testFlagBase, root, manifestPath,
+	}, fs)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	assert.Equal(t, []string{testFileTxt}, manifestPaths(t, fs, manifestPath))
+
+	stderr := testStderr(t, opts)
+	assert.Contains(t, stderr, "skipping pipe: not a regular file")
+	assert.Contains(t, stderr, "skipping link: not a regular file")
+}

internal/cli/signing.go

@@ -0,0 +1,86 @@
+package cli
+
+import (
+	"errors"
+	"fmt"
+	"os"
+
+	"github.com/spf13/afero"
+	"golang.org/x/term"
+	"sneak.berlin/go/mfer/internal/log"
+	"sneak.berlin/go/mfer/mfer"
+)
+
+// envSignKeyPassphrase names the environment variable holding the
+// passphrase of a protected signing key.
+//
+//nolint:gosec // G101: the name of a variable, not a credential
+const envSignKeyPassphrase = "MFER_SIGN_KEY_PASSPHRASE"
+
+// errNoPassphrase indicates a protected signing key whose passphrase is
+// neither in the environment nor can be asked for on a terminal.
+var errNoPassphrase = errors.New(
+	"signing key is protected: set " + envSignKeyPassphrase + " to its passphrase")
+
+// signingOptions returns the signing options for the OpenPGP secret key in
+// the file path, which must be able to sign. The passphrase of a protected
+// key comes from MFER_SIGN_KEY_PASSPHRASE, or else from the terminal on
+// stdin, and must unlock the key.
+func (mfa *CLIApp) signingOptions(path string) (*mfer.SigningOptions, error) {
+	secretKey, err := afero.ReadFile(mfa.Fs, path)
+	if err != nil {
+		return nil, fmt.Errorf("read signing key: %w", err)
+	}
+
+	protected, err := mfer.SecretKeyIsProtected(secretKey)
+	if err != nil {
+		return nil, fmt.Errorf("%s: %w", path, err)
+	}
+
+	log.Infof("signing manifest with the OpenPGP key in %s", path)
+
+	opts := &mfer.SigningOptions{SecretKey: secretKey}
+	if protected {
+		opts.Passphrase, err = mfa.readPassphrase(path)
+		if err != nil {
+			return nil, err
+		}
+	}
+
+	// gen and freshen read the signing options before any file, so a key
+	// that cannot sign, or a wrong passphrase, stops them before they hash
+	// anything.
+	err = mfer.CheckSigningKey(opts)
+	if err != nil {
+		return nil, fmt.Errorf("%s: %w", path, err)
+	}
+
+	return opts, nil
+}
+
+// readPassphrase returns MFER_SIGN_KEY_PASSPHRASE when it is set, or else
+// asks for the passphrase of the key in the file path on the terminal on
+// stdin.
+func (mfa *CLIApp) readPassphrase(path string) ([]byte, error) {
+	passphrase := os.Getenv(envSignKeyPassphrase)
+	if passphrase != "" {
+		return []byte(passphrase), nil
+	}
+
+	stdin, ok := mfa.Stdin.(*os.File)
+	if !ok || !term.IsTerminal(int(stdin.Fd())) {
+		return nil, errNoPassphrase
+	}
+
+	_, _ = fmt.Fprintf(mfa.Stderr, "Passphrase for %s: ", path)
+
+	typed, err := term.ReadPassword(int(stdin.Fd()))
+
+	_, _ = fmt.Fprintln(mfa.Stderr)
+
+	if err != nil {
+		return nil, fmt.Errorf("read passphrase: %w", err)
+	}
+
+	return typed, nil
+}

internal/cli/signing_test.go

@@ -0,0 +1,412 @@
+//nolint:testpackage // white-box tests exercise unexported internals
+package cli
+
+import (
+	"bufio"
+	"io"
+	"net/http"
+	"net/http/httptest"
+	"path/filepath"
+	"slices"
+	"strings"
+	"sync/atomic"
+	"testing"
+	"time"
+
+	"github.com/ProtonMail/go-crypto/openpgp/packet"
+	"github.com/creack/pty"
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+const (
+	testFlagSignKey = "--sign-key"
+	testKeyFile     = "/key.asc"
+)
+
+// TestGenAndFreshenSignWithKeyFile runs gen, then freshen after a file is
+// added, with --sign-key naming a key file: one key with no passphrase and
+// one protected by the passphrase in MFER_SIGN_KEY_PASSPHRASE. check
+// --require-signature must accept each manifest as signed by that key.
+// freshen leaves its manifest out of the listing only on the real
+// filesystem, so the test uses that.
+func TestGenAndFreshenSignWithKeyFile(t *testing.T) {
+	for name, passphrase := range map[string][]byte{
+		"unprotected": nil,
+		"protected":   []byte("passphrase"),
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Setenv(envSignKeyPassphrase, string(passphrase))
+
+			secretKey, fingerprint := testSecretKey(t, passphrase, nil)
+
+			fs := afero.NewOsFs()
+			keyFile := filepath.Join(t.TempDir(), "key.asc")
+			root := t.TempDir()
+			manifestPath := filepath.Join(root, defaultManifestName)
+
+			require.NoError(t, afero.WriteFile(fs, keyFile, secretKey, 0o600))
+			writeTestFile(t, fs, filepath.Join(root, testFileTxt), "hello")
+
+			opts := testOpts([]string{
+				testApp, cmdGenerate, "-q", testFlagSignKey, keyFile,
+				"-o", manifestPath, root,
+			}, fs)
+			require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+			check := []string{
+				testApp, cmdCheck, "-q",
+				"--" + flagRequireSignature, fingerprint, manifestPath,
+			}
+
+			opts = testOpts(check, fs)
+			require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+			writeTestFile(t, fs, filepath.Join(root, "added.txt"), "added")
+
+			opts = testOpts([]string{
+				testApp, cmdFreshen, "-q", testFlagSignKey, keyFile, manifestPath,
+			}, fs)
+			require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+			opts = testOpts(check, fs)
+			require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+			assert.Len(t, manifestFiles(t, fs, manifestPath), 2)
+		})
+	}
+}
+
+// TestFreshenSignedManifestNeedsSignKey runs freshen on a signed manifest
+// after a file is added. Without --sign-key it must fail, naming the
+// signer and --sign-key, and leave the manifest as it was; with --sign-key
+// it must rewrite the manifest, signed.
+func TestFreshenSignedManifestNeedsSignKey(t *testing.T) {
+	t.Setenv(envSignKeyPassphrase, "")
+
+	secretKey, fingerprint := testSecretKey(t, nil, nil)
+
+	fs := afero.NewOsFs()
+	keyFile := filepath.Join(t.TempDir(), "key.asc")
+	root := t.TempDir()
+	manifestPath := filepath.Join(root, defaultManifestName)
+
+	require.NoError(t, afero.WriteFile(fs, keyFile, secretKey, 0o600))
+	writeTestFile(t, fs, filepath.Join(root, testFileTxt), "hello")
+
+	opts := testOpts([]string{
+		testApp, cmdGenerate, "-q", testFlagSignKey, keyFile,
+		"-o", manifestPath, root,
+	}, fs)
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+	before, err := afero.ReadFile(fs, manifestPath)
+	require.NoError(t, err)
+
+	writeTestFile(t, fs, filepath.Join(root, "added.txt"), "added")
+
+	opts = testOpts([]string{testApp, cmdFreshen, "-q", manifestPath}, fs)
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts), fingerprint)
+	assert.Contains(t, testStderr(t, opts), testFlagSignKey)
+
+	after, err := afero.ReadFile(fs, manifestPath)
+	require.NoError(t, err)
+	assert.Equal(t, before, after)
+
+	opts = testOpts([]string{
+		testApp, cmdFreshen, "-q", testFlagSignKey, keyFile, manifestPath,
+	}, fs)
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+	opts = testOpts([]string{
+		testApp, cmdCheck, "-q",
+		"--" + flagRequireSignature, fingerprint, manifestPath,
+	}, fs)
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+	assert.Len(t, manifestFiles(t, fs, manifestPath), 2)
+}
+
+// TestFreshenSignsUnchangedTree runs freshen with --sign-key on a tree that
+// has not changed since gen made its unsigned manifest. freshen must
+// rewrite the manifest signed by that key. Run again with the same key it
+// must leave the manifest as it is; with another key it must rewrite it
+// signed by that one.
+func TestFreshenSignsUnchangedTree(t *testing.T) {
+	t.Setenv(envSignKeyPassphrase, "")
+
+	fs := afero.NewOsFs()
+	_, manifestPath := setupFreshenDir(t, fs, map[string]string{testFileTxt: "hello"})
+
+	newKeyFile := func() (string, string) {
+		secretKey, fingerprint := testSecretKey(t, nil, nil)
+		keyFile := filepath.Join(t.TempDir(), "key.asc")
+		require.NoError(t, afero.WriteFile(fs, keyFile, secretKey, 0o600))
+
+		return keyFile, fingerprint
+	}
+
+	freshenAndCheckSignedBy := func(keyFile, fingerprint string) {
+		opts := testOpts([]string{
+			testApp, cmdFreshen, "-q", testFlagSignKey, keyFile, manifestPath,
+		}, fs)
+		require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+		opts = testOpts([]string{
+			testApp, cmdCheck, "-q",
+			"--" + flagRequireSignature, fingerprint, manifestPath,
+		}, fs)
+		require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+	}
+
+	keyFile, fingerprint := newKeyFile()
+	freshenAndCheckSignedBy(keyFile, fingerprint)
+
+	before, err := afero.ReadFile(fs, manifestPath)
+	require.NoError(t, err)
+
+	freshenAndCheckSignedBy(keyFile, fingerprint)
+
+	after, err := afero.ReadFile(fs, manifestPath)
+	require.NoError(t, err)
+	assert.Equal(t, before, after, "manifest already signed by the key was rewritten")
+
+	freshenAndCheckSignedBy(newKeyFile())
+}
+
+// TestSignWithProtectedKeyNeedsPassphrase runs gen with a protected key,
+// with MFER_SIGN_KEY_PASSPHRASE empty and no terminal to ask on. gen must
+// fail, naming the variable, and write no manifest.
+func TestSignWithProtectedKeyNeedsPassphrase(t *testing.T) {
+	t.Setenv(envSignKeyPassphrase, "")
+
+	secretKey, _ := testSecretKey(t, []byte("secret"), nil)
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, afero.WriteFile(fs, testKeyFile, secretKey, 0o600))
+	require.NoError(t, fs.MkdirAll(testDir, 0o755))
+	writeTestFile(t, fs, testFile1, "hello")
+
+	opts := testOpts([]string{
+		testApp, cmdGenerate, "-q", testFlagSignKey, testKeyFile,
+		"-o", testMF, testDir,
+	}, fs)
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts),
+		"signing key is protected: set MFER_SIGN_KEY_PASSPHRASE to its passphrase")
+
+	exists, err := afero.Exists(fs, testMF)
+	require.NoError(t, err)
+	assert.False(t, exists)
+}
+
+// TestSignWithKeyThatCannotSignFailsFirst runs gen on a directory and
+// freshen on a manifest, neither of which exists, with keys that cannot
+// sign: a protected key with a wrong MFER_SIGN_KEY_PASSPHRASE, a key that
+// expired in 2020, and a version 6 key. Each run must fail on the key: it
+// checks the key before it reads any file, so a missing file goes
+// unnoticed.
+func TestSignWithKeyThatCannotSignFailsFirst(t *testing.T) {
+	t.Setenv(envSignKeyPassphrase, "wrong")
+
+	wrongPassphrase, _ := testSecretKey(t, []byte("right"), nil)
+
+	made := time.Date(2020, 1, 1, 0, 0, 0, 0, time.UTC)
+	expired, _ := testSecretKey(t, nil, &packet.Config{
+		Algorithm:       packet.PubKeyAlgoEdDSA,
+		Time:            func() time.Time { return made },
+		KeyLifetimeSecs: uint32((24 * time.Hour).Seconds()),
+	})
+
+	version6, _ := testSecretKey(t, nil, &packet.Config{
+		Algorithm: packet.PubKeyAlgoEd25519,
+		V6Keys:    true,
+	})
+
+	for want, secretKey := range map[string][]byte{
+		"unlock signing key":                           wrongPassphrase,
+		"signing key cannot sign":                      expired,
+		"signing key must be an OpenPGP version 4 key": version6,
+	} {
+		fs := afero.NewMemMapFs()
+		require.NoError(t, afero.WriteFile(fs, testKeyFile, secretKey, 0o600))
+
+		for _, args := range [][]string{
+			{
+				testApp, cmdGenerate, "-q", testFlagSignKey, testKeyFile,
+				"-o", testMF, "/missing",
+			},
+			{testApp, cmdFreshen, "-q", testFlagSignKey, testKeyFile, "/missing.mf"},
+		} {
+			opts := testOpts(args, fs)
+			assert.Equal(t, 1, runCLI(opts), args[1], want)
+			assert.Contains(t, testStderr(t, opts), testKeyFile+": "+want, args[1])
+		}
+	}
+}
+
+// TestGenAsksForPassphraseOnTerminal runs gen with a protected key, no
+// MFER_SIGN_KEY_PASSPHRASE, and a terminal as stdin and stderr. gen must
+// ask for the passphrase on stderr, and sign with what is typed after the
+// prompt.
+func TestGenAsksForPassphraseOnTerminal(t *testing.T) {
+	t.Setenv(envSignKeyPassphrase, "")
+
+	secretKey, fingerprint := testSecretKey(t, []byte("passphrase"), nil)
+
+	fs := afero.NewOsFs()
+	keyFile := filepath.Join(t.TempDir(), "key.asc")
+	root := t.TempDir()
+	manifestPath := filepath.Join(root, defaultManifestName)
+
+	require.NoError(t, afero.WriteFile(fs, keyFile, secretKey, 0o600))
+	writeTestFile(t, fs, filepath.Join(root, testFileTxt), "hello")
+
+	terminal, tty, err := pty.Open()
+	require.NoError(t, err)
+
+	t.Cleanup(func() { _ = terminal.Close() })
+
+	opts := testOpts([]string{
+		testApp, cmdGenerate, "-q", testFlagSignKey, keyFile,
+		"-o", manifestPath, root,
+	}, fs)
+	opts.Stdin = tty
+	opts.Stderr = tty
+
+	exitCode := make(chan int, 1)
+
+	go func() {
+		exitCode <- runCLI(opts)
+
+		// Once gen has ended, reading the terminal fails instead of
+		// waiting for a prompt that will not come.
+		_ = tty.Close()
+	}()
+
+	prompt := "Passphrase for " + keyFile + ": "
+	output := bufio.NewReader(terminal)
+	written := ""
+
+	for !strings.HasSuffix(written, prompt) {
+		b, err := output.ReadByte()
+		require.NoError(t, err, "gen wrote %q and no prompt", written)
+
+		written += string(b)
+	}
+
+	_, err = terminal.WriteString("passphrase\n")
+	require.NoError(t, err)
+
+	code := <-exitCode
+	rest, _ := io.ReadAll(output)
+	require.Equal(t, 0, code, "gen wrote %q", rest)
+
+	check := testOpts([]string{
+		testApp, cmdCheck, "-q",
+		"--" + flagRequireSignature, fingerprint, manifestPath,
+	}, fs)
+	require.Equal(t, 0, runCLI(check), testStderr(t, check))
+}
+
+// assertEmptySignKeyRefused runs gen and freshen, each with flags, on a
+// directory holding a file and an unsigned manifest. Each must fail,
+// naming --sign-key, and leave the manifest as it was.
+func assertEmptySignKeyRefused(t *testing.T, flags ...string) {
+	t.Helper()
+
+	manifest := manifestOf(t, map[string][]byte{testFileTxt: []byte("listed")})
+
+	for command, rest := range map[string][]string{
+		cmdGenerate: {"-q", "-f", "-o", testMF, testDir},
+		cmdFreshen:  {"-q", testMF},
+	} {
+		fs := afero.NewMemMapFs()
+		require.NoError(t, fs.MkdirAll(testDir, 0o755))
+		writeTestFile(t, fs, testFile1, "hello")
+		require.NoError(t, afero.WriteFile(fs, testMF, manifest, 0o644))
+
+		opts := testOpts(slices.Concat([]string{testApp, command}, flags, rest), fs)
+		assert.Equal(t, 1, runCLI(opts), command)
+		assert.Contains(t, testStderr(t, opts), errEmptySignKey.Error(), command)
+
+		content, err := afero.ReadFile(fs, testMF)
+		require.NoError(t, err)
+		assert.Equal(t, manifest, content, command)
+	}
+}
+
+// TestGenAndFreshenRefuseEmptySignKey runs gen and freshen with --sign-key
+// given an empty value, as an unset shell variable gives it.
+func TestGenAndFreshenRefuseEmptySignKey(t *testing.T) {
+	t.Parallel()
+
+	assertEmptySignKeyRefused(t, testFlagSignKey, "")
+}
+
+// TestGenAndFreshenRefuseEmptySignKeyFromEnvironment runs gen and freshen
+// with MFER_SIGN_KEY set to an empty string.
+func TestGenAndFreshenRefuseEmptySignKeyFromEnvironment(t *testing.T) {
+	t.Setenv("MFER_SIGN_KEY", "")
+
+	assertEmptySignKeyRefused(t)
+}
+
+// assertEmptyFingerprintRefused runs check on an unsigned manifest, and
+// fetch of that manifest from a server, each with flags. Each must refuse
+// the empty fingerprint as malformed, and fetch must request nothing.
+func assertEmptyFingerprintRefused(t *testing.T, flags ...string) {
+	t.Helper()
+
+	const want = "invalid fingerprint: must be exactly 40 hex characters, got 0"
+
+	files := map[string][]byte{testFileTxt: []byte("listed")}
+	manifest := manifestOf(t, files)
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll(testDir, 0o755))
+	writeTestFile(t, fs, filepath.Join(testDir, testFileTxt), "listed")
+	require.NoError(t, afero.WriteFile(fs, testMF, manifest, 0o644))
+
+	opts := testOpts(slices.Concat(
+		[]string{testApp, cmdCheck, "-q"}, flags, []string{testMF},
+	), fs)
+	assert.Equal(t, 1, runCLI(opts), cmdCheck)
+	assert.Contains(t, testStderr(t, opts), want, cmdCheck)
+
+	var requests atomic.Int32
+
+	tree := fetchTestHandler(manifest, files)
+
+	server := httptest.NewServer(
+		http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+			requests.Add(1)
+			tree.ServeHTTP(w, r)
+		}))
+	defer server.Close()
+
+	opts = testOpts(slices.Concat(
+		[]string{testApp, cmdFetch, "-q", "--" + flagDest, t.TempDir()},
+		flags, []string{server.URL},
+	), afero.NewOsFs())
+	assert.Equal(t, 1, runCLI(opts), cmdFetch)
+	assert.Contains(t, testStderr(t, opts), want, cmdFetch)
+	assert.Zero(t, requests.Load(), "fetch made a request")
+}
+
+// TestCheckAndFetchRefuseEmptyRequireSignature runs check and fetch with
+// --require-signature given an empty value, as an unset shell variable
+// gives it.
+func TestCheckAndFetchRefuseEmptyRequireSignature(t *testing.T) {
+	t.Parallel()
+
+	assertEmptyFingerprintRefused(t, "--"+flagRequireSignature, "")
+}
+
+// TestCheckAndFetchRefuseEmptyRequireSignatureFromEnvironment runs check
+// and fetch with MFER_REQUIRE_SIGNATURE set to an empty string.
+func TestCheckAndFetchRefuseEmptyRequireSignatureFromEnvironment(t *testing.T) {
+	t.Setenv("MFER_REQUIRE_SIGNATURE", "")
+
+	assertEmptyFingerprintRefused(t)
+}

mfer/builder.go

@@ -34,10 +34,12 @@ var (
 	errPathAbsolute     = errors.New("is absolute; must be relative")
 	errPathEmptySegment = errors.New("contains empty segment")
 	errPathDotDot       = errors.New("contains '..' segment")
+	errPathDot          = errors.New("contains '.' segment")
 	errSizeMismatch     = errors.New("size mismatch")
 	errNegativeSize     = errors.New("size cannot be negative")
 	errHashNotMultihash = errors.New("hash is not a valid multihash")
 	errHashTooShort     = errors.New("hash digest is too short")
+	errDuplicatePath    = errors.New("duplicate path")
 )
 
 // ValidatePath checks that a file path conforms to manifest path invariants:
@@ -45,6 +47,7 @@ var (
 //   - Must use forward slashes only (no backslashes)
 //   - Must be relative (no leading /)
 //   - Must not contain ".." segments
+//   - Must not contain "." segments
 //   - Must not contain empty segments (no "//")
 //   - Must not be empty
 func ValidatePath(p string) error {
@@ -72,6 +75,10 @@ func ValidatePath(p string) error {
 		if seg == ".." {
 			return fmt.Errorf("path %q %w", p, errPathDotDot)
 		}
+
+		if seg == "." {
+			return fmt.Errorf("path %q %w", p, errPathDot)
+		}
 	}
 
 	return nil
@@ -115,6 +122,7 @@ type FileHashProgress struct {
 type Builder struct {
 	mu                sync.Mutex
 	files             []*MFFilePath
+	paths             map[string]bool // the path of each entry in files
 	createdAt         time.Time
 	includeTimestamps bool
 	signingOptions    *SigningOptions
@@ -125,6 +133,7 @@ type Builder struct {
 func NewBuilder() *Builder {
 	return &Builder{
 		files:     make([]*MFFilePath, 0),
+		paths:     make(map[string]bool),
 		createdAt: time.Now(),
 	}
 }
@@ -138,6 +147,7 @@ func (b *Builder) SetSeed(seed string) {
 }
 
 // AddFile reads file content from reader, computes hashes, and adds to manifest.
+// A path already added is refused once the file is read.
 // Only mode's permission bits (mode.Perm()) are recorded; 0 records none.
 // Progress updates are sent to the progress channel (if non-nil) without blocking.
 // Returns the number of bytes read.
@@ -204,11 +214,7 @@ func (b *Builder) AddFile(
 		Mode:  uint32(mode.Perm()),
 	}
 
-	b.mu.Lock()
+	return totalRead, b.addEntry(entry)
-	b.files = append(b.files, entry)
-	b.mu.Unlock()
-
-	return totalRead, nil
 }
 
 // sendFileHashProgress sends a progress update without blocking.
@@ -234,8 +240,9 @@ func (b *Builder) FileCount() int {
 // AddFileWithHash adds a file entry with a pre-computed hash.
 // This is useful when the hash is already known (e.g., from an existing manifest).
 // Only mode's permission bits (mode.Perm()) are recorded; 0 records none.
-// Returns an error if path is invalid, size is negative, or hash is not a
+// Returns an error if path is invalid or already added, size is negative,
-// multihash with a digest of at least 32 bytes, as long as SHA-256's.
+// or hash is not a multihash with a digest of at least 32 bytes, as long
+// as SHA-256's.
 func (b *Builder) AddFileWithHash(
 	path RelFilePath,
 	size FileSize,
@@ -245,7 +252,7 @@ func (b *Builder) AddFileWithHash(
 ) error {
 	err := ValidatePath(string(path))
 	if err != nil {
-		return fmt.Errorf("add file: %w", err)
+		return err
 	}
 
 	if size < 0 {
@@ -277,11 +284,7 @@ func (b *Builder) AddFileWithHash(
 		Mode:  uint32(mode.Perm()),
 	}
 
-	b.mu.Lock()
+	return b.addEntry(entry)
-	b.files = append(b.files, entry)
-	b.mu.Unlock()
-
-	return nil
 }
 
 // SetIncludeTimestamps controls whether the manifest includes a createdAt timestamp.
@@ -293,7 +296,7 @@ func (b *Builder) SetIncludeTimestamps(include bool) {
 	b.includeTimestamps = include
 }
 
-// SetSigningOptions sets the GPG signing options for the manifest.
+// SetSigningOptions sets the key the manifest is signed with.
 // If opts is non-nil, the manifest will be signed when Build() is called.
 func (b *Builder) SetSigningOptions(opts *SigningOptions) {
 	b.mu.Lock()
@@ -302,8 +305,8 @@ func (b *Builder) SetSigningOptions(opts *SigningOptions) {
 	b.signingOptions = opts
 }
 
-// Build finalizes the manifest and writes it to the writer. ctx bounds the
+// Build finalizes the manifest and writes it to the writer. When signing
-// gpg runs that sign the manifest when signing options are set.
+// options are set, it does not sign once ctx has ended.
 func (b *Builder) Build(ctx context.Context, w io.Writer) error {
 	b.mu.Lock()
 	defer b.mu.Unlock()
@@ -332,20 +335,33 @@ func (b *Builder) Build(ctx context.Context, w io.Writer) error {
 	// Generate outer wrapper
 	err := m.generateOuter(ctx)
 	if err != nil {
-		return fmt.Errorf("build: generate outer: %w", err)
+		return err
 	}
 
 	// Generate final output
 	err = m.generate(ctx)
 	if err != nil {
-		return fmt.Errorf("build: generate: %w", err)
+		return err
 	}
 
 	// Write to output
 	_, err = w.Write(m.output.Bytes())
-	if err != nil {
+
-		return fmt.Errorf("build: write output: %w", err)
+	return err
+}
+
+// addEntry adds entry to the manifest unless an entry with its path is
+// already there.
+func (b *Builder) addEntry(entry *MFFilePath) error {
+	b.mu.Lock()
+	defer b.mu.Unlock()
+
+	if b.paths[entry.GetPath()] {
+		return fmt.Errorf("%w %q", errDuplicatePath, entry.GetPath())
 	}
 
+	b.paths[entry.GetPath()] = true
+	b.files = append(b.files, entry)
+
 	return nil
 }

mfer/builder_test.go

@@ -125,6 +125,32 @@ func TestBuilderAddFileWithHashRejectsBadHashes(t *testing.T) {
 	}
 }
 
+// TestBuilderRefusesPathAlreadyAdded adds a path, then adds it again with
+// AddFile and with AddFileWithHash. Each must refuse it, naming it, and
+// keep the one entry already added.
+func TestBuilderRefusesPathAlreadyAdded(t *testing.T) {
+	t.Parallel()
+
+	hash, err := multihash.Encode(make([]byte, sha256.Size), multihash.SHA2_256)
+	require.NoError(t, err)
+
+	b := NewBuilder()
+	require.NoError(t, b.AddFileWithHash("dir/a.txt", 4, ModTime{}, 0, hash))
+
+	content := []byte("data")
+	_, err = b.AddFile(
+		"dir/a.txt", FileSize(len(content)), ModTime{}, 0, bytes.NewReader(content), nil,
+	)
+	require.ErrorIs(t, err, errDuplicatePath)
+	require.EqualError(t, err, `duplicate path "dir/a.txt"`)
+
+	err = b.AddFileWithHash("dir/a.txt", 4, ModTime{}, 0, hash)
+	require.ErrorIs(t, err, errDuplicatePath)
+	require.EqualError(t, err, `duplicate path "dir/a.txt"`)
+
+	assert.Equal(t, 1, b.FileCount())
+}
+
 func TestBuilderBuild(t *testing.T) {
 	t.Parallel()
 
@@ -260,6 +286,9 @@ func TestValidatePath(t *testing.T) {
 		{"has/../traversal", "dot-dot segment"},
 		{"has//double", "empty segment"},
 		{"..", "just dot-dot"},
+		{"./a.txt", "leading dot segment"},
+		{"has/./dot", "interior dot segment"},
+		{".", "just dot"},
 		{string([]byte{0xff, 0xfe}), "invalid UTF-8"},
 	}
 	for _, tt := range invalid {

mfer/checker.go

@@ -15,7 +15,6 @@ import (
 )
 
 var (
-	errNoSigningPubKey   = errors.New("manifest has no signing public key")
 	errManifestPathEmpty = errors.New("manifest path cannot be empty")
 	errBasePathEmpty     = errors.New("base path cannot be empty")
 )
@@ -173,8 +172,14 @@ func (c *Checker) IsSigned() bool {
 	return len(c.signature) > 0
 }
 
-// Signer returns the signer fingerprint if the manifest is signed, nil otherwise.
+// Signer returns the fingerprint of the key that made the manifest's
+// signature, which loading the manifest checked, or nil if the manifest is
+// not signed.
 func (c *Checker) Signer() []byte {
+	if !c.IsSigned() {
+		return nil
+	}
+
 	return c.signer
 }
 
@@ -184,17 +189,6 @@ func (c *Checker) SigningPubKey() []byte {
 	return c.signingPubKey
 }
 
-// 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(ctx context.Context) (string, error) {
-	if len(c.signingPubKey) == 0 {
-		return "", errNoSigningPubKey
-	}
-
-	return gpgExtractPubKeyFingerprint(ctx, c.signingPubKey)
-}
-
 // Check verifies all files against the manifest.
 // Results are sent to the results channel as files are checked.
 // Progress updates are sent to the progress channel approximately once per second.
@@ -270,11 +264,12 @@ func (c *Checker) Check(
 	return nil
 }
 
-// FindExtraFiles walks the filesystem and reports files not in the manifest,
+// FindExtraFiles walks the filesystem and reports the regular files, and
-// hidden files and directories included. The manifest file itself is not
+// symlinks to them, that are not in the manifest, hidden files and
-// reported. Anything the search cannot read, such as a directory that cannot
+// directories included. The manifest file itself is not reported. Anything
-// be listed, is reported with StatusError and the search goes on. Results are
+// the search cannot read, such as a directory that cannot be listed, is
-// sent to the results channel. The channel is closed when done.
+// 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)
@@ -333,6 +328,13 @@ func (c *Checker) FindExtraFiles(ctx context.Context, results chan<- Result) err
 			}
 		}
 
+		// gen lists regular files and symlinks to them only, so a named
+		// pipe, a socket, a device, a symlink to a directory and a broken
+		// symlink are never reported.
+		if !info.Mode().IsRegular() {
+			return nil
+		}
+
 		// Skip the manifest file itself, however its path is spelled
 		if os.SameFile(info, c.manifestInfo) {
 			return nil
@@ -377,6 +379,15 @@ func (c *Checker) checkFile(entry *MFFilePath, checkedBytes *FileSize) Result {
 		return Result{Path: relPath, Status: StatusError, Message: err.Error()}
 	}
 
+	// Opening a named pipe can block, and reading a device may never end.
+	if !info.Mode().IsRegular() {
+		return Result{
+			Path:    relPath,
+			Status:  StatusError,
+			Message: "not a regular file",
+		}
+	}
+
 	// Check size
 	if info.Size() != entry.GetSize() {
 		*checkedBytes += FileSize(info.Size())

mfer/constants.go

@@ -1,12 +1,6 @@
 package mfer
 
 const (
-	// Version is the current mfer release version.
-	Version = "0.1.0"
-
-	// ReleaseDate is the date on which Version was released.
-	ReleaseDate = "2025-12-17"
-
 	// MaxDecompressedSize is the maximum allowed size of decompressed manifest
 	// data (256 MiB). This prevents decompression bombs from consuming excessive
 	// memory.

mfer/deserialize.go

@@ -2,11 +2,11 @@ package mfer
 
 import (
 	"bytes"
-	"context"
 	"crypto/sha256"
 	"errors"
 	"fmt"
 	"io"
+	"strings"
 
 	"github.com/klauspost/compress/zstd"
 	"github.com/spf13/afero"
@@ -23,12 +23,14 @@ var (
 	errCompressedHashWrong  = errors.New("compressed data hash mismatch")
 	errSignatureNoPubKey    = errors.New("signature present but no public key")
 	errDecompressedTooLarge = errors.New("decompressed data exceeds maximum allowed size")
-	errManifestTooLarge     = errors.New("manifest exceeds maximum allowed size")
+	errManifestTooLarge     = errors.New("file 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")
+	errInvalidManifestPath  = errors.New("invalid file entry")
-	errDecodedTooLarge      = errors.New(
+	errEntryMissingHash     = errors.New("file entry has no hash")
-		"manifest would take too much memory to decode")
+	errDecodedTooLarge      = errors.New("too much memory needed")
+	errSignerNotSigningKey  = errors.New(
+		"signer is not the fingerprint of the key that made the signature")
 )
 
 // validateUUID checks that the byte slice is the 16 bytes of a binary UUID.
@@ -55,20 +57,22 @@ func (m *manifest) validateOuterHeader() error {
 	// Validate outer UUID before any decompression
 	err := validateUUID(m.pbOuter.GetUuid())
 	if err != nil {
-		return fmt.Errorf("outer UUID invalid: %w", err)
+		return fmt.Errorf("outer message: %w", err)
 	}
 
 	return nil
 }
 
-// verifyOuterIntegrity checks the hash of the compressed payload and,
+// verifyOuterIntegrity checks the hash of the compressed payload and, if a
-// if a signature is present, verifies it against the embedded public key.
+// signature is present, verifies it against the embedded public key, which
+// must be one key, and checks that the signer field is that key's
+// fingerprint.
 func (m *manifest) verifyOuterIntegrity() error {
 	h := sha256.New()
 
 	_, err := h.Write(m.pbOuter.GetInnerMessage())
 	if err != nil {
-		return fmt.Errorf("deserialize: hash write: %w", err)
+		return fmt.Errorf("hash inner message: %w", err)
 	}
 
 	sha256Hash := h.Sum(nil)
@@ -86,20 +90,21 @@ func (m *manifest) verifyOuterIntegrity() error {
 
 	sigString, err := m.signatureString()
 	if err != nil {
-		return fmt.Errorf(
+		return fmt.Errorf("build signature string: %w", err)
-			"failed to generate signature string for verification: %w", err,
-		)
 	}
 
-	// Loading a manifest takes no context; gpgTimeout still bounds gpg.
+	signingKey, err := verifySignature(
-	err = gpgVerify(
-		context.Background(),
 		[]byte(sigString),
 		m.pbOuter.GetSignature(),
 		m.pbOuter.GetSigningPubKey(),
 	)
 	if err != nil {
-		return fmt.Errorf("signature verification failed: %w", err)
+		return err
+	}
+
+	if !strings.EqualFold(string(m.pbOuter.GetSigner()), signingKey) {
+		return fmt.Errorf("%w: signer %q, signing key %s",
+			errSignerNotSigningKey, m.pbOuter.GetSigner(), signingKey)
 	}
 
 	log.Infof("signature verified successfully")
@@ -125,7 +130,7 @@ func (m *manifest) decompressInner() ([]byte, error) {
 		zstd.WithDecodeBuffersBelow(0),
 		zstd.WithDecoderMaxWindow(zstdWindowSize))
 	if err != nil {
-		return nil, fmt.Errorf("deserialize: zstd reader: %w", err)
+		return nil, fmt.Errorf("create decompressor: %w", err)
 	}
 	defer zr.Close()
 
@@ -140,7 +145,7 @@ func (m *manifest) decompressInner() ([]byte, error) {
 
 	dat, err := io.ReadAll(limitedReader)
 	if err != nil {
-		return nil, fmt.Errorf("deserialize: decompress: %w", err)
+		return nil, fmt.Errorf("decompress inner message: %w", err)
 	}
 
 	if int64(len(dat)) >= MaxDecompressedSize {
@@ -256,7 +261,7 @@ func (m *manifest) deserializeInner() error {
 
 	err = checkDecodedSize(dat)
 	if err != nil {
-		return fmt.Errorf("deserialize: unmarshal inner: %w", err)
+		return fmt.Errorf("unmarshal inner message: %w", err)
 	}
 
 	// Deserialize inner message
@@ -265,13 +270,17 @@ func (m *manifest) deserializeInner() error {
 	// Unknown fields would cost memory; mfer never writes a loaded manifest out.
 	err = proto.UnmarshalOptions{DiscardUnknown: true}.Unmarshal(dat, m.pbInner)
 	if err != nil {
-		return fmt.Errorf("deserialize: unmarshal inner: %w", err)
+		return fmt.Errorf("unmarshal inner message: %w", err)
+	}
+
+	if m.pbInner.GetVersion() != MFFile_VERSION_ONE {
+		return errUnknownVersion
 	}
 
 	// Validate inner UUID
 	err = validateUUID(m.pbInner.GetUuid())
 	if err != nil {
-		return fmt.Errorf("inner UUID invalid: %w", err)
+		return fmt.Errorf("inner message: %w", err)
 	}
 
 	// Verify UUIDs match
@@ -284,12 +293,26 @@ func (m *manifest) deserializeInner() error {
 	// 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.
+	// check. A path listed twice is refused too: check would check the one
+	// file against both entries. So is an entry with no hash: there is
+	// nothing to check the file against.
+	seen := make(map[string]bool, len(m.pbInner.GetFiles()))
+
 	for _, f := range m.pbInner.GetFiles() {
 		err = ValidatePath(f.GetPath())
 		if err != nil {
 			return fmt.Errorf("%w: %w", errInvalidManifestPath, err)
 		}
+
+		if len(f.GetHashes()) == 0 {
+			return fmt.Errorf("%w: %q", errEntryMissingHash, f.GetPath())
+		}
+
+		if seen[f.GetPath()] {
+			return fmt.Errorf("%w %q", errDuplicatePath, f.GetPath())
+		}
+
+		seen[f.GetPath()] = true
 	}
 
 	log.Infof("loaded manifest with %d files", len(m.pbInner.GetFiles()))

mfer/deserialize_fuzz_test.go

@@ -19,14 +19,6 @@ import (
 // input and of the decompressed data it may read, plus room for the
 // decoder's window buffers. A panic or a hang fails the test on its own.
 func FuzzNewManifestFromReader(f *testing.F) {
-	// A signed manifest makes the parser write the key and signature to a
-	// temporary directory and run gpg on them. With gpg off the PATH and
-	// temporary files kept in the test's own directory, no process is
-	// started and nothing is written elsewhere; such input ends in an
-	// error instead.
-	f.Setenv("PATH", "")
-	f.Setenv("TMPDIR", f.TempDir())
-
 	f.Fuzz(func(t *testing.T, data []byte) {
 		var before, after runtime.MemStats
 

mfer/deserialize_path_test.go

@@ -7,7 +7,6 @@ import (
 	"crypto/sha256"
 	"fmt"
 	"strconv"
-	"strings"
 	"testing"
 	"time"
 	"uuid"
@@ -81,6 +80,8 @@ func TestDeserializeRejectsInvalidEntryPaths(t *testing.T) {
 	}{
 		{"parent traversal", "../escape"},
 		{"interior traversal", "a/../../escape"},
+		{"leading dot segment", "./a.txt"},
+		{"interior dot segment", "dir/./a.txt"},
 		{"absolute path", "/etc/passwd"},
 		{"backslash path", `a\b`},
 		{"double slash", "a//b"},
@@ -118,12 +119,79 @@ func TestDeserializeRejectsInvalidEntryPaths(t *testing.T) {
 	}
 }
 
+// A manifest that lists a path twice is refused as it is loaded, naming the
+// path. Paths are compared byte for byte: two that differ only in letter case
+// load, and fetch refuses those itself. Each entry has a hash, as entries mfer
+// writes do; entries of a path alone would take too much memory to decode.
+func TestDeserializeRefusesPathListedTwice(t *testing.T) {
+	t.Parallel()
+
+	hash, err := multihash.Encode(make([]byte, sha256.Size), multihash.SHA2_256)
+	require.NoError(t, err)
+
+	tests := []struct {
+		name    string
+		paths   []string
+		refused bool
+	}{
+		{"same path twice", []string{"dir/a.txt", "other.txt", "dir/a.txt"}, true},
+		{"paths differing in letter case", []string{"dir/b.txt", "dir/B.txt"}, false},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+
+			id := uuid.NewV4()
+			inner := &MFFile{Version: MFFile_VERSION_ONE, Uuid: id[:]}
+
+			for _, p := range tt.paths {
+				inner.Files = append(inner.Files, &MFFilePath{
+					Path:   p,
+					Hashes: []*MFFileChecksum{{MultiHash: hash}},
+				})
+			}
+
+			innerData, err := proto.Marshal(inner)
+			require.NoError(t, err)
+
+			m, err := NewManifestFromReader(bytes.NewReader(wrapInner(t, id, innerData)))
+			if tt.refused {
+				require.ErrorIs(t, err, errDuplicatePath)
+				require.EqualError(t, err, `duplicate path "dir/a.txt"`)
+			} else {
+				require.NoError(t, err)
+				assert.Len(t, m.Files(), len(tt.paths))
+			}
+		})
+	}
+}
+
+// A manifest holding a file entry with no hash is refused as it is loaded,
+// naming the path: there is nothing to check the file against.
+func TestDeserializeRefusesEntryWithNoHash(t *testing.T) {
+	t.Parallel()
+
+	id := uuid.NewV4()
+	inner, err := proto.Marshal(&MFFile{
+		Version: MFFile_VERSION_ONE,
+		Files:   []*MFFilePath{{Path: "x", Size: 1}},
+		Uuid:    id[:],
+	})
+	require.NoError(t, err)
+
+	_, err = NewManifestFromReader(bytes.NewReader(wrapInner(t, id, inner)))
+	require.ErrorIs(t, err, errEntryMissingHash)
+	require.EqualError(t, err, `file entry has no hash: "x"`)
+}
+
 // Entries of a path, an empty hash, an empty MIME type and empty modification
 // and change times are counted at 432 bytes each (176 + 112 + 16 + 64 + 64)
 // and take 16 bytes plus the path to encode. A 37-character path makes that
 // 53 bytes, about 8.2 times: refused, and leaving any one of the five
 // uncounted, even the MIME type, brings it under 8. A 39-character path makes
-// it 55 bytes, about 7.9 times: loaded.
+// it 55 bytes, about 7.9 times: loaded. Each entry's path is its number,
+// padded with zeros to that length, since a manifest lists a path only once.
 func TestDeserializeRefusesEntriesThatDecodeTooLarge(t *testing.T) {
 	t.Parallel()
 
@@ -139,22 +207,24 @@ func TestDeserializeRefusesEntriesThatDecodeTooLarge(t *testing.T) {
 		t.Run(strconv.Itoa(tt.pathLen), func(t *testing.T) {
 			t.Parallel()
 
-			entry := protowire.AppendTag(nil, 1, protowire.BytesType) // MFFilePath.path
-			entry = protowire.AppendString(entry, strings.Repeat("a", tt.pathLen))
-			entry = protowire.AppendTag(entry, 3, protowire.BytesType) // MFFilePath.hashes
-			entry = protowire.AppendBytes(entry, nil)
-			entry = protowire.AppendTag(entry, 301, protowire.BytesType) // MFFilePath.mimeType
-			entry = protowire.AppendBytes(entry, nil)
-			entry = protowire.AppendTag(entry, 302, protowire.BytesType) // MFFilePath.mtime
-			entry = protowire.AppendBytes(entry, nil)
-			entry = protowire.AppendTag(entry, 303, protowire.BytesType) // MFFilePath.ctime
-			entry = protowire.AppendBytes(entry, nil)
-
 			id := uuid.NewV4()
-			inner := protowire.AppendTag(nil, 102, protowire.BytesType) // MFFile.uuid
+			inner := protowire.AppendTag(nil, 100, protowire.VarintType) // MFFile.version
+			inner = protowire.AppendVarint(inner, uint64(MFFile_VERSION_ONE))
+			inner = protowire.AppendTag(inner, 102, protowire.BytesType) // MFFile.uuid
 			inner = protowire.AppendBytes(inner, id[:])
 
-			for range 1000 {
+			for i := range 1000 {
+				entry := protowire.AppendTag(nil, 1, protowire.BytesType) // MFFilePath.path
+				entry = protowire.AppendString(entry, fmt.Sprintf("%0*d", tt.pathLen, i))
+				entry = protowire.AppendTag(entry, 3, protowire.BytesType) // MFFilePath.hashes
+				entry = protowire.AppendBytes(entry, nil)
+				entry = protowire.AppendTag(entry, 301, protowire.BytesType) // MFFilePath.mimeType
+				entry = protowire.AppendBytes(entry, nil)
+				entry = protowire.AppendTag(entry, 302, protowire.BytesType) // MFFilePath.mtime
+				entry = protowire.AppendBytes(entry, nil)
+				entry = protowire.AppendTag(entry, 303, protowire.BytesType) // MFFilePath.ctime
+				entry = protowire.AppendBytes(entry, nil)
+
 				inner = protowire.AppendTag(inner, 101, protowire.BytesType) // MFFile.files
 				inner = protowire.AppendBytes(inner, entry)
 			}
@@ -179,10 +249,14 @@ func TestDeserializeDropsUnknownFields(t *testing.T) {
 
 	entry := protowire.AppendTag(nil, 1, protowire.BytesType) // MFFilePath.path
 	entry = protowire.AppendString(entry, "a")
+	entry = protowire.AppendTag(entry, 3, protowire.BytesType) // MFFilePath.hashes
+	entry = protowire.AppendBytes(entry, nil)
 	entry = append(entry, unknown...)
 
 	id := uuid.NewV4()
-	inner := protowire.AppendTag(nil, 101, protowire.BytesType) // MFFile.files
+	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[:])

mfer/deserialize_test.go

@@ -3,12 +3,36 @@ package mfer
 
 import (
 	"bytes"
+	"crypto/sha256"
+	"encoding/hex"
+	"os"
 	"testing"
+	"uuid"
 
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
+	"google.golang.org/protobuf/proto"
 )
 
+// An inner message whose version is not VERSION_ONE, whether version 0 or a
+// later one, is refused with the same error as an outer message's.
+func TestDeserializeRefusesUnknownInnerVersion(t *testing.T) {
+	t.Parallel()
+
+	for _, version := range []MFFile_Version{MFFile_VERSION_NONE, MFFile_VERSION_ONE + 1} {
+		t.Run(version.String(), func(t *testing.T) {
+			t.Parallel()
+
+			id := uuid.NewV4()
+			inner, err := proto.Marshal(&MFFile{Version: version, Uuid: id[:]})
+			require.NoError(t, err)
+
+			_, err = NewManifestFromReader(bytes.NewReader(wrapInner(t, id, inner)))
+			require.ErrorIs(t, err, errUnknownVersion)
+		})
+	}
+}
+
 // TestReadAtMost gives readAtMost exactly its maximum, which it must
 // return whole, and twice its maximum, which it must refuse after reading
 // one byte past the maximum, and no more. NewManifestFromReader reads
@@ -28,6 +52,41 @@ func TestReadAtMost(t *testing.T) {
 	_, err = readAtMost(input, maxSize)
 	require.ErrorIs(t, err, errManifestTooLarge)
 	require.EqualError(t, err,
-		"manifest exceeds maximum allowed size of 65536 bytes")
+		"file exceeds maximum allowed size of 65536 bytes")
 	assert.Equal(t, maxSize-1, input.Len(), "bytes left unread")
 }
+
+// TestFormatTestVector checks the test vector that docs/FORMAT.md shows: the
+// SHA-256 of the whole file, so that any change to the file fails, then loads
+// it, verifies its signature, and checks the canonical string and the signer
+// the document gives for it.
+func TestFormatTestVector(t *testing.T) {
+	t.Parallel()
+
+	const (
+		path       = "testdata/test-vector.mf"
+		fileSHA256 = "5864187d671b2a55f8e015f858248f92c51956b549cf548b6bb54477c2407fd4"
+		signer     = "5E962A37590D855B467D20294947A60319611E6F"
+	)
+
+	data, err := os.ReadFile(path)
+	require.NoError(t, err)
+
+	sum := sha256.Sum256(data)
+	require.Equal(t, fileSHA256, hex.EncodeToString(sum[:]))
+
+	m, err := NewManifestFromFile(&ManifestFromFileOptions{Path: path})
+	require.NoError(t, err)
+
+	canonicalString, err := m.signatureString()
+	require.NoError(t, err)
+	assert.Equal(t, "ZNAVSRFG-92197fd532bc40908aa9f86e5518b56c-"+
+		"12202353553205f036a88cefee3d0d9049ccd8e68bb24011a0b462b5867f1fcc6352",
+		canonicalString)
+
+	keyFingerprint, err := verifySignature([]byte(canonicalString),
+		m.pbOuter.GetSignature(), m.pbOuter.GetSigningPubKey())
+	require.NoError(t, err)
+	assert.Equal(t, signer, keyFingerprint)
+	assert.Equal(t, signer, string(m.pbOuter.GetSigner()))
+}

mfer/errmsg_test.go

@@ -62,6 +62,12 @@ func TestValidatePathMessagesVerbatim(t *testing.T) {
 			want: `path "a/../b" contains '..' segment`,
 			is:   errPathDotDot,
 		},
+		{
+			name: "dot segment",
+			path: "a/./b",
+			want: `path "a/./b" contains '.' segment`,
+			is:   errPathDot,
+		},
 	} {
 		t.Run(tc.name, func(t *testing.T) {
 			t.Parallel()
@@ -74,14 +80,18 @@ func TestValidatePathMessagesVerbatim(t *testing.T) {
 	}
 }
 
-// TestSerializeInternalErrorMessagesVerbatim pins the two distinct
+// TestSerializeInnerNotSetMessagesVerbatim pins the messages generate and
-// "internal error" messages, which differ between generate and
+// generateOuter return when the inner message is missing.
-// generateOuter and have always done so.
+func TestSerializeInnerNotSetMessagesVerbatim(t *testing.T) {
-func TestSerializeInternalErrorMessagesVerbatim(t *testing.T) {
 	t.Parallel()
 
 	m := &manifest{}
-	require.EqualError(t, m.generate(context.Background()),
+
-		"internal error: pbInner not set")
+	err := m.generate(context.Background())
-	require.EqualError(t, m.generateOuter(context.Background()), "internal error")
+	require.ErrorIs(t, err, errInnerNotSet)
+	require.EqualError(t, err, "inner message not set")
+
+	err = m.generateOuter(context.Background())
+	require.ErrorIs(t, err, errInternal)
+	require.EqualError(t, err, "inner message not set")
 }

mfer/gpg.go

@@ -1,309 +0,0 @@
-package mfer
-
-import (
-	"bytes"
-	"context"
-	"errors"
-	"fmt"
-	"io"
-	"os"
-	"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
-
-	// gpgWaitDelay is how long a gpg run keeps waiting for gpg's stdout
-	// and stderr to close once gpg has been killed or has exited. Reading
-	// what gpg itself wrote takes far less; only a process gpg left behind
-	// holds them open longer.
-	gpgWaitDelay = time.Second
-
-	// privateDirPerms is the permission mode for temporary GPG home
-	// directories.
-	privateDirPerms os.FileMode = 0o700
-
-	// privateFilePerms is the permission mode for temporary key,
-	// signature, and data files.
-	privateFilePerms os.FileMode = 0o600
-
-	// gpgFingerprintField is the record type tag for fingerprint lines
-	// in gpg --with-colons output.
-	gpgFingerprintField = "fpr"
-
-	// gpgFingerprintMinFields is the minimum number of colon-separated
-	// fields in a gpg fingerprint record (the fingerprint is field 10).
-	gpgFingerprintMinFields = 10
-
-	// gpg option names used from more than one call site.
-	gpgOptArmor   = "--armor"
-	gpgOptHomedir = "--homedir"
-	gpgOptVerify  = "--verify"
-)
-
-var (
-	errGPGKeyNotFound      = errors.New("gpg key not found")
-	errFingerprintNotFound = errors.New("fingerprint not found for key")
-	errImportedFPRNotFound = errors.New("fingerprint not found in imported key")
-)
-
-// GPGKeyID represents a GPG key identifier (fingerprint or key ID).
-type GPGKeyID string
-
-// SigningOptions contains options for GPG signing.
-type SigningOptions struct {
-	KeyID GPGKeyID
-}
-
-// gpgArgs builds a gpg argument list from opts followed by positional
-// arguments, separated by an explicit "--" end-of-options marker.
-//
-// This matters because key IDs reach gpg as bare positional arguments
-// (from --sign-key / MFER_SIGN_KEY) and gpg would otherwise parse a value
-// beginning with "-" as one of its own options. Callers must route every
-// non-option argument through here.
-func gpgArgs(opts []string, positional ...string) []string {
-	args := make([]string, 0, len(opts)+1+len(positional))
-	args = append(args, opts...)
-	args = append(args, "--")
-	args = append(args, positional...)
-
-	return args
-}
-
-// runGPG runs the gpg binary in batch mode with the given arguments and
-// optional stdin, returning captured stdout and stderr. gpg is killed when
-// 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. A gpg-agent that gpg
-	// starts runs detached and holds none of gpg's output, but another
-	// process gpg leaves behind (a wrapper script that runs the real gpg
-	// without exec, for example) can keep gpg's stdout or stderr open, and
-	// Run would wait for it to exit. WaitDelay stops that wait
-	// gpgWaitDelay after the kill; that process is left running.
-	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
-	// are not, so the guarantee that matters is placement: every
-	// caller-supplied value is passed either as the value of a named
-	// 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
-		ctx, "gpg", fullArgs...)
-	cmd.WaitDelay = gpgWaitDelay
-	cmd.Stdin = stdin
-
-	var stdout, stderr bytes.Buffer
-
-	cmd.Stdout = &stdout
-	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
-}
-
-// parseFingerprint extracts the first fingerprint from gpg --with-colons
-// output, or returns ok=false if none is present.
-func parseFingerprint(colonOutput string) (string, bool) {
-	for line := range strings.SplitSeq(colonOutput, "\n") {
-		fields := strings.Split(line, ":")
-		if len(fields) >= gpgFingerprintMinFields &&
-			fields[0] == gpgFingerprintField {
-			return fields[9], true
-		}
-	}
-
-	return "", false
-}
-
-// gpgSign creates a detached signature of the data using the specified key.
-// Returns the armored detached signature.
-func gpgSign(ctx context.Context, data []byte, keyID GPGKeyID) ([]byte, error) {
-	stdout, stderr, err := runGPG(ctx, bytes.NewReader(data),
-		"--detach-sign",
-		gpgOptArmor,
-		"--local-user", string(keyID),
-	)
-	if err != nil {
-		return nil, fmt.Errorf("gpg sign failed: %w: %s", err, stderr.String())
-	}
-
-	return stdout.Bytes(), nil
-}
-
-// gpgExportPublicKey exports the public key for the specified key ID.
-// Returns the armored public key.
-func gpgExportPublicKey(ctx context.Context, keyID GPGKeyID) ([]byte, error) {
-	stdout, stderr, err := runGPG(ctx, nil,
-		gpgArgs([]string{"--export", gpgOptArmor}, string(keyID))...,
-	)
-	if err != nil {
-		return nil, fmt.Errorf("gpg export failed: %w: %s", err, stderr.String())
-	}
-
-	if stdout.Len() == 0 {
-		return nil, fmt.Errorf("%w: %s", errGPGKeyNotFound, keyID)
-	}
-
-	return stdout.Bytes(), nil
-}
-
-// gpgGetKeyFingerprint gets the full fingerprint for a key ID.
-func gpgGetKeyFingerprint(ctx context.Context, keyID GPGKeyID) ([]byte, error) {
-	stdout, stderr, err := runGPG(ctx, nil,
-		gpgArgs([]string{"--with-colons", "--fingerprint"}, string(keyID))...,
-	)
-	if err != nil {
-		return nil, fmt.Errorf(
-			"gpg fingerprint lookup failed: %w: %s", err, stderr.String(),
-		)
-	}
-
-	fpr, ok := parseFingerprint(stdout.String())
-	if !ok {
-		return nil, fmt.Errorf("%w: %s", errFingerprintNotFound, keyID)
-	}
-
-	return []byte(fpr), nil
-}
-
-// 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(ctx context.Context, pubKey []byte) (string, error) {
-	// Create temporary directory for GPG operations
-	tmpDir, err := os.MkdirTemp("", "mfer-gpg-fingerprint-*")
-	if err != nil {
-		return "", fmt.Errorf("failed to create temp dir: %w", err)
-	}
-
-	defer func() { _ = os.RemoveAll(tmpDir) }()
-
-	// Set restrictive permissions
-	err = os.Chmod(tmpDir, privateDirPerms)
-	if err != nil {
-		return "", fmt.Errorf("failed to set temp dir permissions: %w", err)
-	}
-
-	// Write public key to temp file
-	pubKeyFile := filepath.Join(tmpDir, "pubkey.asc")
-
-	err = os.WriteFile(pubKeyFile, pubKey, privateFilePerms)
-	if err != nil {
-		return "", fmt.Errorf("failed to write public key: %w", err)
-	}
-
-	// Import the public key into the temporary keyring
-	_, importStderr, err := runGPG(ctx, nil,
-		gpgArgs([]string{gpgOptHomedir, tmpDir, "--import"}, pubKeyFile)...,
-	)
-	if err != nil {
-		return "", fmt.Errorf(
-			"failed to import public key: %w: %s", err, importStderr.String(),
-		)
-	}
-
-	// List keys to get fingerprint
-	listStdout, listStderr, err := runGPG(ctx, nil,
-		"--homedir", tmpDir,
-		"--with-colons",
-		"--fingerprint",
-	)
-	if err != nil {
-		return "", fmt.Errorf(
-			"failed to list keys: %w: %s", err, listStderr.String(),
-		)
-	}
-
-	fpr, ok := parseFingerprint(listStdout.String())
-	if !ok {
-		return "", errImportedFPRNotFound
-	}
-
-	return fpr, nil
-}
-
-// 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(ctx context.Context, data, signature, pubKey []byte) error {
-	// Create temporary directory for GPG operations
-	tmpDir, err := os.MkdirTemp("", "mfer-gpg-verify-*")
-	if err != nil {
-		return fmt.Errorf("failed to create temp dir: %w", err)
-	}
-
-	defer func() { _ = os.RemoveAll(tmpDir) }()
-
-	// Set restrictive permissions
-	err = os.Chmod(tmpDir, privateDirPerms)
-	if err != nil {
-		return fmt.Errorf("failed to set temp dir permissions: %w", err)
-	}
-
-	// Write public key to temp file
-	pubKeyFile := filepath.Join(tmpDir, "pubkey.asc")
-
-	err = os.WriteFile(pubKeyFile, pubKey, privateFilePerms)
-	if err != nil {
-		return fmt.Errorf("failed to write public key: %w", err)
-	}
-
-	// Write signature to temp file
-	sigFile := filepath.Join(tmpDir, "signature.asc")
-
-	err = os.WriteFile(sigFile, signature, privateFilePerms)
-	if err != nil {
-		return fmt.Errorf("failed to write signature: %w", err)
-	}
-
-	// Write data to temp file
-	dataFile := filepath.Join(tmpDir, "data")
-
-	err = os.WriteFile(dataFile, data, privateFilePerms)
-	if err != nil {
-		return fmt.Errorf("failed to write data: %w", err)
-	}
-
-	// Import the public key into the temporary keyring
-	_, importStderr, err := runGPG(ctx, nil,
-		gpgArgs([]string{gpgOptHomedir, tmpDir, "--import"}, pubKeyFile)...,
-	)
-	if err != nil {
-		return fmt.Errorf(
-			"failed to import public key: %w: %s", err, importStderr.String(),
-		)
-	}
-
-	// Verify the signature
-	_, verifyStderr, err := runGPG(ctx, nil,
-		gpgArgs([]string{gpgOptHomedir, tmpDir, gpgOptVerify},
-			sigFile, dataFile)...,
-	)
-	if err != nil {
-		return fmt.Errorf(
-			"signature verification failed: %w: %s", err, verifyStderr.String(),
-		)
-	}
-
-	return nil
-}

mfer/gpg_test.go

@@ -1,488 +0,0 @@
-//nolint:testpackage // white-box tests exercise unexported internals
-package mfer
-
-import (
-	"bytes"
-	"context"
-	"io"
-	"os"
-	"os/exec"
-	"path/filepath"
-	"strconv"
-	"strings"
-	"syscall"
-	"testing"
-	"time"
-
-	"github.com/spf13/afero"
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-// testGPGEnv sets up a temporary GPG home directory with a test key.
-// Returns the key ID and the GPG home directory; callers must point
-// GNUPGHOME at the returned directory (via t.Setenv) before using the
-// gpg helpers under test.
-func testGPGEnv(t *testing.T) (GPGKeyID, string) {
-	t.Helper()
-
-	// Check if gpg is installed
-	_, err := exec.LookPath("gpg")
-	if err != nil {
-		t.Skip("gpg not installed, skipping signing test")
-	}
-
-	// Create temporary GPG home directory (0700 by default)
-	gpgHome := t.TempDir()
-
-	// Generate a test key with no passphrase
-	keyParams := `%no-protection
-Key-Type: RSA
-Key-Length: 2048
-Name-Real: MFER Test Key
-Name-Email: test@mfer.test
-Expire-Date: 0
-%commit
-`
-	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(ctx, "gpg",
-		"--batch", "--gen-key", paramsFile)
-
-	cmd.Env = append(os.Environ(), "GNUPGHOME="+gpgHome)
-
-	output, err := cmd.CombinedOutput()
-	if err != nil {
-		t.Skipf("failed to generate test GPG key: %v: %s", err, output)
-	}
-
-	// Get the key fingerprint
-	cmd = exec.CommandContext(ctx, "gpg",
-		"--list-keys", "--with-colons", "test@mfer.test")
-
-	cmd.Env = append(os.Environ(), "GNUPGHOME="+gpgHome)
-
-	output, err = cmd.Output()
-	if err != nil {
-		t.Fatalf("failed to list test key: %v", err)
-	}
-
-	// Parse fingerprint from output
-	var keyID string
-
-	for line := range strings.SplitSeq(string(output), "\n") {
-		fields := strings.Split(line, ":")
-		if len(fields) >= gpgFingerprintMinFields &&
-			fields[0] == gpgFingerprintField {
-			keyID = fields[9]
-
-			break
-		}
-	}
-
-	if keyID == "" {
-		t.Fatal("failed to find test key fingerprint")
-	}
-
-	return GPGKeyID(keyID), gpgHome
-}
-
-func TestGPGSign(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	data := []byte("test data to sign")
-	sig, err := gpgSign(context.Background(), data, keyID)
-	require.NoError(t, err)
-	assert.NotEmpty(t, sig)
-	assert.Contains(t, string(sig), "-----BEGIN PGP SIGNATURE-----")
-	assert.Contains(t, string(sig), "-----END PGP SIGNATURE-----")
-}
-
-func TestGPGExportPublicKey(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	pubKey, err := gpgExportPublicKey(context.Background(), keyID)
-	require.NoError(t, err)
-	assert.NotEmpty(t, pubKey)
-	assert.Contains(t, string(pubKey), "-----BEGIN PGP PUBLIC KEY BLOCK-----")
-	assert.Contains(t, string(pubKey), "-----END PGP PUBLIC KEY BLOCK-----")
-}
-
-func TestGPGGetKeyFingerprint(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	fingerprint, err := gpgGetKeyFingerprint(context.Background(), keyID)
-	require.NoError(t, err)
-	assert.NotEmpty(t, fingerprint)
-	// The fingerprint should be 40 hex chars
-	assert.Len(t, fingerprint, 40, "fingerprint should be 40 hex chars")
-}
-
-// TestGPGArgsSeparatesPositionals pins that caller-supplied values are
-// placed after an end-of-options marker. Key IDs arrive from --sign-key
-// and MFER_SIGN_KEY as bare positional arguments, so without the marker
-// a value beginning with "-" would be parsed by gpg as one of its own
-// options.
-func TestGPGArgsSeparatesPositionals(t *testing.T) {
-	t.Parallel()
-
-	assert.Equal(t,
-		[]string{"--opt-a", "--opt-b", "--", "--version"},
-		gpgArgs([]string{"--opt-a", "--opt-b"}, "--version"))
-
-	assert.Equal(t,
-		[]string{"--opt-c", "--", "sig", "data"},
-		gpgArgs([]string{"--opt-c"}, "sig", "data"))
-
-	assert.Equal(t, []string{"--opt-d", "--"},
-		gpgArgs([]string{"--opt-d"}))
-}
-
-// TestGPGOptionLikeKeyIDIsNotAnOption drives real gpg with a key ID that
-// looks like an option and asserts it is treated as a (nonexistent) key
-// rather than executed as gpg's own --version.
-func TestGPGOptionLikeKeyIDIsNotAnOption(t *testing.T) {
-	_, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	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(context.Background(), GPGKeyID("--version"))
-	require.Error(t, err)
-	assert.NotContains(t, string(fpr), "gpg (GnuPG)")
-}
-
-func TestGPGSignInvalidKey(t *testing.T) {
-	// Set up test environment (we need GNUPGHOME set)
-	_, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	data := []byte("test data")
-	_, err := gpgSign(context.Background(), data,
-		GPGKeyID("NONEXISTENT_KEY_ID_12345"))
-	assert.Error(t, err)
-}
-
-func TestBuilderWithSigning(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	// Create a builder with signing options
-	b := NewBuilder()
-	b.SetSigningOptions(&SigningOptions{
-		KeyID: keyID,
-	})
-
-	// Add a test file
-	content := []byte("test file content")
-	reader := bytes.NewReader(content)
-	_, err := b.AddFile("test.txt", FileSize(len(content)), ModTime{}, 0, reader, nil)
-	require.NoError(t, err)
-
-	// Build the manifest
-	var buf bytes.Buffer
-
-	err = b.Build(context.Background(), &buf)
-	require.NoError(t, err)
-
-	// Parse the manifest and verify signature fields are populated
-	manifest, err := NewManifestFromReader(&buf)
-	require.NoError(t, err)
-	require.NotNil(t, manifest.pbOuter)
-
-	assert.NotEmpty(t, manifest.pbOuter.GetSignature(),
-		"signature should be populated")
-	assert.NotEmpty(t, manifest.pbOuter.GetSigner(), "signer should be populated")
-	assert.NotEmpty(t, manifest.pbOuter.GetSigningPubKey(),
-		"signing public key should be populated")
-
-	// Verify signature is a valid PGP signature
-	assert.Contains(t, string(manifest.pbOuter.GetSignature()),
-		"-----BEGIN PGP SIGNATURE-----")
-
-	// Verify public key is a valid PGP public key block
-	assert.Contains(t, string(manifest.pbOuter.GetSigningPubKey()),
-		"-----BEGIN PGP PUBLIC KEY BLOCK-----")
-}
-
-func TestScannerWithSigning(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	// Create in-memory filesystem with test files
-	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t,
-		afero.WriteFile(fs, "/testdir/file1.txt", []byte("content1"), 0o644))
-	require.NoError(t,
-		afero.WriteFile(fs, "/testdir/file2.txt", []byte("content2"), 0o644))
-
-	// Create scanner with signing options
-	opts := &ScannerOptions{
-		Fs: fs,
-		SigningOptions: &SigningOptions{
-			KeyID: keyID,
-		},
-	}
-	s := NewScannerWithOptions(opts)
-
-	// Enumerate files
-	require.NoError(t, s.EnumeratePath("/testdir", nil))
-	assert.Equal(t, FileCount(2), s.FileCount())
-
-	// Generate signed manifest
-	var buf bytes.Buffer
-	require.NoError(t, s.ToManifest(context.Background(), &buf, nil))
-
-	// Parse and verify
-	manifest, err := NewManifestFromReader(&buf)
-	require.NoError(t, err)
-
-	assert.NotEmpty(t, manifest.pbOuter.GetSignature())
-	assert.NotEmpty(t, manifest.pbOuter.GetSigner())
-	assert.NotEmpty(t, manifest.pbOuter.GetSigningPubKey())
-}
-
-func TestGPGVerify(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	data := []byte("test data to sign and verify")
-	sig, err := gpgSign(context.Background(), data, keyID)
-	require.NoError(t, err)
-
-	pubKey, err := gpgExportPublicKey(context.Background(), keyID)
-	require.NoError(t, err)
-
-	// Verify the signature
-	err = gpgVerify(context.Background(), data, sig, pubKey)
-	require.NoError(t, err)
-}
-
-func TestGPGVerifyInvalidSignature(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	data := []byte("test data to sign")
-	sig, err := gpgSign(context.Background(), data, keyID)
-	require.NoError(t, err)
-
-	pubKey, err := gpgExportPublicKey(context.Background(), keyID)
-	require.NoError(t, err)
-
-	// Try to verify with different data - should fail
-	wrongData := []byte("different data")
-	err = gpgVerify(context.Background(), wrongData, sig, pubKey)
-	assert.Error(t, err)
-}
-
-func TestGPGVerifyBadPublicKey(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	data := []byte("test data")
-	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(context.Background(), data, sig, badPubKey)
-	assert.Error(t, err)
-}
-
-func TestManifestSignatureVerification(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	// Create a builder with signing options
-	b := NewBuilder()
-	b.SetSigningOptions(&SigningOptions{
-		KeyID: keyID,
-	})
-
-	// Add a test file
-	content := []byte("test file content for verification")
-	reader := bytes.NewReader(content)
-	_, err := b.AddFile("test.txt", FileSize(len(content)), ModTime{}, 0, reader, nil)
-	require.NoError(t, err)
-
-	// Build the manifest
-	var buf bytes.Buffer
-
-	err = b.Build(context.Background(), &buf)
-	require.NoError(t, err)
-
-	// Parse the manifest - signature should be verified during load
-	manifest, err := NewManifestFromReader(&buf)
-	require.NoError(t, err)
-	require.NotNil(t, manifest)
-
-	// Signature should be present and valid
-	assert.NotEmpty(t, manifest.pbOuter.GetSignature())
-}
-
-func TestManifestTamperedSignatureFails(t *testing.T) {
-	keyID, gpgHome := testGPGEnv(t)
-	t.Setenv("GNUPGHOME", gpgHome)
-
-	// Create a signed manifest
-	b := NewBuilder()
-	b.SetSigningOptions(&SigningOptions{
-		KeyID: keyID,
-	})
-
-	content := []byte("test file content")
-	reader := bytes.NewReader(content)
-	_, err := b.AddFile("test.txt", FileSize(len(content)), ModTime{}, 0, reader, nil)
-	require.NoError(t, err)
-
-	var buf bytes.Buffer
-
-	err = b.Build(context.Background(), &buf)
-	require.NoError(t, err)
-
-	// Tamper with the signature by replacing some bytes
-	data := buf.Bytes()
-	// Find and modify a byte in the signature portion
-	for i := range data {
-		if i > 100 && data[i] == 'A' {
-			data[i] = 'B'
-
-			break
-		}
-	}
-
-	// Try to load the tampered manifest - should fail
-	_, err = NewManifestFromReader(bytes.NewReader(data))
-	assert.Error(t, err)
-}
-
-func TestBuilderWithoutSigning(t *testing.T) {
-	t.Parallel()
-
-	// Create a builder without signing options
-	b := NewBuilder()
-
-	// Add a test file
-	content := []byte("test file content")
-	reader := bytes.NewReader(content)
-	_, err := b.AddFile("test.txt", FileSize(len(content)), ModTime{}, 0, reader, nil)
-	require.NoError(t, err)
-
-	// Build the manifest
-	var buf bytes.Buffer
-
-	err = b.Build(context.Background(), &buf)
-	require.NoError(t, err)
-
-	// Parse the manifest and verify signature fields are empty
-	manifest, err := NewManifestFromReader(&buf)
-	require.NoError(t, err)
-	require.NotNil(t, manifest.pbOuter)
-
-	assert.Empty(t, manifest.pbOuter.GetSignature(),
-		"signature should be empty when not signing")
-	assert.Empty(t, manifest.pbOuter.GetSigner(),
-		"signer should be empty when not signing")
-	assert.Empty(t, manifest.pbOuter.GetSigningPubKey(),
-		"signing public key should be empty when not signing")
-}
-
-// fakeGPGPath writes script as an executable named gpg into a temporary
-// directory and returns a PATH value with that directory first.
-func fakeGPGPath(t *testing.T, script string) string {
-	t.Helper()
-
-	binDir := t.TempDir()
-	//nolint:gosec // G306: the fake gpg has to be executable
-	require.NoError(t, os.WriteFile(filepath.Join(binDir, "gpg"),
-		[]byte(script), 0o700))
-
-	return binDir + string(os.PathListSeparator) + os.Getenv("PATH")
-}
-
-// 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) {
-	t.Setenv("PATH", fakeGPGPath(t, "#!/bin/sh\nexec sleep 10\n"))
-
-	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")
-}
-
-// TestGPGCancelWhenChildHoldsOutput uses a fake gpg that runs sleep as a
-// child instead of exec-ing it, the way a wrapper script around the real
-// gpg might. Killing the fake gpg leaves sleep holding its stdout and
-// stderr open; the call must still return once ctx ends instead of waiting
-// for sleep to exit. The fake gpg writes the process ID of sleep to a named
-// pipe; the test ends ctx only after reading it, so sleep is running by
-// then, and kills sleep before returning.
-func TestGPGCancelWhenChildHoldsOutput(t *testing.T) {
-	pidPipe := filepath.Join(t.TempDir(), "sleep.pid")
-	require.NoError(t, syscall.Mkfifo(pidPipe, 0o600))
-	// sleep outlasts the 10 s wait below, so a call that waits for it fails.
-	t.Setenv("PATH", fakeGPGPath(t,
-		"#!/bin/sh\nsleep 60 &\necho $! >'"+pidPipe+"'\nwait\n"))
-
-	ctx, cancel := context.WithCancel(context.Background())
-	defer cancel()
-
-	signErr := make(chan error, 1)
-
-	go func() {
-		_, err := gpgSign(ctx, []byte("data"), GPGKeyID("any"))
-		signErr <- err
-	}()
-
-	pid, err := os.ReadFile(pidPipe) //nolint:gosec // G304: path inside t.TempDir()
-	require.NoError(t, err)
-
-	n, err := strconv.Atoi(strings.TrimSpace(string(pid)))
-	require.NoError(t, err)
-
-	sleep, err := os.FindProcess(n)
-	require.NoError(t, err)
-	t.Cleanup(func() { require.NoError(t, sleep.Kill()) })
-
-	cancel()
-
-	// The call should return about gpgWaitDelay (one second) after the
-	// cancel. 10 s is far above that and well under the 30 s test timeout,
-	// which would abort the whole package before the cleanup kills sleep.
-	select {
-	case err := <-signErr:
-		require.ErrorIs(t, err, context.Canceled)
-	case <-time.After(10 * time.Second):
-		t.Fatal("the call waited for the child holding gpg's output to exit")
-	}
-}
-
-// 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/manifest.go

@@ -10,7 +10,7 @@ import (
 )
 
 var (
-	errOuterNotSet  = errors.New("pbOuter not set")
+	errOuterNotSet  = errors.New("outer message not set")
 	errUUIDNotSet   = errors.New("UUID not set")
 	errSHA256NotSet = errors.New("SHA256 hash not set")
 )
@@ -47,6 +47,23 @@ func (m *manifest) Files() []*MFFilePath {
 	return m.pbInner.GetFiles()
 }
 
+// Signer returns the fingerprint of the key that made a loaded manifest's
+// signature, which loading the manifest checked, or nil if the manifest is
+// not signed.
+func (m *manifest) Signer() []byte {
+	if len(m.pbOuter.GetSignature()) == 0 {
+		return nil
+	}
+
+	return m.pbOuter.GetSigner()
+}
+
+// CreatedAt returns the createdAt timestamp of a loaded manifest, or nil
+// if the manifest has none.
+func (m *manifest) CreatedAt() *Timestamp {
+	return m.pbInner.GetCreatedAt()
+}
+
 // signatureString generates the canonical string used for signing/verification.
 // Format: MAGIC-UUID-MULTIHASH where UUID and multihash are hex-encoded.
 // Requires pbOuter to be set with Uuid and Sha256 fields.
@@ -65,7 +82,7 @@ func (m *manifest) signatureString() (string, error) {
 
 	mh, err := multihash.Encode(m.pbOuter.GetSha256(), multihash.SHA2_256)
 	if err != nil {
-		return "", fmt.Errorf("failed to encode multihash: %w", err)
+		return "", fmt.Errorf("encode multihash: %w", err)
 	}
 
 	uuidStr := hex.EncodeToString(m.pbOuter.GetUuid())

mfer/manifest_test.go

@@ -0,0 +1,30 @@
+//nolint:testpackage // white-box tests exercise unexported internals
+package mfer
+
+import (
+	"encoding/hex"
+	"testing"
+	"uuid"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// TestSignatureString checks the canonical string for the UUID and sha256
+// of the example in the Signature Scheme section of docs/FORMAT.md, which
+// shows the same string.
+func TestSignatureString(t *testing.T) {
+	t.Parallel()
+
+	manifestUUID := uuid.MustParse("b0fb6918-6298-443b-ada2-1b162f4dc0b3")
+	sha256Hash, err := hex.DecodeString(
+		"e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855")
+	require.NoError(t, err)
+
+	m := &manifest{pbOuter: &MFFileOuter{Uuid: manifestUUID[:], Sha256: sha256Hash}}
+
+	got, err := m.signatureString()
+	require.NoError(t, err)
+	assert.Equal(t, "ZNAVSRFG-b0fb69186298443bada21b162f4dc0b3-"+
+		"1220e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", got)
+}

mfer/mf.pb.go

@@ -223,11 +223,14 @@ type MFFileOuter struct {
 	// uuid must match the uuid in the inner message
 	Uuid         []byte `protobuf:"bytes,105,opt,name=uuid,proto3" json:"uuid,omitempty"`
 	InnerMessage []byte `protobuf:"bytes,199,opt,name=innerMessage,proto3" json:"innerMessage,omitempty"`
-	//detached signature, ascii or binary
+	// one OpenPGP signature, armored or binary, over the canonical string
+	// ZNAVSRFG-<uuid>-<sha256 as a multihash>, with the uuid as 32
+	// lower-case hex digits and no hyphens, and the multihash in lower-case
+	// hex (see docs/FORMAT.md). A signature is never stored anywhere else.
 	Signature []byte `protobuf:"bytes,201,opt,name=signature,proto3,oneof" json:"signature,omitempty"`
-	//full GPG key id
+	// fingerprint of the signing primary key, in upper-case hex
 	Signer []byte `protobuf:"bytes,202,opt,name=signer,proto3,oneof" json:"signer,omitempty"`
-	//full GPG signing public key, ascii or binary
+	// OpenPGP public key of the signer, one primary key, armored or binary
 	SigningPubKey []byte `protobuf:"bytes,203,opt,name=signingPubKey,proto3,oneof" json:"signingPubKey,omitempty"`
 	unknownFields protoimpl.UnknownFields
 	sizeCache     protoimpl.SizeCache
@@ -330,8 +333,8 @@ type MFFilePath struct {
 	state protoimpl.MessageState `protogen:"open.v1"`
 	// required attributes:
 	// Path invariants: must be valid UTF-8, use forward slashes only,
-	// be relative (no leading /), contain no ".." segments, and no
+	// be relative (no leading /), contain no ".." or "." segments, and
-	// empty segments (no "//").
+	// no empty segments (no "//").
 	Path string `protobuf:"bytes,1,opt,name=path,proto3" json:"path,omitempty"`
 	Size int64  `protobuf:"varint,2,opt,name=size,proto3" json:"size,omitempty"`
 	// gotta have at least one:

mfer/mf.proto

@@ -32,23 +32,25 @@ message MFFileOuter {
     bytes uuid = 105;
 
     bytes innerMessage = 199;
-    // 2xx for optional manifest root attributes
-    // think we might use gosignify instead of gpg:
-    // github.com/frankbraun/gosignify
 
-    //detached signature, ascii or binary
+    // 2xx for optional manifest root attributes
+
+    // one OpenPGP signature, armored or binary, over the canonical string
+    // ZNAVSRFG-<uuid>-<sha256 as a multihash>, with the uuid as 32
+    // lower-case hex digits and no hyphens, and the multihash in lower-case
+    // hex (see docs/FORMAT.md). A signature is never stored anywhere else.
     optional bytes signature = 201;
-    //full GPG key id
+    // fingerprint of the signing primary key, in upper-case hex
     optional bytes signer = 202;
-    //full GPG signing public key, ascii or binary
+    // OpenPGP public key of the signer, one primary key, armored or binary
     optional bytes signingPubKey = 203;
 }
 
 message MFFilePath {
     // required attributes:
     // Path invariants: must be valid UTF-8, use forward slashes only,
-    // be relative (no leading /), contain no ".." segments, and no
+    // be relative (no leading /), contain no ".." or "." segments, and
-    // empty segments (no "//").
+    // no empty segments (no "//").
     string path = 1;
     int64 size = 2;
 

mfer/mf.proto.sha256

@@ -1 +1 @@
-3d4dcb0b2f4640dd3ae6bb48b833e9f26ae9771e2d3e88bd646e7f1724dda654  mf.proto
+1668b2f6b8639a9213873474e58dbacb3a4ef77cc27c42253cad8dd076e5f206  mf.proto

mfer/openpgp.go

@@ -0,0 +1,419 @@
+package mfer
+
+import (
+	"bytes"
+	"encoding/hex"
+	"errors"
+	"fmt"
+	"io"
+	"slices"
+	"strings"
+	"time"
+
+	"github.com/ProtonMail/go-crypto/openpgp"
+	"github.com/ProtonMail/go-crypto/openpgp/armor"
+	pgperrors "github.com/ProtonMail/go-crypto/openpgp/errors"
+	"github.com/ProtonMail/go-crypto/openpgp/packet"
+)
+
+const (
+	// The tags of OpenPGP signature, key and subkey packets (RFC 9580,
+	// section 5). Subkeys have tags of their own, so each secret or public
+	// key packet is one primary key.
+	signaturePacketTag    = 2
+	secretKeyPacketTag    = 5
+	publicKeyPacketTag    = 6
+	secretSubkeyPacketTag = 7
+	publicSubkeyPacketTag = 14
+
+	// In the body of a key or subkey packet the algorithm octet follows
+	// the version octet and the four-octet creation time, and from version
+	// 5 on a four-octet length as well (RFC 9580, section 5.5.2).
+	keyAlgorithmOffset            = 5
+	firstKeyVersionWithLength     = 5
+	keyAlgorithmOffsetAfterLength = 9
+
+	// signingKeyVersion is the only OpenPGP key version mfer signs with.
+	// Its fingerprints are 40 hex characters, the length
+	// --require-signature takes.
+	signingKeyVersion = 4
+
+	// armorBegin and armorEnd start the lines that begin and end an
+	// armored block.
+	armorBegin = "-----BEGIN "
+	armorEnd   = "-----END "
+)
+
+var (
+	errKeyCount    = errors.New("must hold exactly one key")
+	errDSAKey      = errors.New("must not hold a DSA key")
+	errSecretKey   = errors.New("must not hold a secret key")
+	errNoSecretKey = errors.New("signing key file holds no secret key")
+	errNotV4Key    = errors.New("signing key must be an OpenPGP version 4 key, " +
+		"the only kind whose fingerprint --require-signature takes")
+	errNoPassphrase = errors.New(
+		"signing key is protected and no passphrase was given")
+	errNotOneSignature = errors.New(
+		"signature must hold exactly one signature")
+	errNotOneArmoredBlock = errors.New(
+		"must be exactly one armored block and nothing else")
+	errMalformedArmor        = errors.New("armor is malformed")
+	errKeyNotValidWhenSigned = errors.New(
+		"signature was made when its key was not valid")
+)
+
+// SigningOptions holds the key a manifest is signed with.
+type SigningOptions struct {
+	// SecretKey is an OpenPGP secret key, armored or binary, as
+	// gpg --export-secret-keys writes it. It must hold one primary key.
+	SecretKey []byte
+	// Passphrase unlocks SecretKey when it is protected.
+	Passphrase []byte
+}
+
+// SecretKeyIsProtected reports whether the OpenPGP secret key secretKey,
+// armored or binary, needs a passphrase to sign. It fails unless
+// secretKey holds one version 4 primary key with its secret key.
+func SecretKeyIsProtected(secretKey []byte) (bool, error) {
+	key, err := readSecretKey(secretKey)
+	if err != nil {
+		return false, err
+	}
+
+	return isProtected(key), nil
+}
+
+// SecretKeyFingerprint returns the fingerprint of the OpenPGP secret key
+// secretKey, armored or binary, as a manifest signed with it records its
+// signer. It fails unless secretKey holds one version 4 primary key with
+// its secret key.
+func SecretKeyFingerprint(secretKey []byte) (string, error) {
+	key, err := readSecretKey(secretKey)
+	if err != nil {
+		return "", err
+	}
+
+	return fingerprint(key), nil
+}
+
+// CheckSigningKey fails unless opts can sign now: opts.SecretKey must hold
+// one version 4 primary key with a secret key that may sign and has not
+// expired or been revoked, and opts.Passphrase must unlock it when it is
+// protected. It lets a caller find a key that cannot sign before it builds
+// a manifest.
+func CheckSigningKey(opts *SigningOptions) error {
+	key, err := readSigningKey(opts)
+	if err != nil {
+		return err
+	}
+
+	// Signing nothing fails wherever signing the manifest would.
+	err = openpgp.DetachSign(io.Discard, key, bytes.NewReader(nil), nil)
+	if err != nil {
+		return fmt.Errorf("signing key cannot sign: %w", err)
+	}
+
+	return nil
+}
+
+// readSigningKey returns the key in opts.SecretKey, unlocked with
+// opts.Passphrase if it is protected.
+func readSigningKey(opts *SigningOptions) (*openpgp.Entity, error) {
+	key, err := readSecretKey(opts.SecretKey)
+	if err != nil {
+		return nil, err
+	}
+
+	if !isProtected(key) {
+		return key, nil
+	}
+
+	if len(opts.Passphrase) == 0 {
+		return nil, errNoPassphrase
+	}
+
+	err = key.DecryptPrivateKeys(opts.Passphrase)
+	if err != nil {
+		return nil, fmt.Errorf("unlock signing key: %w", err)
+	}
+
+	return key, nil
+}
+
+// readSecretKey returns the one key in secretKey, armored or binary,
+// which must be a version 4 key and include its secret key.
+func readSecretKey(secretKey []byte) (*openpgp.Entity, error) {
+	key, err := readOneKey(secretKey, "signing key file", false)
+	if err != nil {
+		return nil, err
+	}
+
+	if key.PrimaryKey.Version != signingKeyVersion {
+		return nil, fmt.Errorf("%w; this key is version %d",
+			errNotV4Key, key.PrimaryKey.Version)
+	}
+
+	if key.PrivateKey == nil {
+		return nil, errNoSecretKey
+	}
+
+	return key, nil
+}
+
+// readOneKey returns the key in data, armored or binary, which must hold
+// exactly one primary key and no DSA key or subkey, and when publicOnly no
+// secret key or subkey either. what names data in errors.
+func readOneKey(data []byte, what string, publicOnly bool) (*openpgp.Entity, error) {
+	packets, err := dearmor(data)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", what, err)
+	}
+
+	keys, err := countPackets(packets, secretKeyPacketTag, publicKeyPacketTag)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", what, err)
+	}
+
+	if keys != 1 {
+		return nil, fmt.Errorf("%s %w, found %d", what, errKeyCount, keys)
+	}
+
+	// openpgp.ReadKeyRing checks the numbers of every secret key it reads,
+	// and an ElGamal secret subkey with a very large prime makes that take
+	// minutes.
+	secretKeys, err := countPackets(packets, secretKeyPacketTag, secretSubkeyPacketTag)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", what, err)
+	}
+
+	if publicOnly && secretKeys != 0 {
+		return nil, fmt.Errorf("%s %w", what, errSecretKey)
+	}
+
+	// openpgp.ReadKeyRing also checks every self-signature, and a DSA key
+	// with very large numbers makes each check take seconds to minutes.
+	dsa, err := holdsDSAKey(packets)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", what, err)
+	}
+
+	if dsa {
+		return nil, fmt.Errorf("%s %w", what, errDSAKey)
+	}
+
+	keyring, err := openpgp.ReadKeyRing(bytes.NewReader(packets))
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", what, err)
+	}
+
+	// openpgp.ReadKeyRing also reads a subkey packet at the start as a
+	// primary key.
+	if len(keyring) != 1 {
+		return nil, fmt.Errorf("%s %w, found %d", what, errKeyCount, len(keyring))
+	}
+
+	return keyring[0], nil
+}
+
+// isProtected reports whether any secret key in key needs a passphrase.
+func isProtected(key *openpgp.Entity) bool {
+	if key.PrivateKey.Encrypted {
+		return true
+	}
+
+	for _, subkey := range key.Subkeys {
+		if subkey.PrivateKey != nil && subkey.PrivateKey.Encrypted {
+			return true
+		}
+	}
+
+	return false
+}
+
+// armoredPublicKey returns the public part of key, armored.
+func armoredPublicKey(key *openpgp.Entity) ([]byte, error) {
+	var buf bytes.Buffer
+
+	w, err := armor.Encode(&buf, openpgp.PublicKeyType, nil)
+	if err != nil {
+		return nil, err
+	}
+
+	err = key.Serialize(w)
+	if err != nil {
+		return nil, fmt.Errorf("write public key: %w", err)
+	}
+
+	err = w.Close()
+	if err != nil {
+		return nil, err
+	}
+
+	return buf.Bytes(), nil
+}
+
+// fingerprint returns the fingerprint of key's primary key in upper-case
+// hex, as gpg prints it.
+func fingerprint(key *openpgp.Entity) string {
+	return strings.ToUpper(hex.EncodeToString(key.PrimaryKey.Fingerprint))
+}
+
+// verifySignature checks that signature is one good, unexpired OpenPGP
+// signature over data, made by the one primary key in pubKey or one of its
+// subkeys while that key was valid, and returns that primary key's
+// fingerprint. The key may have expired since. signature and pubKey may
+// each be armored or binary.
+func verifySignature(data, signature, pubKey []byte) (string, error) {
+	key, err := readOneKey(pubKey, "embedded public key block", true)
+	if err != nil {
+		return "", err
+	}
+
+	sigData, err := dearmor(signature)
+	if err != nil {
+		return "", fmt.Errorf("read signature: %w", err)
+	}
+
+	sigs, err := countPackets(sigData, signaturePacketTag)
+	if err != nil {
+		return "", fmt.Errorf("read signature: %w", err)
+	}
+
+	if sigs != 1 {
+		return "", fmt.Errorf("%w, found %d", errNotOneSignature, sigs)
+	}
+
+	sig, _, err := openpgp.VerifyDetachedSignature(openpgp.EntityList{key},
+		bytes.NewReader(data), bytes.NewReader(sigData), nil)
+	// A manifest outlives its signing key, so a signature by a key that
+	// has expired since is still good, unless the signature has expired
+	// itself. The library does not check that once it finds the key
+	// expired.
+	if errors.Is(err, pgperrors.ErrKeyExpired) && sig.SigExpired(time.Now()) {
+		err = pgperrors.ErrSignatureExpired
+	}
+
+	if err != nil && !errors.Is(err, pgperrors.ErrKeyExpired) {
+		return "", fmt.Errorf("verify signature: %w", err)
+	}
+
+	// The check above judges the key as of now. Checking the signature a
+	// second time with the library's clock set to its creation time
+	// requires the primary key, and the subkey that made the signature, to
+	// have been valid then under the key validity rules of RFC 9580. The
+	// key is judged by its current self-signatures and binding signatures:
+	// for a version 4 key the newest self-signature on its primary user
+	// ID, for a version 6 key its newest direct-key signature, and for a
+	// subkey its newest binding signature with the signature embedded in
+	// it. So a signature made before the newest of those is refused.
+	signedAt := &packet.Config{
+		Time: func() time.Time { return sig.CreationTime },
+	}
+
+	_, _, err = openpgp.VerifyDetachedSignature(openpgp.EntityList{key},
+		bytes.NewReader(data), bytes.NewReader(sigData), signedAt)
+	if err != nil {
+		return "", fmt.Errorf("verify signature: %w: %w",
+			errKeyNotValidWhenSigned, err)
+	}
+
+	return fingerprint(key), nil
+}
+
+// dearmor returns the binary OpenPGP data in data: data itself when it is
+// not armored, or else the body of its armored block. Armored data must be
+// one block and nothing else: its first line is the only BEGIN line and
+// its last line the only END line, white space around them aside.
+// armor.Decode skips any text before a BEGIN line and reads only the first
+// block, so without this a second key or signature would go unseen.
+func dearmor(data []byte) ([]byte, error) {
+	if !bytes.Contains(data, []byte(armorBegin)) {
+		return data, nil
+	}
+
+	text := bytes.TrimSpace(data)
+	lastLine := text[bytes.LastIndexByte(text, '\n')+1:]
+
+	if !bytes.HasPrefix(text, []byte(armorBegin)) ||
+		bytes.Count(text, []byte(armorBegin)) != 1 ||
+		!bytes.HasPrefix(lastLine, []byte(armorEnd)) ||
+		bytes.Count(text, []byte(armorEnd)) != 1 {
+		return nil, errNotOneArmoredBlock
+	}
+
+	// armor.Decode passes over a block it cannot read, such as one with a
+	// header line that has no colon, and returns io.EOF on finding no
+	// other.
+	block, err := armor.Decode(bytes.NewReader(text))
+	if err != nil {
+		return nil, errMalformedArmor
+	}
+
+	body, err := io.ReadAll(block.Body)
+	if err != nil {
+		return nil, fmt.Errorf("%w: %w", errMalformedArmor, err)
+	}
+
+	return body, nil
+}
+
+// countPackets returns how many packets in the binary OpenPGP data have
+// one of tags. It reads only each packet's header, so it also counts
+// packets that openpgp.ReadKeyRing skips, such as a key with no user ID
+// or of an algorithm it does not know.
+func countPackets(data []byte, tags ...uint8) (int, error) {
+	packets := packet.NewOpaqueReader(bytes.NewReader(data))
+	count := 0
+
+	for {
+		p, err := packets.Next()
+		if errors.Is(err, io.EOF) {
+			return count, nil
+		}
+
+		if err != nil {
+			return 0, err
+		}
+
+		if slices.Contains(tags, p.Tag) {
+			count++
+		}
+	}
+}
+
+// holdsDSAKey reports whether any key or subkey packet in the binary
+// OpenPGP data holds a DSA key. It reads each packet's algorithm octet
+// rather than parsing the packet, since parsing a secret key packet checks
+// its numbers, which for a DSA key with very large numbers is as slow as
+// checking a self-signature.
+func holdsDSAKey(data []byte) (bool, error) {
+	packets := packet.NewOpaqueReader(bytes.NewReader(data))
+
+	for {
+		p, err := packets.Next()
+		if errors.Is(err, io.EOF) {
+			return false, nil
+		}
+
+		if err != nil {
+			return false, err
+		}
+
+		if !slices.Contains([]uint8{
+			secretKeyPacketTag, publicKeyPacketTag,
+			secretSubkeyPacketTag, publicSubkeyPacketTag,
+		}, p.Tag) {
+			continue
+		}
+
+		offset := keyAlgorithmOffset
+		if len(p.Contents) > 0 && p.Contents[0] >= firstKeyVersionWithLength {
+			offset = keyAlgorithmOffsetAfterLength
+		}
+
+		if len(p.Contents) > offset &&
+			packet.PublicKeyAlgorithm(p.Contents[offset]) == packet.PubKeyAlgoDSA {
+			return true, nil
+		}
+	}
+}

mfer/openpgp_test.go

@@ -0,0 +1,972 @@
+//nolint:testpackage // white-box tests exercise unexported internals
+package mfer
+
+import (
+	"bytes"
+	"context"
+	"crypto"
+	"crypto/dsa" //nolint:staticcheck // SA1019: tests need a DSA key to refuse
+	"io"
+	"math/big"
+	"os"
+	"path/filepath"
+	"slices"
+	"strconv"
+	"strings"
+	"testing"
+	"time"
+
+	"github.com/ProtonMail/go-crypto/openpgp"
+	"github.com/ProtonMail/go-crypto/openpgp/armor"
+	"github.com/ProtonMail/go-crypto/openpgp/elgamal"
+	pgperrors "github.com/ProtonMail/go-crypto/openpgp/errors"
+	"github.com/ProtonMail/go-crypto/openpgp/packet"
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"google.golang.org/protobuf/proto"
+)
+
+// newTestKey returns a new Ed25519 key, which is quick to make, for
+// "MFER Test Key <test@mfer.test>". config may set when it is made and how
+// long it lasts.
+func newTestKey(t *testing.T, config *packet.Config) *openpgp.Entity {
+	t.Helper()
+
+	if config == nil {
+		config = &packet.Config{}
+	}
+
+	config.Algorithm = packet.PubKeyAlgoEdDSA
+
+	key, err := openpgp.NewEntity("MFER Test Key", "", "test@mfer.test", config)
+	require.NoError(t, err)
+
+	return key
+}
+
+// armoredSecretKeys returns keys with their secret keys in one armored
+// block, as gpg --export-secret-keys --armor writes them.
+func armoredSecretKeys(t *testing.T, keys ...*openpgp.Entity) []byte {
+	t.Helper()
+
+	var buf bytes.Buffer
+
+	w, err := armor.Encode(&buf, openpgp.PrivateKeyType, nil)
+	require.NoError(t, err)
+
+	for _, key := range keys {
+		require.NoError(t, key.SerializePrivateWithoutSigning(w, nil))
+	}
+
+	require.NoError(t, w.Close())
+
+	return buf.Bytes()
+}
+
+// armoredPublicKeys returns the public parts of keys in one armored block,
+// as gpg --export --armor writes them.
+func armoredPublicKeys(t *testing.T, keys ...*openpgp.Entity) []byte {
+	t.Helper()
+
+	var buf bytes.Buffer
+
+	w, err := armor.Encode(&buf, openpgp.PublicKeyType, nil)
+	require.NoError(t, err)
+
+	for _, key := range keys {
+		require.NoError(t, key.Serialize(w))
+	}
+
+	require.NoError(t, w.Close())
+
+	return buf.Bytes()
+}
+
+// testSigningOptions returns signing options for a new key with no
+// passphrase.
+func testSigningOptions(t *testing.T) *SigningOptions {
+	t.Helper()
+
+	return &SigningOptions{SecretKey: armoredSecretKeys(t, newTestKey(t, nil))}
+}
+
+// joinArmored returns the armored block first followed by the armored
+// block second on the next line. armor.Encode ends a block without a
+// newline, unlike gpg, and a block only starts at the start of a line.
+func joinArmored(first, second []byte) []byte {
+	return slices.Concat(first, []byte("\n"), second)
+}
+
+// signedTestManifest returns a manifest of one file signed with opts.
+func signedTestManifest(t *testing.T, opts *SigningOptions) []byte {
+	t.Helper()
+
+	b := NewBuilder()
+	b.SetSigningOptions(opts)
+
+	content := []byte("signed file content")
+	_, err := b.AddFile("test.txt", FileSize(len(content)), ModTime{}, 0,
+		bytes.NewReader(content), nil)
+	require.NoError(t, err)
+
+	var buf bytes.Buffer
+
+	require.NoError(t, b.Build(context.Background(), &buf))
+
+	return buf.Bytes()
+}
+
+// rewriteOuter returns manifest with its outer message changed by edit.
+// A signature stays good as long as edit leaves the UUID and hash alone.
+func rewriteOuter(t *testing.T, manifest []byte, edit func(*MFFileOuter)) []byte {
+	t.Helper()
+
+	outer := new(MFFileOuter)
+	require.NoError(t, proto.Unmarshal(manifest[len(MAGIC):], outer))
+
+	edit(outer)
+
+	data, err := proto.Marshal(outer)
+	require.NoError(t, err)
+
+	return append([]byte(MAGIC), data...)
+}
+
+func TestBuilderWithSigning(t *testing.T) {
+	t.Parallel()
+
+	key := newTestKey(t, nil)
+
+	// Create a builder with signing options
+	b := NewBuilder()
+	b.SetSigningOptions(&SigningOptions{SecretKey: armoredSecretKeys(t, key)})
+
+	// Add a test file
+	content := []byte("test file content")
+	reader := bytes.NewReader(content)
+	_, err := b.AddFile("test.txt", FileSize(len(content)), ModTime{}, 0, reader, nil)
+	require.NoError(t, err)
+
+	// Build the manifest
+	var buf bytes.Buffer
+
+	err = b.Build(context.Background(), &buf)
+	require.NoError(t, err)
+
+	// Parse the manifest and verify signature fields are populated
+	manifest, err := NewManifestFromReader(&buf)
+	require.NoError(t, err)
+	require.NotNil(t, manifest.pbOuter)
+
+	assert.NotEmpty(t, manifest.pbOuter.GetSignature(),
+		"signature should be populated")
+	assert.NotEmpty(t, manifest.pbOuter.GetSigningPubKey(),
+		"signing public key should be populated")
+
+	// The signer is the key's fingerprint in 40 upper-case hex characters.
+	assert.Equal(t, fingerprint(key), string(manifest.pbOuter.GetSigner()))
+	assert.Regexp(t, "^[0-9A-F]{40}$", string(manifest.pbOuter.GetSigner()))
+
+	// Verify signature is a valid PGP signature
+	assert.Contains(t, string(manifest.pbOuter.GetSignature()),
+		"-----BEGIN PGP SIGNATURE-----")
+
+	// Verify public key is a valid PGP public key block
+	assert.Contains(t, string(manifest.pbOuter.GetSigningPubKey()),
+		"-----BEGIN PGP PUBLIC KEY BLOCK-----")
+}
+
+// TestManifestSigner checks that Signer gives the signing key's
+// fingerprint for a signed manifest, and nil once the signature is taken
+// out, although the signer field is still there.
+func TestManifestSigner(t *testing.T) {
+	t.Parallel()
+
+	key := newTestKey(t, nil)
+	data := signedTestManifest(t, &SigningOptions{SecretKey: armoredSecretKeys(t, key)})
+
+	signed, err := NewManifestFromReader(bytes.NewReader(data))
+	require.NoError(t, err)
+	assert.Equal(t, fingerprint(key), string(signed.Signer()))
+
+	unsigned, err := NewManifestFromReader(bytes.NewReader(
+		rewriteOuter(t, data, func(outer *MFFileOuter) { outer.Signature = nil })))
+	require.NoError(t, err)
+	assert.Nil(t, unsigned.Signer())
+}
+
+func TestScannerWithSigning(t *testing.T) {
+	t.Parallel()
+
+	// Create in-memory filesystem with test files
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
+	require.NoError(t,
+		afero.WriteFile(fs, "/testdir/file1.txt", []byte("content1"), 0o644))
+	require.NoError(t,
+		afero.WriteFile(fs, "/testdir/file2.txt", []byte("content2"), 0o644))
+
+	// Create scanner with signing options
+	opts := &ScannerOptions{
+		Fs:             fs,
+		SigningOptions: testSigningOptions(t),
+	}
+	s := NewScannerWithOptions(opts)
+
+	// Enumerate files
+	require.NoError(t, s.EnumeratePath("/testdir", nil))
+	assert.Equal(t, FileCount(2), s.FileCount())
+
+	// Generate signed manifest
+	var buf bytes.Buffer
+	require.NoError(t, s.ToManifest(context.Background(), &buf, nil))
+
+	// Parse and verify
+	manifest, err := NewManifestFromReader(&buf)
+	require.NoError(t, err)
+
+	assert.NotEmpty(t, manifest.pbOuter.GetSignature())
+	assert.NotEmpty(t, manifest.pbOuter.GetSigner())
+	assert.NotEmpty(t, manifest.pbOuter.GetSigningPubKey())
+}
+
+// TestSigningWithBinarySecretKey signs with a secret key that is not
+// armored, as gpg --export-secret-keys writes it without --armor.
+func TestSigningWithBinarySecretKey(t *testing.T) {
+	t.Parallel()
+
+	var secretKey bytes.Buffer
+
+	require.NoError(t, newTestKey(t, nil).SerializePrivateWithoutSigning(&secretKey, nil))
+
+	_, err := NewManifestFromReader(bytes.NewReader(
+		signedTestManifest(t, &SigningOptions{SecretKey: secretKey.Bytes()})))
+	require.NoError(t, err)
+}
+
+// TestSigningWithProtectedKey signs with a key protected by a passphrase:
+// with the passphrase, without one, and with a wrong one.
+func TestSigningWithProtectedKey(t *testing.T) {
+	t.Parallel()
+
+	key := newTestKey(t, nil)
+	require.NoError(t, key.EncryptPrivateKeys([]byte("right"), nil))
+	secretKey := armoredSecretKeys(t, key)
+
+	protected, err := SecretKeyIsProtected(secretKey)
+	require.NoError(t, err)
+	assert.True(t, protected)
+
+	_, err = NewManifestFromReader(bytes.NewReader(signedTestManifest(t,
+		&SigningOptions{SecretKey: secretKey, Passphrase: []byte("right")})))
+	require.NoError(t, err)
+
+	b := NewBuilder()
+	b.SetSigningOptions(&SigningOptions{SecretKey: secretKey})
+	require.ErrorIs(t, b.Build(context.Background(), io.Discard), errNoPassphrase)
+
+	b.SetSigningOptions(&SigningOptions{
+		SecretKey: secretKey, Passphrase: []byte("wrong"),
+	})
+	assert.ErrorContains(t, b.Build(context.Background(), io.Discard),
+		"unlock signing key")
+}
+
+func TestSecretKeyIsProtectedWithoutPassphrase(t *testing.T) {
+	t.Parallel()
+
+	protected, err := SecretKeyIsProtected(testSigningOptions(t).SecretKey)
+	require.NoError(t, err)
+	assert.False(t, protected)
+}
+
+// TestSecretKeyFingerprint checks that SecretKeyFingerprint gives the
+// signer that a manifest signed with the key records.
+func TestSecretKeyFingerprint(t *testing.T) {
+	t.Parallel()
+
+	opts := testSigningOptions(t)
+
+	got, err := SecretKeyFingerprint(opts.SecretKey)
+	require.NoError(t, err)
+
+	m, err := NewManifestFromReader(bytes.NewReader(signedTestManifest(t, opts)))
+	require.NoError(t, err)
+	assert.Equal(t, string(m.Signer()), got)
+}
+
+// TestSigningKeyFileWithTwoKeys signs with a key file that holds two keys,
+// as gpg writes it for a user ID that two keys have. It names no one key
+// to sign with, so signing must fail.
+func TestSigningKeyFileWithTwoKeys(t *testing.T) {
+	t.Parallel()
+
+	b := NewBuilder()
+	b.SetSigningOptions(&SigningOptions{SecretKey: armoredSecretKeys(t,
+		newTestKey(t, nil), newTestKey(t, nil))})
+
+	err := b.Build(context.Background(), io.Discard)
+	require.ErrorIs(t, err, errKeyCount)
+	assert.EqualError(t, err, "signing key file must hold exactly one key, found 2")
+}
+
+// TestSigningKeyFileWithoutSecretKey signs with a file that holds only a
+// public key.
+func TestSigningKeyFileWithoutSecretKey(t *testing.T) {
+	t.Parallel()
+
+	b := NewBuilder()
+	b.SetSigningOptions(&SigningOptions{
+		SecretKey: armoredPublicKeys(t, newTestKey(t, nil)),
+	})
+	require.ErrorIs(t, b.Build(context.Background(), io.Discard), errNoSecretKey)
+}
+
+// TestCheckSigningKeyRefusesKeyThatCannotSign checks a key that can sign,
+// and keys that read and need no passphrase but cannot sign now: one that
+// expired in 2020 and one that has been revoked. CheckSigningKey must
+// refuse each of the two, as signing a manifest with it would fail.
+func TestCheckSigningKeyRefusesKeyThatCannotSign(t *testing.T) {
+	t.Parallel()
+
+	require.NoError(t, CheckSigningKey(testSigningOptions(t)))
+
+	made := time.Date(2020, 1, 1, 0, 0, 0, 0, time.UTC)
+	expired := newTestKey(t, &packet.Config{
+		Time:            func() time.Time { return made },
+		KeyLifetimeSecs: uint32((24 * time.Hour).Seconds()),
+	})
+
+	revoked := newTestKey(t, nil)
+	require.NoError(t, revoked.RevokeKey(packet.KeyRetired, "", nil))
+
+	for name, key := range map[string]*openpgp.Entity{
+		"expired": expired,
+		"revoked": revoked,
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			assert.ErrorContains(t, CheckSigningKey(
+				&SigningOptions{SecretKey: armoredSecretKeys(t, key)}),
+				"signing key cannot sign")
+		})
+	}
+}
+
+// TestSigningRefusesVersion6Key signs with an OpenPGP version 6 key, whose
+// fingerprint is 64 hex characters. mfer signs only with version 4 keys.
+func TestSigningRefusesVersion6Key(t *testing.T) {
+	t.Parallel()
+
+	key, err := openpgp.NewEntity("MFER Test Key", "", "test@mfer.test",
+		&packet.Config{V6Keys: true, Algorithm: packet.PubKeyAlgoEd25519})
+	require.NoError(t, err)
+
+	secretKey := armoredSecretKeys(t, key)
+
+	_, err = SecretKeyIsProtected(secretKey)
+	require.ErrorIs(t, err, errNotV4Key)
+
+	b := NewBuilder()
+	b.SetSigningOptions(&SigningOptions{SecretKey: secretKey})
+	require.ErrorIs(t, b.Build(context.Background(), io.Discard), errNotV4Key)
+}
+
+// TestMalformedArmorIsNamed reads a signing key file, a signature and an
+// embedded public key block whose armor is malformed: a header line with
+// no colon, or no blank line after the BEGIN line. Each must fail saying
+// the armor is malformed.
+func TestMalformedArmorIsNamed(t *testing.T) {
+	t.Parallel()
+
+	opts := testSigningOptions(t)
+	manifest := signedTestManifest(t, opts)
+
+	for name, change := range map[string]func([]byte) []byte{
+		"header line with no colon": func(block []byte) []byte {
+			return bytes.Replace(block,
+				[]byte("-----\n"), []byte("-----\nno colon\n"), 1)
+		},
+		"no blank line after the BEGIN line": func(block []byte) []byte {
+			return bytes.Replace(block, []byte("-----\n\n"), []byte("-----\n"), 1)
+		},
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			_, err := SecretKeyIsProtected(change(opts.SecretKey))
+			require.ErrorIs(t, err, errMalformedArmor)
+
+			for _, changed := range [][]byte{
+				rewriteOuter(t, manifest, func(outer *MFFileOuter) {
+					outer.Signature = change(outer.GetSignature())
+				}),
+				rewriteOuter(t, manifest, func(outer *MFFileOuter) {
+					outer.SigningPubKey = change(outer.GetSigningPubKey())
+				}),
+			} {
+				_, err = NewManifestFromReader(bytes.NewReader(changed))
+				require.ErrorIs(t, err, errMalformedArmor)
+			}
+		})
+	}
+}
+
+func TestVerifySignature(t *testing.T) {
+	t.Parallel()
+
+	key := newTestKey(t, nil)
+	data := []byte("test data to sign and verify")
+
+	var armored, binary bytes.Buffer
+
+	require.NoError(t, openpgp.ArmoredDetachSign(&armored, key,
+		bytes.NewReader(data), nil))
+	require.NoError(t, openpgp.DetachSign(&binary, key, bytes.NewReader(data), nil))
+
+	pubKey, err := armoredPublicKey(key)
+	require.NoError(t, err)
+
+	var binaryPubKey bytes.Buffer
+
+	require.NoError(t, key.Serialize(&binaryPubKey))
+
+	// Verifying names the key that made the signature, whether the
+	// signature and key are armored or not.
+	signer, err := verifySignature(data, armored.Bytes(), pubKey)
+	require.NoError(t, err)
+	assert.Equal(t, fingerprint(key), signer)
+
+	signer, err = verifySignature(data, binary.Bytes(), binaryPubKey.Bytes())
+	require.NoError(t, err)
+	assert.Equal(t, fingerprint(key), signer)
+
+	// A signature over other data is bad.
+	_, err = verifySignature([]byte("different data"), armored.Bytes(), pubKey)
+	require.Error(t, err)
+
+	// A public key that is not one cannot verify anything.
+	_, err = verifySignature(data, armored.Bytes(), []byte("not a public key"))
+	assert.Error(t, err)
+}
+
+// TestVerifySignatureKeyExpiredSince verifies two signatures made in 2020
+// by a key that expired a day after it was made. A signature with no
+// expiry time is still good, as is one made then by a signing subkey that
+// expired a day after it was made. One that expired an hour after it was
+// made is refused, although the key has expired too.
+func TestVerifySignatureKeyExpiredSince(t *testing.T) {
+	t.Parallel()
+
+	made := time.Date(2020, 1, 1, 0, 0, 0, 0, time.UTC)
+	config := &packet.Config{
+		Time:            func() time.Time { return made },
+		KeyLifetimeSecs: uint32((24 * time.Hour).Seconds()),
+	}
+	key := newTestKey(t, config)
+	data := []byte("signed in 2020")
+
+	var sig, expiringSig bytes.Buffer
+
+	require.NoError(t, openpgp.ArmoredDetachSign(&sig, key, bytes.NewReader(data), config))
+	require.NoError(t, openpgp.ArmoredDetachSign(&expiringSig, key,
+		bytes.NewReader(data), &packet.Config{
+			Time:            config.Time,
+			SigLifetimeSecs: uint32(time.Hour.Seconds()),
+		}))
+
+	pubKey, err := armoredPublicKey(key)
+	require.NoError(t, err)
+
+	signer, err := verifySignature(data, sig.Bytes(), pubKey)
+	require.NoError(t, err)
+	assert.Equal(t, fingerprint(key), signer)
+
+	withSubkey := newTestKey(t, &packet.Config{Time: config.Time})
+	require.NoError(t, withSubkey.AddSigningSubkey(&packet.Config{
+		Algorithm: packet.PubKeyAlgoEdDSA, Time: config.Time,
+		KeyLifetimeSecs: config.KeyLifetimeSecs,
+	}))
+
+	var subkeySig bytes.Buffer
+
+	require.NoError(t, openpgp.ArmoredDetachSign(&subkeySig, withSubkey,
+		bytes.NewReader(data), config))
+
+	subkeyPubKey, err := armoredPublicKey(withSubkey)
+	require.NoError(t, err)
+
+	_, err = verifySignature(data, subkeySig.Bytes(), subkeyPubKey)
+	require.NoError(t, err)
+
+	_, err = verifySignature(data, expiringSig.Bytes(), pubKey)
+	require.ErrorIs(t, err, pgperrors.ErrSignatureExpired)
+}
+
+// signDated returns a detached signature over data by signer, dated when.
+// openpgp.DetachSign signs only with a key that is valid at the time its
+// config gives, so this makes the signature packet without that check.
+func signDated(t *testing.T, signer *packet.PrivateKey, data []byte,
+	when time.Time,
+) []byte {
+	t.Helper()
+
+	sig := &packet.Signature{
+		SigType:      packet.SigTypeBinary,
+		PubKeyAlgo:   signer.PubKeyAlgo,
+		Hash:         crypto.SHA256,
+		CreationTime: when,
+		IssuerKeyId:  &signer.KeyId,
+	}
+
+	h, err := sig.PrepareSign(nil)
+	require.NoError(t, err)
+
+	_, err = h.Write(data)
+	require.NoError(t, err)
+
+	require.NoError(t, sig.Sign(h, signer, nil))
+
+	var buf bytes.Buffer
+
+	require.NoError(t, sig.Serialize(&buf))
+
+	return buf.Bytes()
+}
+
+// TestVerifySignatureRefusesKeyNotValidWhenSigned verifies signatures
+// dated when the key or subkey that made them was not valid: after the key
+// expired; after the key's self-signature, or the signing subkey's binding
+// signature, expired, the key or subkey having expired since as well; and
+// before the key was made, also by a key made in 2100. Each must be
+// refused.
+func TestVerifySignatureRefusesKeyNotValidWhenSigned(t *testing.T) {
+	t.Parallel()
+
+	made := time.Date(2020, 1, 1, 0, 0, 0, 0, time.UTC)
+	twoDaysLater := made.Add(48 * time.Hour)
+	day := uint32((24 * time.Hour).Seconds())
+	clock := func(when time.Time) func() time.Time {
+		return func() time.Time { return when }
+	}
+
+	expiredAfterADay := newTestKey(t, &packet.Config{
+		Time: clock(made), KeyLifetimeSecs: day,
+	})
+	selfSignatureExpiredAfterADay := newTestKey(t, &packet.Config{
+		Time: clock(made), KeyLifetimeSecs: 30 * day, SigLifetimeSecs: day,
+	})
+
+	withSubkey := newTestKey(t, &packet.Config{Time: clock(made)})
+	require.NoError(t, withSubkey.AddSigningSubkey(&packet.Config{
+		Algorithm: packet.PubKeyAlgoEdDSA, Time: clock(made),
+		KeyLifetimeSecs: 30 * day, SigLifetimeSecs: day,
+	}))
+	subkey := withSubkey.Subkeys[len(withSubkey.Subkeys)-1].PrivateKey
+
+	madeADayLater := newTestKey(t, &packet.Config{
+		Time: clock(made.Add(24 * time.Hour)),
+	})
+	madeIn2100 := newTestKey(t, &packet.Config{
+		Time: clock(time.Date(2100, 1, 1, 0, 0, 0, 0, time.UTC)),
+	})
+
+	for name, test := range map[string]struct {
+		key    *openpgp.Entity
+		signer *packet.PrivateKey
+		when   time.Time
+	}{
+		"after the key expired": {
+			expiredAfterADay, expiredAfterADay.PrivateKey, twoDaysLater,
+		},
+		"after the self-signature expired": {
+			selfSignatureExpiredAfterADay,
+			selfSignatureExpiredAfterADay.PrivateKey, twoDaysLater,
+		},
+		"after the binding signature expired": {
+			withSubkey, subkey, twoDaysLater,
+		},
+		"before the key was made": {
+			madeADayLater, madeADayLater.PrivateKey, made,
+		},
+		"before a key made in 2100": {
+			madeIn2100, madeIn2100.PrivateKey, made,
+		},
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			data := []byte("signed in 2020")
+
+			pubKey, err := armoredPublicKey(test.key)
+			require.NoError(t, err)
+
+			_, err = verifySignature(data,
+				signDated(t, test.signer, data, test.when), pubKey)
+			require.ErrorIs(t, err, errKeyNotValidWhenSigned)
+		})
+	}
+}
+
+func TestManifestSignatureVerification(t *testing.T) {
+	t.Parallel()
+
+	// Parse the manifest - signature should be verified during load
+	manifest, err := NewManifestFromReader(bytes.NewReader(
+		signedTestManifest(t, testSigningOptions(t))))
+	require.NoError(t, err)
+	require.NotNil(t, manifest)
+
+	// Signature should be present and valid
+	assert.NotEmpty(t, manifest.pbOuter.GetSignature())
+}
+
+func TestManifestTamperedSignatureFails(t *testing.T) {
+	t.Parallel()
+
+	// Change one character of the signature's base64 body, which starts
+	// after the blank line that ends the armor headers.
+	data := rewriteOuter(t, signedTestManifest(t, testSigningOptions(t)),
+		func(outer *MFFileOuter) {
+			sig := outer.GetSignature()
+			i := bytes.Index(sig, []byte("\n\n")) + len("\n\n") + 20
+
+			sig[i]++
+		})
+
+	// Try to load the tampered manifest - should fail
+	_, err := NewManifestFromReader(bytes.NewReader(data))
+	assert.Error(t, err)
+}
+
+// TestManifestSignedByGPGLoads loads the signed seed of
+// FuzzNewManifestFromReader, a manifest signed with gpg before mfer signed
+// and verified manifests itself.
+func TestManifestSignedByGPGLoads(t *testing.T) {
+	t.Parallel()
+
+	seed, err := os.ReadFile(filepath.Join(
+		"testdata", "fuzz", "FuzzNewManifestFromReader", "signed"))
+	require.NoError(t, err)
+
+	// After its header line the seed holds the manifest as []byte("...").
+	_, quoted, found := strings.Cut(string(seed), "[]byte(")
+	require.True(t, found)
+
+	manifest, err := strconv.Unquote(
+		strings.TrimSuffix(strings.TrimSpace(quoted), ")"))
+	require.NoError(t, err)
+
+	m, err := NewManifestFromReader(strings.NewReader(manifest))
+	require.NoError(t, err)
+	assert.Equal(t, "4F562BFB863FDC6B51B4EE88872A51176CEF23AE",
+		string(m.pbOuter.GetSigner()))
+}
+
+// TestManifestRefusesSecondEmbeddedKey loads manifests whose embedded
+// public key block holds another key besides the key that signed it: as a
+// public key, as a secret key with no user ID, which openpgp.ReadKeyRing
+// skips, and written as a subkey packet at the start of the block, which
+// openpgp.ReadKeyRing reads as a primary key. Loading must refuse each,
+// although the signature is good and the signer field names the key that
+// made it.
+func TestManifestRefusesSecondEmbeddedKey(t *testing.T) {
+	t.Parallel()
+
+	other := newTestKey(t, nil)
+	signer := newTestKey(t, nil)
+	manifest := signedTestManifest(t,
+		&SigningOptions{SecretKey: armoredSecretKeys(t, signer)})
+
+	otherWithoutUserID := newTestKey(t, nil)
+	otherWithoutUserID.Identities = map[string]*openpgp.Identity{}
+
+	otherAsSubkey := newTestKey(t, nil)
+	otherAsSubkey.PrimaryKey.IsSubkey = true
+
+	for name, block := range map[string][]byte{
+		"public key":                 armoredPublicKeys(t, other, signer),
+		"secret key without user ID": armoredSecretKeys(t, signer, otherWithoutUserID),
+		"subkey packet first":        armoredPublicKeys(t, otherAsSubkey, signer),
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			embedded := rewriteOuter(t, manifest, func(outer *MFFileOuter) {
+				outer.SigningPubKey = block
+			})
+
+			_, err := NewManifestFromReader(bytes.NewReader(embedded))
+			require.ErrorIs(t, err, errKeyCount)
+		})
+	}
+}
+
+// TestManifestRefusesSecondEmbeddedKeyWithoutUserID loads a manifest whose
+// embedded public key block holds, before the key that signed it, another
+// key with no user ID, which openpgp.ReadKeyRing skips. Loading must
+// refuse it: the block holds two keys.
+func TestManifestRefusesSecondEmbeddedKeyWithoutUserID(t *testing.T) {
+	t.Parallel()
+
+	other := newTestKey(t, nil)
+	other.Identities = map[string]*openpgp.Identity{}
+
+	signer := newTestKey(t, nil)
+
+	manifest := rewriteOuter(t, signedTestManifest(t,
+		&SigningOptions{SecretKey: armoredSecretKeys(t, signer)}),
+		func(outer *MFFileOuter) {
+			outer.SigningPubKey = armoredPublicKeys(t, other, signer)
+		})
+
+	_, err := NewManifestFromReader(bytes.NewReader(manifest))
+	require.ErrorIs(t, err, errKeyCount)
+}
+
+// dsaKeyPacket returns a public key packet holding a DSA key, or a public
+// subkey packet when isSubkey. Its numbers are not a working key: loading
+// must refuse the packet before it uses them.
+func dsaKeyPacket(t *testing.T, isSubkey bool) []byte {
+	t.Helper()
+
+	key := packet.NewDSAPublicKey(time.Now(), &dsa.PublicKey{
+		P: big.NewInt(23), Q: big.NewInt(11), G: big.NewInt(4), Y: big.NewInt(8),
+	})
+	key.IsSubkey = isSubkey
+
+	var buf bytes.Buffer
+
+	require.NoError(t, key.Serialize(&buf))
+
+	return buf.Bytes()
+}
+
+// TestManifestRefusesDSAKey loads manifests whose embedded public key
+// block holds a DSA key: alone, or as a subkey after the key that signed
+// the manifest. openpgp.ReadKeyRing checks a key's self-signatures, which
+// for a DSA key with very large numbers takes minutes each. Loading must
+// refuse each block before that.
+func TestManifestRefusesDSAKey(t *testing.T) {
+	t.Parallel()
+
+	signer := newTestKey(t, nil)
+	manifest := signedTestManifest(t,
+		&SigningOptions{SecretKey: armoredSecretKeys(t, signer)})
+
+	var signerKey bytes.Buffer
+
+	require.NoError(t, signer.Serialize(&signerKey))
+
+	for name, block := range map[string][]byte{
+		"DSA key":    dsaKeyPacket(t, false),
+		"DSA subkey": slices.Concat(signerKey.Bytes(), dsaKeyPacket(t, true)),
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			embedded := rewriteOuter(t, manifest, func(outer *MFFileOuter) {
+				outer.SigningPubKey = block
+			})
+
+			_, err := NewManifestFromReader(bytes.NewReader(embedded))
+			require.ErrorIs(t, err, errDSAKey)
+		})
+	}
+}
+
+// elGamalSecretSubkeyPacket returns a secret subkey packet holding an
+// ElGamal key. Its numbers are not a working key: loading must refuse the
+// packet before it uses them.
+func elGamalSecretSubkeyPacket(t *testing.T) []byte {
+	t.Helper()
+
+	key := packet.NewElGamalPrivateKey(time.Now(), &elgamal.PrivateKey{
+		P: big.NewInt(23), G: big.NewInt(4), Y: big.NewInt(8), X: big.NewInt(3),
+	})
+	key.IsSubkey = true
+
+	var buf bytes.Buffer
+
+	require.NoError(t, key.Serialize(&buf))
+
+	return buf.Bytes()
+}
+
+// TestManifestRefusesSecretKey loads manifests whose embedded public key
+// block holds a secret key: the key that signed the manifest with its
+// secret key, or its public key followed by an ElGamal secret subkey.
+// openpgp.ReadKeyRing checks the numbers of every secret key it reads,
+// which for an ElGamal key with a very large prime takes minutes. Loading
+// must refuse each block before that.
+func TestManifestRefusesSecretKey(t *testing.T) {
+	t.Parallel()
+
+	signer := newTestKey(t, nil)
+	manifest := signedTestManifest(t,
+		&SigningOptions{SecretKey: armoredSecretKeys(t, signer)})
+
+	var signerKey bytes.Buffer
+
+	require.NoError(t, signer.Serialize(&signerKey))
+
+	for _, block := range [][]byte{
+		armoredSecretKeys(t, signer),
+		slices.Concat(signerKey.Bytes(), elGamalSecretSubkeyPacket(t)),
+	} {
+		embedded := rewriteOuter(t, manifest, func(outer *MFFileOuter) {
+			outer.SigningPubKey = block
+		})
+
+		_, err := NewManifestFromReader(bytes.NewReader(embedded))
+		require.ErrorIs(t, err, errSecretKey)
+	}
+}
+
+// TestManifestRefusesTwoSignatures loads a manifest whose signature field
+// holds its good signature twice, not armored. Loading must refuse it.
+func TestManifestRefusesTwoSignatures(t *testing.T) {
+	t.Parallel()
+
+	manifest := rewriteOuter(t, signedTestManifest(t, testSigningOptions(t)),
+		func(outer *MFFileOuter) {
+			sig, err := dearmor(outer.GetSignature())
+			require.NoError(t, err)
+
+			outer.Signature = slices.Concat(sig, sig)
+		})
+
+	_, err := NewManifestFromReader(bytes.NewReader(manifest))
+	require.ErrorIs(t, err, errNotOneSignature)
+}
+
+// TestManifestRefusesFieldNotOneArmoredBlock loads manifests whose
+// signature or embedded public key block holds its good armored block with
+// something else: a second armored block, text after the END line, or many
+// END lines before the block. Decoding the block once for each END line
+// before it would take time and memory that grow with the square of the
+// field's size. Loading must refuse each.
+func TestManifestRefusesFieldNotOneArmoredBlock(t *testing.T) {
+	t.Parallel()
+
+	manifest := signedTestManifest(t, testSigningOptions(t))
+
+	for name, change := range map[string]func([]byte) []byte{
+		"second armored block": func(block []byte) []byte {
+			return joinArmored(block, block)
+		},
+		"text after the END line": func(block []byte) []byte {
+			return slices.Concat(block, []byte("\nmore text\n"))
+		},
+		"END lines before the block": func(block []byte) []byte {
+			return slices.Concat(
+				[]byte(strings.Repeat(armorEnd+"\n", 1000)), block)
+		},
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			for _, changed := range [][]byte{
+				rewriteOuter(t, manifest, func(outer *MFFileOuter) {
+					outer.Signature = change(outer.GetSignature())
+				}),
+				rewriteOuter(t, manifest, func(outer *MFFileOuter) {
+					outer.SigningPubKey = change(outer.GetSigningPubKey())
+				}),
+			} {
+				_, err := NewManifestFromReader(bytes.NewReader(changed))
+				require.ErrorIs(t, err, errNotOneArmoredBlock)
+			}
+		})
+	}
+}
+
+// TestManifestSignedWithSubkey signs with a key that has a signing subkey,
+// which signs in place of the primary key. The manifest must load, with
+// the primary key's fingerprint as signer.
+func TestManifestSignedWithSubkey(t *testing.T) {
+	t.Parallel()
+
+	key := newTestKey(t, nil)
+	require.NoError(t, key.AddSigningSubkey(
+		&packet.Config{Algorithm: packet.PubKeyAlgoEdDSA}))
+
+	m, err := NewManifestFromReader(bytes.NewReader(signedTestManifest(t,
+		&SigningOptions{SecretKey: armoredSecretKeys(t, key)})))
+	require.NoError(t, err)
+	assert.Equal(t, fingerprint(key), string(m.pbOuter.GetSigner()))
+
+	block, err := armor.Decode(bytes.NewReader(m.pbOuter.GetSignature()))
+	require.NoError(t, err)
+
+	p, err := packet.Read(block.Body)
+	require.NoError(t, err)
+
+	sig, ok := p.(*packet.Signature)
+	require.True(t, ok)
+
+	subkey := key.Subkeys[len(key.Subkeys)-1].PublicKey
+	assert.Equal(t, subkey.KeyId, *sig.IssuerKeyId,
+		"the signing subkey made the signature")
+}
+
+// TestManifestRefusesSignerOtherThanSigningKey loads a manifest whose
+// signer field names a key other than the one that made the signature.
+func TestManifestRefusesSignerOtherThanSigningKey(t *testing.T) {
+	t.Parallel()
+
+	manifest := rewriteOuter(t, signedTestManifest(t, testSigningOptions(t)),
+		func(outer *MFFileOuter) {
+			outer.Signer = []byte(strings.Repeat("A", len(outer.GetSigner())))
+		})
+
+	_, err := NewManifestFromReader(bytes.NewReader(manifest))
+	require.ErrorIs(t, err, errSignerNotSigningKey)
+}
+
+func TestBuilderWithoutSigning(t *testing.T) {
+	t.Parallel()
+
+	// Create a builder without signing options
+	b := NewBuilder()
+
+	// Add a test file
+	content := []byte("test file content")
+	reader := bytes.NewReader(content)
+	_, err := b.AddFile("test.txt", FileSize(len(content)), ModTime{}, 0, reader, nil)
+	require.NoError(t, err)
+
+	// Build the manifest
+	var buf bytes.Buffer
+
+	err = b.Build(context.Background(), &buf)
+	require.NoError(t, err)
+
+	// Parse the manifest and verify signature fields are empty
+	manifest, err := NewManifestFromReader(&buf)
+	require.NoError(t, err)
+	require.NotNil(t, manifest.pbOuter)
+
+	assert.Empty(t, manifest.pbOuter.GetSignature(),
+		"signature should be empty when not signing")
+	assert.Empty(t, manifest.pbOuter.GetSigner(),
+		"signer should be empty when not signing")
+	assert.Empty(t, manifest.pbOuter.GetSigningPubKey(),
+		"signing public key should be empty when not signing")
+}
+
+// TestBuildPassesContextToSigning checks that Build does not sign once the
+// context given to it has ended.
+func TestBuildPassesContextToSigning(t *testing.T) {
+	t.Parallel()
+
+	b := NewBuilder()
+	b.SetSigningOptions(&SigningOptions{SecretKey: []byte("any")})
+
+	ctx, cancel := context.WithCancel(context.Background())
+	cancel()
+
+	require.ErrorIs(t, b.Build(ctx, io.Discard), context.Canceled)
+}

mfer/pipe_test.go

@@ -0,0 +1,123 @@
+//go:build unix
+
+//nolint:testpackage // white-box tests exercise unexported internals
+package mfer
+
+import (
+	"bytes"
+	"context"
+	"os"
+	"path/filepath"
+	"syscall"
+	"testing"
+	"time"
+
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// pipeDeadline is how long a test lets a run go before it opens the test's
+// named pipes for writing.
+const pipeDeadline = 5 * time.Second
+
+// makePipe makes a named pipe at path. Opening a named pipe for reading
+// blocks until it is opened for writing, so once pipeDeadline has passed,
+// unless the test has ended, makePipe opens it for writing and closes it
+// again. A run that wrongly reads the pipe then ends, and the test fails on
+// what it reports instead of hanging. That lets one read through, so each
+// path a wrong run would read gets a pipe of its own.
+func makePipe(t *testing.T, path string) {
+	t.Helper()
+
+	require.NoError(t, syscall.Mkfifo(path, 0o600))
+
+	timer := time.AfterFunc(pipeDeadline, func() {
+		f, err := os.OpenFile(path, os.O_WRONLY, 0) //nolint:gosec // test-controlled path
+		if err == nil {
+			_ = f.Close()
+		}
+	})
+
+	t.Cleanup(func() { timer.Stop() })
+}
+
+// TestScannerSkipsPipes scans a tree holding a named pipe and a symlink to
+// another one, following symlinks: the manifest lists the regular file only.
+func TestScannerSkipsPipes(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, testFile1), []byte("a"), 0o600))
+	makePipe(t, filepath.Join(dir, "pipe"))
+
+	// The symlink points outside the tree, so no pipe is read twice.
+	target := filepath.Join(t.TempDir(), "pipe")
+	makePipe(t, target)
+	require.NoError(t, os.Symlink(target, filepath.Join(dir, "link")))
+
+	s := NewScannerWithOptions(&ScannerOptions{FollowSymLinks: true})
+	require.NoError(t, s.EnumeratePath(dir, nil))
+
+	var buf bytes.Buffer
+	require.NoError(t, s.ToManifest(context.Background(), &buf, nil))
+
+	m, err := NewManifestFromReader(&buf)
+	require.NoError(t, err)
+	require.Len(t, m.Files(), 1)
+	assert.Equal(t, testFile1, m.Files()[0].GetPath())
+}
+
+// TestCheckPipes checks a tree against a manifest that lists, as an empty
+// file, a path that is a named pipe on disk. The tree holds another pipe the
+// manifest does not list. check reports the listed pipe as an error without
+// reading it, and the search for extra files does not report the other.
+func TestCheckPipes(t *testing.T) {
+	t.Parallel()
+
+	dir := t.TempDir()
+	manifestPath := filepath.Join(dir, "index.mf")
+	content := []byte("in manifest")
+	listedPipe := RelFilePath("listed-pipe")
+
+	fs := afero.NewOsFs()
+	createTestManifest(t, fs, manifestPath, map[string][]byte{
+		testFile1:          content,
+		string(listedPipe): {},
+	})
+	require.NoError(t, afero.WriteFile(fs, filepath.Join(dir, testFile1), content, 0o600))
+	makePipe(t, filepath.Join(dir, string(listedPipe)))
+	makePipe(t, filepath.Join(dir, "unlisted-pipe"))
+
+	chk, err := NewChecker(&CheckerOptions{
+		ManifestPath: manifestPath,
+		BasePath:     dir,
+		Fs:           fs,
+	})
+	require.NoError(t, err)
+
+	results := make(chan Result, 10)
+	require.NoError(t, chk.Check(context.Background(), results, nil))
+
+	byPath := map[RelFilePath]Result{}
+	for r := range results {
+		byPath[r.Path] = r
+	}
+
+	assert.Equal(t, StatusOK, byPath[testFile1].Status)
+	assert.Equal(t, Result{
+		Path:    listedPipe,
+		Status:  StatusError,
+		Message: "not a regular file",
+	}, byPath[listedPipe])
+
+	extras := make(chan Result, 10)
+	require.NoError(t, chk.FindExtraFiles(context.Background(), extras))
+
+	var extraPaths []RelFilePath
+	for r := range extras {
+		extraPaths = append(extraPaths, r.Path)
+	}
+
+	assert.Empty(t, extraPaths)
+}

mfer/scanner.go

@@ -2,6 +2,7 @@ package mfer
 
 import (
 	"context"
+	"fmt"
 	"io"
 	"io/fs"
 	"os"
@@ -57,7 +58,7 @@ type ScannerOptions struct {
 	IncludePermissions bool
 	// Fs is the filesystem to use, defaults to OsFs if nil.
 	Fs afero.Fs
-	// SigningOptions holds GPG signing options (nil = no signing).
+	// SigningOptions holds the key to sign with (nil = no signing).
 	SigningOptions *SigningOptions
 	// Seed, if set, derives a deterministic UUID from this seed.
 	Seed string
@@ -79,7 +80,8 @@ type FileEntry struct {
 type Scanner struct {
 	mu         sync.RWMutex
 	files      []*FileEntry
-	totalBytes FileSize // cached sum of all file sizes
+	paths      map[RelFilePath]AbsFilePath // the file at each path in files
+	totalBytes FileSize                    // cached sum of all file sizes
 	options    *ScannerOptions
 	fs         afero.Fs
 	excluded   []fs.FileInfo // the files named in ExcludePaths that exist
@@ -103,6 +105,7 @@ func NewScannerWithOptions(opts *ScannerOptions) *Scanner {
 
 	s := &Scanner{
 		files:   make([]*FileEntry, 0),
+		paths:   make(map[RelFilePath]AbsFilePath),
 		options: opts,
 		fs:      fs,
 	}
@@ -136,28 +139,20 @@ func (s *Scanner) EnumerateFile(filePath string) error {
 	return s.enumerateFileWithInfo(filepath.Base(abs), basePath, info, nil)
 }
 
-// EnumeratePath walks a directory path and adds all files to the scanner.
+// EnumeratePath adds inputPath, a directory or a file, to the scanner as
+// EnumeratePaths adds each of its paths.
 // If progress is non-nil, status updates are sent as files are discovered.
 // The progress channel is closed when the method returns.
 func (s *Scanner) EnumeratePath(
 	inputPath string,
 	progress chan<- EnumerateStatus,
 ) error {
-	if progress != nil {
+	return s.EnumeratePaths(progress, inputPath)
-		defer close(progress)
-	}
-
-	abs, err := filepath.Abs(inputPath)
-	if err != nil {
-		return err
-	}
-
-	afs := afero.NewReadOnlyFs(afero.NewBasePathFs(s.fs, abs))
-
-	return s.enumerateFS(afs, abs, progress)
 }
 
-// EnumeratePaths walks multiple directory paths and adds all files to the scanner.
+// EnumeratePaths adds to the scanner the files under each directory path,
+// listed by their paths under it, and each file path, listed by its name
+// as EnumerateFile lists it.
 // If progress is non-nil, status updates are sent as files are discovered.
 // The progress channel is closed when the method returns.
 func (s *Scanner) EnumeratePaths(
@@ -174,9 +169,27 @@ func (s *Scanner) EnumeratePaths(
 			return err
 		}
 
-		afs := afero.NewReadOnlyFs(afero.NewBasePathFs(s.fs, abs))
+		info, err := s.fs.Stat(abs)
+		if err != nil {
+			return err
+		}
+
+		if info.IsDir() {
+			// The walk does not follow a symlink at its top, so a directory
+			// named through one is resolved first. If that fails, the
+			// directory is walked as named and the walk reports the problem.
+			resolved, evalErr := filepath.EvalSymlinks(abs)
+			if evalErr == nil {
+				abs = resolved
+			}
+
+			afs := afero.NewReadOnlyFs(afero.NewBasePathFs(s.fs, abs))
+			err = s.enumerateFS(afs, abs, progress)
+		} else {
+			err = s.enumerateFileWithInfo(
+				filepath.Base(abs), filepath.Dir(abs), info, progress)
+		}
 
-		err = s.enumerateFS(afs, abs, progress)
 		if err != nil {
 			return err
 		}
@@ -461,6 +474,13 @@ func (s *Scanner) enumerateFileWithInfo(
 		info = realInfo
 	}
 
+	// Opening a named pipe can block, and reading a device may never end.
+	if !info.Mode().IsRegular() {
+		log.Verbosef("skipping %s: not a regular file", cleanPath)
+
+		return nil
+	}
+
 	for _, excluded := range s.excluded {
 		if os.SameFile(info, excluded) {
 			return nil
@@ -478,6 +498,18 @@ func (s *Scanner) enumerateFileWithInfo(
 	}
 
 	s.mu.Lock()
+
+	// Each path is relative to the input path it was found under, so files
+	// under two input paths can share one.
+	first, ok := s.paths[entry.Path]
+	if ok {
+		s.mu.Unlock()
+
+		return fmt.Errorf("%w %q: %s and %s",
+			errDuplicatePath, entry.Path, first, entry.AbsPath)
+	}
+
+	s.paths[entry.Path] = entry.AbsPath
 	s.files = append(s.files, entry)
 	s.totalBytes += entry.Size
 	filesFound := FileCount(len(s.files))

mfer/scanner_test.go

@@ -118,6 +118,27 @@ func TestScannerEnumeratePathWithProgress(t *testing.T) {
 	assert.Equal(t, FileSize(6), final.BytesFound)
 }
 
+// TestScannerEnumeratePathFile gives EnumeratePath a file: it is listed
+// by its name, as EnumerateFile lists it, and the manifest can be built.
+func TestScannerEnumeratePathFile(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll("/dir", 0o755))
+	require.NoError(t, afero.WriteFile(fs, "/dir/one.txt", []byte("1"), 0o644))
+
+	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
+	require.NoError(t, s.EnumeratePath("/dir/one.txt", nil))
+
+	var buf bytes.Buffer
+	require.NoError(t, s.ToManifest(context.Background(), &buf, nil))
+
+	m, err := NewManifestFromReader(&buf)
+	require.NoError(t, err)
+	require.Len(t, m.Files(), 1)
+	assert.Equal(t, "one.txt", m.Files()[0].GetPath())
+}
+
 func TestScannerEnumeratePaths(t *testing.T) {
 	t.Parallel()
 
@@ -134,6 +155,28 @@ func TestScannerEnumeratePaths(t *testing.T) {
 	assert.Equal(t, FileCount(2), s.FileCount())
 }
 
+// TestScannerEnumeratePathsFile gives EnumeratePaths a directory and a
+// file: the file is listed by its name, as EnumerateFile lists it.
+func TestScannerEnumeratePathsFile(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll("/dir/sub", 0o755))
+	require.NoError(t, fs.MkdirAll("/other", 0o755))
+	require.NoError(t, afero.WriteFile(fs, "/dir/sub/one.txt", []byte("1"), 0o644))
+	require.NoError(t, afero.WriteFile(fs, "/other/two.txt", []byte("2"), 0o644))
+
+	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
+	require.NoError(t, s.EnumeratePaths(nil, "/dir", "/other/two.txt"))
+
+	paths := make([]RelFilePath, 0, s.FileCount())
+	for _, f := range s.Files() {
+		paths = append(paths, f.Path)
+	}
+
+	assert.Equal(t, []RelFilePath{"sub/one.txt", "two.txt"}, paths)
+}
+
 func TestScannerExcludeDotfiles(t *testing.T) {
 	t.Parallel()
 

mfer/serialize.go

@@ -7,9 +7,11 @@ import (
 	"errors"
 	"fmt"
 	"math"
+	"strings"
 	"time"
 	"uuid"
 
+	"github.com/ProtonMail/go-crypto/openpgp"
 	"github.com/klauspost/compress/zstd"
 	"google.golang.org/protobuf/proto"
 )
@@ -20,11 +22,9 @@ const MAGIC string = "ZNAVSRFG"
 var (
 	// errInnerNotSet is returned by generate when the inner manifest is
 	// missing.
-	errInnerNotSet = errors.New("internal error: pbInner not set")
+	errInnerNotSet = errors.New("inner message not set")
 	// errInternal is returned by generateOuter for the same condition.
-	// The two messages differ, and both are load-bearing for callers that
+	errInternal = errors.New("inner message not set")
-	// match on text, so they are kept distinct.
-	errInternal = errors.New("internal error")
 )
 
 // nanosecondsInt32 converts t's nanosecond component to int32.
@@ -65,14 +65,14 @@ func (m *manifest) generate(ctx context.Context) error {
 
 	dat, err := proto.MarshalOptions{Deterministic: true}.Marshal(m.pbOuter)
 	if err != nil {
-		return fmt.Errorf("serialize: marshal outer: %w", err)
+		return fmt.Errorf("marshal outer message: %w", err)
 	}
 
 	m.output = bytes.NewBufferString(MAGIC)
 
 	_, err = m.output.Write(dat)
 	if err != nil {
-		return fmt.Errorf("serialize: write output: %w", err)
+		return fmt.Errorf("write outer message: %w", err)
 	}
 
 	return nil
@@ -95,7 +95,7 @@ func (m *manifest) generateOuter(ctx context.Context) error {
 
 	innerData, err := proto.MarshalOptions{Deterministic: true}.Marshal(m.pbInner)
 	if err != nil {
-		return fmt.Errorf("serialize: marshal inner: %w", err)
+		return fmt.Errorf("marshal inner message: %w", err)
 	}
 
 	// Compress the inner data
@@ -103,12 +103,12 @@ func (m *manifest) generateOuter(ctx context.Context) error {
 
 	zw, err := zstd.NewWriter(idc, zstd.WithEncoderLevel(zstd.SpeedBestCompression))
 	if err != nil {
-		return fmt.Errorf("serialize: create compressor: %w", err)
+		return fmt.Errorf("create compressor: %w", err)
 	}
 
 	_, err = zw.Write(innerData)
 	if err != nil {
-		return fmt.Errorf("serialize: compress: %w", err)
+		return fmt.Errorf("compress inner message: %w", err)
 	}
 
 	_ = zw.Close()
@@ -120,7 +120,7 @@ func (m *manifest) generateOuter(ctx context.Context) error {
 
 	_, err = h.Write(compressedData)
 	if err != nil {
-		return fmt.Errorf("serialize: hash write: %w", err)
+		return fmt.Errorf("hash inner message: %w", err)
 	}
 
 	sha256Hash := h.Sum(nil)
@@ -135,40 +135,48 @@ func (m *manifest) generateOuter(ctx context.Context) error {
 	}
 
 	// Sign the manifest if signing options are provided
-	if m.signingOptions != nil && m.signingOptions.KeyID != "" {
+	if m.signingOptions != nil {
 		return m.signOuter(ctx)
 	}
 
 	return nil
 }
 
-// signOuter signs the outer message with the configured GPG key and
+// signOuter signs the outer message with the secret key in the signing
-// embeds the signature, signer fingerprint, and public key.
+// options and embeds the signature, the key's fingerprint and its public
+// key.
 func (m *manifest) signOuter(ctx context.Context) error {
+	// Unlocking a protected key can take a while; do not start once ctx
+	// has ended.
+	err := ctx.Err()
+	if err != nil {
+		return err
+	}
+
 	sigString, err := m.signatureString()
 	if err != nil {
-		return fmt.Errorf("failed to generate signature string: %w", err)
+		return fmt.Errorf("build signature string: %w", err)
 	}
 
-	sig, err := gpgSign(ctx, []byte(sigString), m.signingOptions.KeyID)
+	key, err := readSigningKey(m.signingOptions)
 	if err != nil {
-		return fmt.Errorf("failed to sign manifest: %w", err)
+		return err
 	}
 
-	m.pbOuter.Signature = sig
+	var sig bytes.Buffer
 
-	fingerprint, err := gpgGetKeyFingerprint(ctx, m.signingOptions.KeyID)
+	err = openpgp.ArmoredDetachSign(&sig, key, strings.NewReader(sigString), nil)
 	if err != nil {
-		return fmt.Errorf("failed to get key fingerprint: %w", err)
+		return fmt.Errorf("sign manifest: %w", err)
 	}
 
-	m.pbOuter.Signer = fingerprint
+	pubKey, err := armoredPublicKey(key)
-
-	pubKey, err := gpgExportPublicKey(ctx, m.signingOptions.KeyID)
 	if err != nil {
-		return fmt.Errorf("failed to export public key: %w", err)
+		return err
 	}
 
+	m.pbOuter.Signature = sig.Bytes()
+	m.pbOuter.Signer = []byte(fingerprint(key))
 	m.pbOuter.SigningPubKey = pubKey
 
 	return nil