fix: handle errcheck warnings in gpg.go and gpg_test.go, fix gofmt

path.Clean(".") returns "." which starts with a dot, causing IsHiddenPath
to incorrectly treat the current directory as hidden. Add explicit checks
for "." and "/" before the dot-prefix check.

Fixed in both mfer/scanner.go and internal/scanner/scanner.go.

.gitignore

@@ -1,4 +1,4 @@
-/mfer.cmd
+/bin/
 /tmp
 *.tmp
 *.dockerimage

CLAUDE.md

@@ -1,20 +1,20 @@
 # Important Rules
 
-* when fixing a bug, write a failing test FIRST.  only after the test fails, write
+- when fixing a bug, write a failing test FIRST. only after the test fails, write
-  the code to fix the bug.  then ensure the test passes.  leave the test in
+  the code to fix the bug. then ensure the test passes. leave the test in
-  place and commit it with the bugfix.  don't run shell commands to test
+  place and commit it with the bugfix. don't run shell commands to test
-  bugfixes or reproduce bugs.  write tests!
+  bugfixes or reproduce bugs. write tests!
 
-* never, ever mention claude or anthropic in commit messages.  do not use attribution
+- never, ever mention claude or anthropic in commit messages. do not use attribution
 
-* after each change, run "make fmt".
+- after each change, run "make fmt".
 
-* after each change, run "make test" and ensure all tests pass.
+- after each change, run "make test" and ensure all tests pass.
 
-* after each change, run "make lint" and ensure no linting errors.  fix any
+- after each change, run "make lint" and ensure no linting errors. fix any
   you find, one by one.
 
-* after each change, commit the files you've changed.  push after
+- after each change, commit the files you've changed. push after
   committing.
 
-* NEVER use `git add -A`.  always add only individual files that you've changed.
+- NEVER use `git add -A`. always add only individual files that you've changed.

Makefile

@@ -17,14 +17,14 @@ GOFLAGS := -ldflags "$(GOLDFLAGS)"
 
 default: fmt test
 
-run: ./mfer.cmd
+run: ./bin/mfer
 	./$<
 	./$< gen
 
 ci: test
 
 test: $(SOURCEFILES) mfer/mf.pb.go
-	go test -v --timeout 3s ./...
+	go test -v --timeout 10s ./...
 
 $(PROTOC_GEN_GO):
 	test -e $(PROTOC_GEN_GO) || go install -v google.golang.org/protobuf/cmd/protoc-gen-go@v1.28.1
@@ -38,12 +38,12 @@ devprereqs:
 mfer/mf.pb.go: mfer/mf.proto
 	cd mfer && go generate .
 
-mfer.cmd: $(SOURCEFILES) mfer/mf.pb.go
+bin/mfer: $(SOURCEFILES) mfer/mf.pb.go
 	protoc --version
-	cd cmd/mfer && go build -tags urfave_cli_no_docs -o ../../mfer.cmd $(GOFLAGS) .
+	cd cmd/mfer && go build -tags urfave_cli_no_docs -o ../../bin/mfer $(GOFLAGS) .
 
 clean:
-	rm -rfv mfer/*.pb.go mfer.cmd cmd/mfer/mfer *.dockerimage
+	rm -rfv mfer/*.pb.go bin/mfer cmd/mfer/mfer *.dockerimage
 
 fmt: mfer/mf.pb.go
 	gofumpt -l -w mfer internal cmd

README.md

@@ -3,25 +3,25 @@
 [mfer](https://git.eeqj.de/sneak/mfer) is a reference implementation library
 and thin wrapper command-line utility written in [Go](https://golang.org)
 and first published in 2022 under the [WTFPL](https://wtfpl.net) (public
-domain) license.  It specifies and generates `.mf` manifest files over a
+domain) license. It specifies and generates `.mf` manifest files over a
 directory tree of files to encapsulate metadata about them (such as
 cryptographic checksums or signatures over same) to aid in archiving,
-downloading, and streaming, or mirroring.  The manifest files' data is
+downloading, and streaming, or mirroring. The manifest files' data is
 serialized with Google's [protobuf serialization
-format](https://developers.google.com/protocol-buffers).  The structure of
+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)
 which is 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)
+there has not yet been any versioned release. [SemVer](https://semver.org)
 will be used for releases.
 
 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 javascript library is planned.
+software. A compatible javascript library is planned.
 
 # Phases
 
@@ -52,188 +52,6 @@ Reading file contents and computing cryptographic hashes for manifest generation
 - **NO_COLOR:** Respect the `NO_COLOR` environment variable for disabling colored output.
 - **Options pattern:** Use `NewWithOptions(opts *Options)` constructor pattern for configurable types.
 
-# Codebase Structure
-
-## cmd/mfer/
-
-### main.go
-- **Variables**
-  - `Appname string` - Application name
-  - `Version string` - Version string (set at build time)
-  - `Gitrev string` - Git revision (set at build time)
-
-## internal/cli/
-
-### entry.go
-- **Variables**
-  - `NO_COLOR bool` - Disables color output when NO_COLOR env var is set
-- **Functions**
-  - `Run(Appname, Version, Gitrev string) int` - Main entry point for the CLI
-
-### mfer.go
-- **Types**
-  - `CLIApp struct` - Main CLI application container
-- **Methods**
-  - `(*CLIApp) VersionString() string` - Returns formatted version string
-
-## internal/log/
-
-### log.go
-- **Functions**
-  - `Init()` - Initializes the logger
-  - `Info(arg string)` - Logs at info level
-  - `Infof(format string, args ...interface{})` - Logs at info level with formatting
-  - `Debug(arg string)` - Logs at debug level with caller info
-  - `Debugf(format string, args ...interface{})` - Logs at debug level with formatting and caller info
-  - `Dump(args ...interface{})` - Logs spew dump at debug level
-  - `Progressf(format string, args ...interface{})` - Prints progress message (overwrites current line)
-  - `ProgressDone()` - Completes progress line with newline
-  - `EnableDebugLogging()` - Sets log level to debug
-  - `SetLevel(arg log.Level)` - Sets log level
-  - `SetLevelFromVerbosity(l int)` - Sets log level from verbosity count
-  - `GetLevel() log.Level` - Returns current log level
-  - `GetLogger() *log.Logger` - Returns underlying logger
-  - `WithError(e error) *log.Entry` - Returns log entry with error attached
-  - `DisableStyling()` - Disables colors and styling (for NO_COLOR)
-
-## internal/scanner/
-
-### scanner.go
-- **Types**
-  - `Options struct` - Options for scanner behavior
-    - `IncludeDotfiles bool` - Include dot (hidden) files (excluded by default)
-    - `FollowSymLinks bool`
-  - `EnumerateStatus struct` - Progress information for enumeration phase
-    - `FilesFound int64`
-    - `BytesFound int64`
-  - `ScanStatus struct` - Progress information for scan phase
-    - `TotalFiles int64`
-    - `ScannedFiles int64`
-    - `TotalBytes int64`
-    - `ScannedBytes int64`
-    - `BytesPerSec float64`
-    - `ETA time.Duration`
-  - `FileEntry struct` - Represents an enumerated file
-    - `Path string` - Relative path (used in manifest)
-    - `AbsPath string` - Absolute path (used for reading file content)
-    - `Size int64`
-    - `Mtime time.Time`
-    - `Ctime time.Time`
-  - `Scanner struct` - Accumulates files and generates manifests
-- **Functions**
-  - `New() *Scanner` - Creates a new Scanner with default options
-  - `NewWithOptions(opts *Options) *Scanner` - Creates a new Scanner with given options
-- **Methods (Enumeration Phase)**
-  - `(*Scanner) EnumerateFile(path string) error` - Enumerates a single file, calling stat() for metadata
-  - `(*Scanner) EnumeratePath(inputPath string, progress chan<- EnumerateStatus) error` - Walks a directory and enumerates all files
-  - `(*Scanner) EnumeratePaths(progress chan<- EnumerateStatus, inputPaths ...string) error` - Walks multiple directories
-  - `(*Scanner) EnumerateFS(afs afero.Fs, basePath string, progress chan<- EnumerateStatus) error` - Walks an afero filesystem
-- **Methods (Accessors)**
-  - `(*Scanner) Files() []*FileEntry` - Returns copy of all enumerated files
-  - `(*Scanner) FileCount() int64` - Returns number of files
-  - `(*Scanner) TotalBytes() int64` - Returns total size of all files
-- **Methods (Scan Phase)**
-  - `(*Scanner) ToManifest(ctx context.Context, w io.Writer, progress chan<- ScanStatus) error` - Reads file contents, computes hashes, generates manifest
-
-## internal/checker/
-
-### checker.go
-- **Types**
-  - `Result struct` - Outcome of checking a single file
-    - `Path string` - File path from manifest
-    - `Status Status` - Verification status
-    - `Message string` - Error or status message
-  - `Status int` - Verification status enumeration
-    - `StatusOK` - File matches manifest
-    - `StatusMissing` - File not found
-    - `StatusSizeMismatch` - File size differs from manifest
-    - `StatusHashMismatch` - File hash differs from manifest
-    - `StatusError` - Error occurred during verification
-  - `CheckStatus struct` - Progress information for check operation
-    - `TotalFiles int64`
-    - `CheckedFiles int64`
-    - `TotalBytes int64`
-    - `CheckedBytes int64`
-    - `BytesPerSec float64`
-    - `ETA time.Duration`
-    - `Failures int64`
-  - `Checker struct` - Verifies files against a manifest
-- **Functions**
-  - `NewChecker(manifestPath string, basePath string) (*Checker, error)` - Creates a new Checker for the given manifest and base path
-- **Methods**
-  - `(s Status) String() string` - Returns string representation of status
-  - `(*Checker) FileCount() int64` - Returns number of files in the manifest
-  - `(*Checker) TotalBytes() int64` - Returns total size of all files in manifest
-  - `(*Checker) Check(ctx context.Context, results chan<- Result, progress chan<- CheckStatus) error` - Verifies all files against the manifest
-
-## mfer/
-
-### manifest.go
-- **Types**
-  - `manifest struct` - Internal representation of a manifest file
-- **Methods**
-  - `(*manifest) Files() []*MFFilePath` - Returns all file entries from a loaded manifest
-
-### builder.go
-- **Types**
-  - `FileHashProgress struct` - Progress info during file hashing (BytesRead int64)
-  - `Builder struct` - Constructs manifests by adding files one at a time
-- **Functions**
-  - `NewBuilder() *Builder` - Creates a new Builder
-- **Methods**
-  - `(*Builder) AddFile(path string, size int64, mtime time.Time, reader io.Reader, progress chan<- FileHashProgress) (int64, error)` - Reads file, computes hash, adds to manifest
-  - `(*Builder) AddFileWithHash(path string, size int64, mtime time.Time, hash []byte)` - Adds file with pre-computed hash
-  - `(*Builder) FileCount() int` - Returns number of files added
-  - `(*Builder) Build(w io.Writer) error` - Finalizes and writes manifest
-
-### serialize.go
-- **Constants**
-  - `MAGIC string` - Magic bytes prefix for manifest files ("ZNAVSRFG")
-
-### deserialize.go
-- **Functions**
-  - `NewManifestFromReader(input io.Reader) (*manifest, error)` - Reads and parses manifest from io.Reader
-  - `NewManifestFromFile(fs afero.Fs, path string) (*manifest, error)` - Reads and parses manifest from file path
-
-### mf.pb.go (generated from mf.proto)
-- **Enum Types**
-  - `MFFileOuter_Version` - Outer file format version
-    - `MFFileOuter_VERSION_NONE`
-    - `MFFileOuter_VERSION_ONE`
-  - `MFFileOuter_CompressionType` - Compression type for inner message
-    - `MFFileOuter_COMPRESSION_NONE`
-    - `MFFileOuter_COMPRESSION_ZSTD`
-  - `MFFile_Version` - Inner file format version
-    - `MFFile_VERSION_NONE`
-    - `MFFile_VERSION_ONE`
-- **Message Types**
-  - `Timestamp struct` - Timestamp with seconds and nanoseconds
-    - `GetSeconds() int64`
-    - `GetNanos() int32`
-  - `MFFileOuter struct` - Outer wrapper containing compressed/signed inner message
-    - `GetVersion() MFFileOuter_Version`
-    - `GetCompressionType() MFFileOuter_CompressionType`
-    - `GetSize() int64`
-    - `GetSha256() []byte`
-    - `GetInnerMessage() []byte`
-    - `GetSignature() []byte`
-    - `GetSigner() []byte`
-    - `GetSigningPubKey() []byte`
-  - `MFFilePath struct` - Individual file entry in manifest
-    - `GetPath() string`
-    - `GetSize() int64`
-    - `GetHashes() []*MFFileChecksum`
-    - `GetMimeType() string`
-    - `GetMtime() *Timestamp`
-    - `GetCtime() *Timestamp`
-    - `GetAtime() *Timestamp`
-  - `MFFileChecksum struct` - File checksum using multihash
-    - `GetMultiHash() []byte`
-  - `MFFile struct` - Inner manifest containing file list
-    - `GetVersion() MFFile_Version`
-    - `GetFiles() []*MFFilePath`
-    - `GetCreatedAt() *Timestamp`
-
 # Build Status
 
 [![Build Status](https://drone.datavi.be/api/badges/sneak/mfer/status.svg)](https://drone.datavi.be/sneak/mfer)
@@ -241,19 +59,18 @@ Reading file contents and computing cryptographic hashes for manifest generation
 # Participation
 
 The community is as yet nonexistent so there are no defined policies or
-norms yet.  Primary development happens on a privately-run Gitea instance at
+norms yet. Primary development happens on a privately-run Gitea instance at
 [https://git.eeqj.de/sneak/mfer](https://git.eeqj.de/sneak/mfer) and issues
 are [tracked there](https://git.eeqj.de/sneak/mfer/issues).
 
 Changes must always be formatted with a standard `go fmt`, syntactically
 valid, and must pass the linting defined in the repository (presently only
-the `golangci-lint` defaults), which can be run with a `make lint`.  The
+the `golangci-lint` defaults), which can be run with a `make lint`. The
 `main` branch is protected and all changes must be made via [pull
 requests](https://git.eeqj.de/sneak/mfer/pulls) and pass CI to be merged.
 Any changes submitted to this project must also be
 [WTFPL-licensed](https://wtfpl.net) to be considered.
 
-
 # Problem Statement
 
 Given a plain URL, there is no standard way to safely and programmatically
@@ -424,13 +241,13 @@ desired username for an account on this Gitea instance.
 
 ## Links
 
-* Repo: [https://git.eeqj.de/sneak/mfer](https://git.eeqj.de/sneak/mfer)
+- Repo: [https://git.eeqj.de/sneak/mfer](https://git.eeqj.de/sneak/mfer)
-* Issues: [https://git.eeqj.de/sneak/mfer/issues](https://git.eeqj.de/sneak/mfer/issues)
+- Issues: [https://git.eeqj.de/sneak/mfer/issues](https://git.eeqj.de/sneak/mfer/issues)
 
 # Authors
 
-* [@sneak &lt;sneak@sneak.berlin&gt;](mailto:sneak@sneak.berlin)
+- [@sneak &lt;sneak@sneak.berlin&gt;](mailto:sneak@sneak.berlin)
 
 # License
 
-* [WTFPL](https://wtfpl.net)
+- [WTFPL](https://wtfpl.net)

TODO.md

@@ -0,0 +1,122 @@
+# TODO: mfer 1.0
+
+## Design Questions
+
+*sneak: please answer inline below each question. These are preserved for posterity.*
+
+### Format Design
+
+**1. Should `MFFileChecksum` be simplified?**
+Currently it's a separate message wrapping a single `bytes multiHash` field. Since multihash already self-describes the algorithm, `repeated bytes hashes` directly on `MFFilePath` would be simpler and reduce per-file protobuf overhead. Is the extra message layer intentional (e.g. planning to add per-hash metadata like `verified_at`)?
+
+> *answer:*
+
+**2. Should file permissions/mode be stored?**
+The format stores mtime/ctime but not Unix file permissions. For archival use (ExFAT, filesystem-independent checksums) this may not matter, but for software distribution or filesystem restoration it's a gap. Should we reserve a field now (e.g. `optional uint32 mode = 305`) even if we don't populate it yet?
+
+> *answer:*
+
+**3. Should `atime` be removed from the schema?**
+Access time is volatile, non-deterministic, and often disabled (`noatime`). Including it means two manifests of the same directory at different times will differ, which conflicts with the determinism goal. Remove it, or document it as "never set by default"?
+
+> *answer:*
+
+**4. What are the path normalization rules?**
+The proto has `string path` with no specification about: always forward-slash? Must be relative? No `..` components allowed? UTF-8 NFC vs NFD normalization (macOS vs Linux)? Max path length? This is a security issue (path traversal) and a cross-platform compatibility issue. What rules should the spec mandate?
+
+> *answer:*
+
+**5. Should we add a version byte after the magic?**
+Currently `ZNAVSRFG` is followed immediately by protobuf. Adding a version byte (`ZNAVSRFG\x01`) would allow future framing changes without requiring protobuf parsing to detect the version. `MFFileOuter.Version` serves this purpose but requires successful deserialization to read. Worth the extra byte?
+
+> *answer:*
+
+**6. Should we add a length-prefix after the magic?**
+Protobuf is not self-delimiting. If we ever want to concatenate manifests or append data after the protobuf, the current framing is insufficient. Add a varint or fixed-width length-prefix?
+
+> *answer:*
+
+### Signature Design
+
+**7. What does the outer SHA-256 hash cover — compressed or uncompressed data?**
+The review notes it currently hashes compressed data (good for verifying before decompression), but this should be explicitly documented. Which is the intended behavior?
+
+> *answer:*
+
+**8. Should `signatureString()` sign raw bytes instead of a hex-encoded string?**
+Currently the canonical string is `MAGIC-UUID-MULTIHASH` with hex encoding, which adds a transformation layer. Signing the raw `sha256` bytes (or compressed `innerMessage` directly) would be simpler. Keep the string format or switch to raw bytes?
+
+> *answer:*
+
+**9. Should we support detached signature files (`.mf.sig`)?**
+Embedded signatures are better for single-file distribution. Detached `.mf.sig` files follow the familiar `SHASUMS`/`SHASUMS.asc` pattern and are simpler for HTTP serving. Support both modes?
+
+> *answer:*
+
+**10. GPG vs pure-Go crypto for signatures?**
+Shelling out to `gpg` is fragile (may not be installed, version-dependent output). `github.com/ProtonMail/go-crypto` provides pure-Go OpenPGP, or we could go Ed25519/signify (simpler, no key management). Which direction?
+
+> *answer:*
+
+### Implementation Design
+
+**11. Should manifests be deterministic by default?**
+This means: sort file entries by path, omit `createdAt` timestamp (or make it opt-in), no `atime`. Should determinism be the default, with a `--include-timestamps` flag to opt in?
+
+> *answer:*
+
+**12. Should we consolidate or keep both scanner/checker implementations?**
+There are two parallel implementations: `mfer/scanner.go` + `mfer/checker.go` (typed with `FileSize`, `RelFilePath`) and `internal/scanner/` + `internal/checker/` (raw `int64`, `string`). The `mfer/` versions are superior. Delete the `internal/` versions?
+
+> *answer:*
+
+**13. Should the `manifest` type be exported?**
+Currently unexported with exported constructors (`New`, `NewFromPaths`, etc.). Consumers can't declare `var m *mfer.manifest`. Export the type, or define an interface?
+
+> *answer:*
+
+**14. What should the Go module path be for 1.0?**
+Currently mixed between `sneak.berlin/go/mfer` and `git.eeqj.de/sneak/mfer`. Which is canonical?
+
+> *answer:*
+
+---
+
+## Implementation Plan
+
+### Phase 1: Foundation (format correctness)
+
+- [ ] Delete `internal/scanner/` and `internal/checker/` — consolidate on `mfer/` package versions; update CLI code
+- [ ] Add deterministic file ordering — sort entries by path (lexicographic, byte-order) in `Builder.Build()`; add test asserting byte-identical output from two runs
+- [ ] Add decompression size limit — `io.LimitReader` in `deserializeInner()` with `m.pbOuter.Size` as bound
+- [ ] Fix `errors.Is` dead code in checker — replace with `os.IsNotExist(err)` or `errors.Is(err, fs.ErrNotExist)`
+- [ ] Fix `AddFile` to verify size — check `totalRead == size` after reading, return error on mismatch
+- [ ] Specify path invariants — add proto comments (UTF-8, forward-slash, relative, no `..`, no leading `/`); validate in `Builder.AddFile` and `Builder.AddFileWithHash`
+
+### Phase 2: CLI polish
+
+- [ ] Fix flag naming — all CLI flags use kebab-case as primary (`--include-dotfiles`, `--follow-symlinks`)
+- [ ] Fix URL construction in fetch — use `BaseURL.JoinPath()` or `url.JoinPath()` instead of string concatenation
+- [ ] Add progress rate-limiting to Checker — throttle to once per second, matching Scanner
+- [ ] Add `--deterministic` flag (or make it default) — omit `createdAt`, sort files
+
+### Phase 3: Robustness
+
+- [ ] Replace GPG subprocess with pure-Go crypto — `github.com/ProtonMail/go-crypto` or Ed25519/signify
+- [ ] Add timeout to any remaining subprocess calls
+- [ ] Add fuzzing tests for `NewManifestFromReader`
+- [ ] Add retry logic to fetch — exponential backoff for transient HTTP errors
+
+### Phase 4: Format finalization
+
+- [ ] Remove or deprecate `atime` from proto (pending design question answer)
+- [ ] Reserve `optional uint32 mode = 305` in `MFFilePath` for future file permissions
+- [ ] Add version byte after magic — `ZNAVSRFG\x01` for format version 1
+- [ ] Write format specification document — separate from README: magic, outer structure, compression, inner structure, path invariants, signature scheme, canonical serialization
+
+### Phase 5: Release prep
+
+- [ ] Finalize Go module path
+- [ ] Audit all error messages for consistency and helpfulness
+- [ ] Add `--version` output matching SemVer
+- [ ] Tag v1.0.0

go.mod

@@ -6,6 +6,7 @@ require (
 	github.com/apex/log v1.9.0
 	github.com/davecgh/go-spew v1.1.1
 	github.com/dustin/go-humanize v1.0.1
+	github.com/google/uuid v1.1.2
 	github.com/klauspost/compress v1.18.2
 	github.com/multiformats/go-multihash v0.2.3
 	github.com/pterm/pterm v0.12.35

go.sum

@@ -135,6 +135,7 @@ github.com/google/pprof v0.0.0-20201203190320-1bf35d6f28c2/go.mod h1:kpwsk12EmLe
 github.com/google/pprof v0.0.0-20201218002935-b9804c9f04c2/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE=
 github.com/google/renameio v0.1.0/go.mod h1:KWCgfxg9yswjAJkECMjeO8J8rahYeXnNhOm40UhjYkI=
 github.com/google/uuid v1.1.1/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
+github.com/google/uuid v1.1.2 h1:EVhdT+1Kseyi1/pUmXKaFxYsDNy9RQYkMWRH68J/W7Y=
 github.com/google/uuid v1.1.2/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
 github.com/googleapis/gax-go/v2 v2.0.4/go.mod h1:0Wqv26UfaUD9n4G6kQubkQ+KchISgw+vpHVxEJEs9eg=
 github.com/googleapis/gax-go/v2 v2.0.5/go.mod h1:DWXyrwAJ9X0FpwwEdw+IPEYBICEFu5mhpdKc/us6bOk=

internal/cli/check.go

@@ -1,8 +1,10 @@
 package cli
 
 import (
+	"encoding/hex"
 	"fmt"
 	"path/filepath"
+	"strings"
 	"time"
 
 	"github.com/dustin/go-humanize"
@@ -68,6 +70,35 @@ func (mfa *CLIApp) checkManifestOperation(ctx *cli.Context) error {
 		return fmt.Errorf("failed to load manifest: %w", err)
 	}
 
+	// Check signature requirement
+	requiredSigner := ctx.String("require-signature")
+	if requiredSigner != "" {
+		// Validate fingerprint format: must be exactly 40 hex characters
+		if len(requiredSigner) != 40 {
+			return fmt.Errorf("invalid fingerprint: must be exactly 40 hex characters, got %d", len(requiredSigner))
+		}
+		if _, err := hex.DecodeString(requiredSigner); err != nil {
+			return fmt.Errorf("invalid fingerprint: must be valid hex: %w", err)
+		}
+
+		if !chk.IsSigned() {
+			return fmt.Errorf("manifest is not signed, but signature from %s is required", requiredSigner)
+		}
+
+		// Extract fingerprint from the embedded public key (not from the signer field)
+		// This validates the key is importable and gets its actual fingerprint
+		embeddedFP, err := chk.ExtractEmbeddedSigningKeyFP()
+		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) {
+			return fmt.Errorf("embedded signing key fingerprint %s does not match required %s", embeddedFP, requiredSigner)
+		}
+		log.Infof("manifest signature verified (signer: %s)", embeddedFP)
+	}
+
 	log.Infof("manifest contains %d files, %s", chk.FileCount(), humanize.IBytes(uint64(chk.TotalBytes())))
 
 	// Set up results channel

internal/cli/entry_test.go

@@ -65,9 +65,9 @@ func TestGenerateCommand(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files in memory filesystem
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("test content"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("test content"), 0o644))
 
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/testdir/test.mf", "/testdir"}, fs)
 
@@ -85,9 +85,9 @@ func TestGenerateAndCheckCommand(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files with subdirectory
-	require.NoError(t, fs.MkdirAll("/testdir/subdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir/subdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/subdir/file2.txt", []byte("test content"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/subdir/file2.txt", []byte("test content"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/testdir/test.mf", "/testdir"}, fs)
@@ -104,8 +104,8 @@ func TestCheckCommandWithMissingFile(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/testdir/test.mf", "/testdir"}, fs)
@@ -125,8 +125,8 @@ func TestCheckCommandWithCorruptedFile(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/testdir/test.mf", "/testdir"}, fs)
@@ -134,7 +134,7 @@ func TestCheckCommandWithCorruptedFile(t *testing.T) {
 	require.Equal(t, 0, exitCode, "generate failed: %s", opts.Stderr.(*bytes.Buffer).String())
 
 	// Corrupt the file (change content but keep same size)
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("HELLO WORLD"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("HELLO WORLD"), 0o644))
 
 	// Check manifest - should fail with hash mismatch
 	opts = testOpts([]string{"mfer", "check", "-q", "--base", "/testdir", "/testdir/test.mf"}, fs)
@@ -146,8 +146,8 @@ func TestCheckCommandWithSizeMismatch(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello world"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/testdir/test.mf", "/testdir"}, fs)
@@ -155,7 +155,7 @@ func TestCheckCommandWithSizeMismatch(t *testing.T) {
 	require.Equal(t, 0, exitCode, "generate failed: %s", opts.Stderr.(*bytes.Buffer).String())
 
 	// Change file size
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("different size content here"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("different size content here"), 0o644))
 
 	// Check manifest - should fail with size mismatch
 	opts = testOpts([]string{"mfer", "check", "-q", "--base", "/testdir", "/testdir/test.mf"}, fs)
@@ -167,8 +167,8 @@ func TestBannerOutput(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
 
 	// Run without -q to see banner
 	opts := testOpts([]string{"mfer", "generate", "-o", "/testdir/test.mf", "/testdir"}, fs)
@@ -193,9 +193,9 @@ func TestGenerateExcludesDotfilesByDefault(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files including dotfiles
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden", []byte("secret"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden", []byte("secret"), 0o644))
 
 	// Generate manifest without --include-dotfiles (default excludes dotfiles)
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/testdir/test.mf", "/testdir"}, fs)
@@ -217,9 +217,9 @@ func TestGenerateWithIncludeDotfiles(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files including dotfiles
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden", []byte("secret"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden", []byte("secret"), 0o644))
 
 	// Generate manifest with --include-dotfiles
 	opts := testOpts([]string{"mfer", "generate", "-q", "--include-dotfiles", "-o", "/testdir/test.mf", "/testdir"}, fs)
@@ -236,10 +236,10 @@ func TestMultipleInputPaths(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files in multiple directories
-	require.NoError(t, fs.MkdirAll("/dir1", 0755))
+	require.NoError(t, fs.MkdirAll("/dir1", 0o755))
-	require.NoError(t, fs.MkdirAll("/dir2", 0755))
+	require.NoError(t, fs.MkdirAll("/dir2", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/dir1/file1.txt", []byte("content1"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/dir1/file1.txt", []byte("content1"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/dir2/file2.txt", []byte("content2"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/dir2/file2.txt", []byte("content2"), 0o644))
 
 	// Generate manifest from multiple paths
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/output.mf", "/dir1", "/dir2"}, fs)
@@ -254,9 +254,9 @@ func TestNoExtraFilesPass(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("world"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/manifest.mf", "/testdir"}, fs)
@@ -273,8 +273,8 @@ func TestNoExtraFilesFail(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/manifest.mf", "/testdir"}, fs)
@@ -282,7 +282,7 @@ func TestNoExtraFilesFail(t *testing.T) {
 	require.Equal(t, 0, exitCode)
 
 	// Add an extra file after manifest generation
-	require.NoError(t, afero.WriteFile(fs, "/testdir/extra.txt", []byte("extra"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/extra.txt", []byte("extra"), 0o644))
 
 	// Check with --no-extra-files (should fail - extra file exists)
 	opts = testOpts([]string{"mfer", "check", "-q", "--no-extra-files", "--base", "/testdir", "/manifest.mf"}, fs)
@@ -294,9 +294,9 @@ func TestNoExtraFilesWithSubdirectory(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test files with subdirectory
-	require.NoError(t, fs.MkdirAll("/testdir/subdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir/subdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/subdir/file2.txt", []byte("world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/subdir/file2.txt", []byte("world"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/manifest.mf", "/testdir"}, fs)
@@ -304,7 +304,7 @@ func TestNoExtraFilesWithSubdirectory(t *testing.T) {
 	require.Equal(t, 0, exitCode)
 
 	// Add extra file in subdirectory
-	require.NoError(t, afero.WriteFile(fs, "/testdir/subdir/extra.txt", []byte("extra"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/subdir/extra.txt", []byte("extra"), 0o644))
 
 	// Check with --no-extra-files (should fail)
 	opts = testOpts([]string{"mfer", "check", "-q", "--no-extra-files", "--base", "/testdir", "/manifest.mf"}, fs)
@@ -316,8 +316,8 @@ func TestCheckWithoutNoExtraFilesIgnoresExtra(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/manifest.mf", "/testdir"}, fs)
@@ -325,7 +325,7 @@ func TestCheckWithoutNoExtraFilesIgnoresExtra(t *testing.T) {
 	require.Equal(t, 0, exitCode)
 
 	// Add extra file
-	require.NoError(t, afero.WriteFile(fs, "/testdir/extra.txt", []byte("extra"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/extra.txt", []byte("extra"), 0o644))
 
 	// Check WITHOUT --no-extra-files (should pass - extra files ignored)
 	opts = testOpts([]string{"mfer", "check", "-q", "--base", "/testdir", "/manifest.mf"}, fs)
@@ -337,8 +337,8 @@ func TestGenerateAtomicWriteNoTempFileOnSuccess(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/output.mf", "/testdir"}, fs)
@@ -360,11 +360,11 @@ func TestGenerateAtomicWriteOverwriteWithForce(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
 
 	// Create existing manifest with different content
-	require.NoError(t, afero.WriteFile(fs, "/output.mf", []byte("old content"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/output.mf", []byte("old content"), 0o644))
 
 	// Generate manifest with --force
 	opts := testOpts([]string{"mfer", "generate", "-q", "-f", "-o", "/output.mf", "/testdir"}, fs)
@@ -386,11 +386,11 @@ func TestGenerateFailsWithoutForceWhenOutputExists(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
 
 	// Create existing manifest
-	require.NoError(t, afero.WriteFile(fs, "/output.mf", []byte("existing"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/output.mf", []byte("existing"), 0o644))
 
 	// Generate manifest WITHOUT --force (should fail)
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/output.mf", "/testdir"}, fs)
@@ -411,8 +411,8 @@ func TestGenerateAtomicWriteUsesTemp(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create test file
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("hello"), 0o644))
 
 	// Generate manifest
 	opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/output.mf", "/testdir"}, fs)
@@ -464,8 +464,8 @@ func TestGenerateAtomicWriteCleansUpOnError(t *testing.T) {
 	baseFs := afero.NewMemMapFs()
 
 	// Create test files - need enough content to trigger the write failure
-	require.NoError(t, baseFs.MkdirAll("/testdir", 0755))
+	require.NoError(t, baseFs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(baseFs, "/testdir/file1.txt", []byte("hello world this is a test file"), 0644))
+	require.NoError(t, afero.WriteFile(baseFs, "/testdir/file1.txt", []byte("hello world this is a test file"), 0o644))
 
 	// Wrap with failing writer that fails after writing some bytes
 	fs := &failingWriterFs{Fs: baseFs, failAfter: 10}
@@ -489,8 +489,8 @@ func TestGenerateValidatesInputPaths(t *testing.T) {
 	fs := afero.NewMemMapFs()
 
 	// Create one valid directory
-	require.NoError(t, fs.MkdirAll("/validdir", 0755))
+	require.NoError(t, fs.MkdirAll("/validdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/validdir/file.txt", []byte("content"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/validdir/file.txt", []byte("content"), 0o644))
 
 	t.Run("nonexistent path fails fast", func(t *testing.T) {
 		opts := testOpts([]string{"mfer", "generate", "-q", "-o", "/output.mf", "/nonexistent"}, fs)
@@ -527,7 +527,7 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 
 	// Create many small files with random names to generate a ~1MB manifest
 	// Each manifest entry is roughly 50-60 bytes, so we need ~20000 files
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
 
 	numFiles := 20000
 	for i := 0; i < numFiles; i++ {
@@ -536,7 +536,7 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 		// Small random content
 		content := make([]byte, 16+rng.Intn(48))
 		rng.Read(content)
-		require.NoError(t, afero.WriteFile(fs, filename, content, 0644))
+		require.NoError(t, afero.WriteFile(fs, filename, content, 0o644))
 	}
 
 	// Generate manifest outside of testdir
@@ -551,7 +551,7 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 	t.Logf("manifest size: %d bytes (%d files)", len(validManifest), numFiles)
 
 	// First corruption: truncate the manifest
-	require.NoError(t, afero.WriteFile(fs, "/manifest.mf", validManifest[:len(validManifest)/2], 0644))
+	require.NoError(t, afero.WriteFile(fs, "/manifest.mf", validManifest[:len(validManifest)/2], 0o644))
 
 	// Check should fail with truncated manifest
 	opts = testOpts([]string{"mfer", "check", "-q", "--base", "/testdir", "/manifest.mf"}, fs)
@@ -559,7 +559,7 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 	assert.Equal(t, 1, exitCode, "check should fail with truncated manifest")
 
 	// Verify check passes with valid manifest
-	require.NoError(t, afero.WriteFile(fs, "/manifest.mf", validManifest, 0644))
+	require.NoError(t, afero.WriteFile(fs, "/manifest.mf", validManifest, 0o644))
 	opts = testOpts([]string{"mfer", "check", "-q", "--base", "/testdir", "/manifest.mf"}, fs)
 	exitCode = RunWithOptions(opts)
 	require.Equal(t, 0, exitCode, "check should pass with valid manifest")
@@ -579,7 +579,7 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 		}
 		corrupted[offset] = newByte
 
-		require.NoError(t, afero.WriteFile(fs, "/manifest.mf", corrupted, 0644))
+		require.NoError(t, afero.WriteFile(fs, "/manifest.mf", corrupted, 0o644))
 
 		// Check should fail with corrupted manifest
 		opts = testOpts([]string{"mfer", "check", "-q", "--base", "/testdir", "/manifest.mf"}, fs)
@@ -588,6 +588,6 @@ func TestCheckDetectsManifestCorruption(t *testing.T) {
 			i, offset, originalByte, newByte)
 
 		// Restore valid manifest for next iteration
-		require.NoError(t, afero.WriteFile(fs, "/manifest.mf", validManifest, 0644))
+		require.NoError(t, afero.WriteFile(fs, "/manifest.mf", validManifest, 0o644))
 	}
 }

internal/cli/fetch.go

@@ -113,7 +113,7 @@ func (mfa *CLIApp) fetchManifestOperation(ctx *cli.Context) error {
 			return fmt.Errorf("invalid path in manifest: %w", err)
 		}
 
-		fileURL := baseURL.String() + f.Path
+		fileURL := baseURL.String() + encodeFilePath(f.Path)
 		log.Infof("fetching %s", f.Path)
 
 		if err := downloadFile(fileURL, localPath, f, progress); err != nil {
@@ -139,6 +139,15 @@ func (mfa *CLIApp) fetchManifestOperation(ctx *cli.Context) error {
 	return nil
 }
 
+// encodeFilePath URL-encodes each segment of a file path while preserving slashes.
+func encodeFilePath(p string) string {
+	segments := strings.Split(p, "/")
+	for i, seg := range segments {
+		segments[i] = url.PathEscape(seg)
+	}
+	return strings.Join(segments, "/")
+}
+
 // sanitizePath validates and sanitizes a file path from the manifest.
 // It prevents path traversal attacks and rejects unsafe paths.
 func sanitizePath(p string) (string, error) {
@@ -257,7 +266,7 @@ func downloadFile(fileURL, localPath string, entry *mfer.MFFilePath, progress ch
 	// Create parent directories if needed
 	dir := filepath.Dir(localPath)
 	if dir != "" && dir != "." {
-		if err := os.MkdirAll(dir, 0755); err != nil {
+		if err := os.MkdirAll(dir, 0o755); err != nil {
 			return err
 		}
 	}

internal/cli/fetch_test.go

@@ -13,10 +13,32 @@ import (
 	"github.com/spf13/afero"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	"sneak.berlin/go/mfer/internal/scanner"
 	"sneak.berlin/go/mfer/mfer"
 )
 
+func TestEncodeFilePath(t *testing.T) {
+	tests := []struct {
+		input    string
+		expected string
+	}{
+		{"file.txt", "file.txt"},
+		{"dir/file.txt", "dir/file.txt"},
+		{"my file.txt", "my%20file.txt"},
+		{"dir/my file.txt", "dir/my%20file.txt"},
+		{"file#1.txt", "file%231.txt"},
+		{"file?v=1.txt", "file%3Fv=1.txt"},
+		{"path/to/file with spaces.txt", "path/to/file%20with%20spaces.txt"},
+		{"100%done.txt", "100%25done.txt"},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.input, func(t *testing.T) {
+			result := encodeFilePath(tt.input)
+			assert.Equal(t, tt.expected, result)
+		})
+	}
+}
+
 func TestSanitizePath(t *testing.T) {
 	// Valid paths that should be accepted
 	validTests := []struct {
@@ -107,15 +129,15 @@ func TestFetchFromHTTP(t *testing.T) {
 	for path, content := range testFiles {
 		fullPath := "/" + path // MemMapFs needs absolute paths
 		dir := filepath.Dir(fullPath)
-		require.NoError(t, sourceFs.MkdirAll(dir, 0755))
+		require.NoError(t, sourceFs.MkdirAll(dir, 0o755))
-		require.NoError(t, afero.WriteFile(sourceFs, fullPath, content, 0644))
+		require.NoError(t, afero.WriteFile(sourceFs, fullPath, content, 0o644))
 	}
 
 	// Generate manifest using scanner
-	opts := &scanner.Options{
+	opts := &mfer.ScannerOptions{
 		Fs: sourceFs,
 	}
-	s := scanner.NewWithOptions(opts)
+	s := mfer.NewScannerWithOptions(opts)
 	require.NoError(t, s.EnumerateFS(sourceFs, "/", nil))
 
 	var manifestBuf bytes.Buffer
@@ -197,11 +219,11 @@ func TestFetchHashMismatch(t *testing.T) {
 	// Create source filesystem with a test file
 	sourceFs := afero.NewMemMapFs()
 	originalContent := []byte("Original content")
-	require.NoError(t, afero.WriteFile(sourceFs, "/file.txt", originalContent, 0644))
+	require.NoError(t, afero.WriteFile(sourceFs, "/file.txt", originalContent, 0o644))
 
 	// Generate manifest
-	opts := &scanner.Options{Fs: sourceFs}
+	opts := &mfer.ScannerOptions{Fs: sourceFs}
-	s := scanner.NewWithOptions(opts)
+	s := mfer.NewScannerWithOptions(opts)
 	require.NoError(t, s.EnumerateFS(sourceFs, "/", nil))
 
 	var manifestBuf bytes.Buffer
@@ -249,11 +271,11 @@ func TestFetchSizeMismatch(t *testing.T) {
 	// Create source filesystem with a test file
 	sourceFs := afero.NewMemMapFs()
 	originalContent := []byte("Original content with specific size")
-	require.NoError(t, afero.WriteFile(sourceFs, "/file.txt", originalContent, 0644))
+	require.NoError(t, afero.WriteFile(sourceFs, "/file.txt", originalContent, 0o644))
 
 	// Generate manifest
-	opts := &scanner.Options{Fs: sourceFs}
+	opts := &mfer.ScannerOptions{Fs: sourceFs}
-	s := scanner.NewWithOptions(opts)
+	s := mfer.NewScannerWithOptions(opts)
 	require.NoError(t, s.EnumerateFS(sourceFs, "/", nil))
 
 	var manifestBuf bytes.Buffer
@@ -298,11 +320,11 @@ func TestFetchProgress(t *testing.T) {
 	sourceFs := afero.NewMemMapFs()
 	// Create content large enough to trigger multiple progress updates
 	content := bytes.Repeat([]byte("x"), 100*1024) // 100KB
-	require.NoError(t, afero.WriteFile(sourceFs, "/large.txt", content, 0644))
+	require.NoError(t, afero.WriteFile(sourceFs, "/large.txt", content, 0o644))
 
 	// Generate manifest
-	opts := &scanner.Options{Fs: sourceFs}
+	opts := &mfer.ScannerOptions{Fs: sourceFs}
-	s := scanner.NewWithOptions(opts)
+	s := mfer.NewScannerWithOptions(opts)
 	require.NoError(t, s.EnumerateFS(sourceFs, "/", nil))
 
 	var manifestBuf bytes.Buffer

internal/cli/freshen.go

@@ -227,6 +227,14 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 
 	builder := mfer.NewBuilder()
 
+	// Set up signing options if sign-key is provided
+	if signKey := ctx.String("sign-key"); signKey != "" {
+		builder.SetSigningOptions(&mfer.SigningOptions{
+			KeyID: mfer.GPGKeyID(signKey),
+		})
+		log.Infof("signing manifest with GPG key: %s", signKey)
+	}
+
 	for _, e := range entries {
 		select {
 		case <-ctx.Done():

internal/cli/freshen_test.go

@@ -8,7 +8,6 @@ import (
 	"github.com/spf13/afero"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	"sneak.berlin/go/mfer/internal/scanner"
 	"sneak.berlin/go/mfer/mfer"
 )
 
@@ -16,20 +15,20 @@ func TestFreshenUnchanged(t *testing.T) {
 	// Create filesystem with test files
 	fs := afero.NewMemMapFs()
 
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("content1"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("content1"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("content2"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("content2"), 0o644))
 
 	// Generate initial manifest
-	opts := &scanner.Options{Fs: fs}
+	opts := &mfer.ScannerOptions{Fs: fs}
-	s := scanner.NewWithOptions(opts)
+	s := mfer.NewScannerWithOptions(opts)
 	require.NoError(t, s.EnumeratePath("/testdir", nil))
 
 	var manifestBuf bytes.Buffer
 	require.NoError(t, s.ToManifest(context.Background(), &manifestBuf, nil))
 
 	// Write manifest to filesystem
-	require.NoError(t, afero.WriteFile(fs, "/testdir/.index.mf", manifestBuf.Bytes(), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/.index.mf", manifestBuf.Bytes(), 0o644))
 
 	// Parse manifest to verify
 	manifest, err := mfer.NewManifestFromFile(fs, "/testdir/.index.mf")
@@ -41,20 +40,20 @@ func TestFreshenWithChanges(t *testing.T) {
 	// Create filesystem with test files
 	fs := afero.NewMemMapFs()
 
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("content1"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("content1"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("content2"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("content2"), 0o644))
 
 	// Generate initial manifest
-	opts := &scanner.Options{Fs: fs}
+	opts := &mfer.ScannerOptions{Fs: fs}
-	s := scanner.NewWithOptions(opts)
+	s := mfer.NewScannerWithOptions(opts)
 	require.NoError(t, s.EnumeratePath("/testdir", nil))
 
 	var manifestBuf bytes.Buffer
 	require.NoError(t, s.ToManifest(context.Background(), &manifestBuf, nil))
 
 	// Write manifest to filesystem
-	require.NoError(t, afero.WriteFile(fs, "/testdir/.index.mf", manifestBuf.Bytes(), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/.index.mf", manifestBuf.Bytes(), 0o644))
 
 	// Verify initial manifest has 2 files
 	manifest, err := mfer.NewManifestFromFile(fs, "/testdir/.index.mf")
@@ -62,10 +61,10 @@ func TestFreshenWithChanges(t *testing.T) {
 	assert.Len(t, manifest.Files(), 2)
 
 	// Add a new file
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file3.txt", []byte("content3"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file3.txt", []byte("content3"), 0o644))
 
 	// Modify file2 (change content and size)
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("modified content2"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("modified content2"), 0o644))
 
 	// Remove file1
 	require.NoError(t, fs.Remove("/testdir/file1.txt"))

internal/cli/gen.go

@@ -25,6 +25,14 @@ func (mfa *CLIApp) generateManifestOperation(ctx *cli.Context) error {
 		Fs:              mfa.Fs,
 	}
 
+	// Set up signing options if sign-key is provided
+	if signKey := ctx.String("sign-key"); signKey != "" {
+		opts.SigningOptions = &mfer.SigningOptions{
+			KeyID: mfer.GPGKeyID(signKey),
+		}
+		log.Infof("signing manifest with GPG key: %s", signKey)
+	}
+
 	s := mfer.NewScannerWithOptions(opts)
 
 	// Phase 1: Enumeration - collect paths and stat files

internal/cli/mfer.go

@@ -148,6 +148,12 @@ func (mfa *CLIApp) run(args []string) {
 						Aliases: []string{"P"},
 						Usage:   "Show progress during enumeration and scanning",
 					},
+					&cli.StringFlag{
+						Name:    "sign-key",
+						Aliases: []string{"s"},
+						Usage:   "GPG key ID to sign the manifest with",
+						EnvVars: []string{"MFER_SIGN_KEY"},
+					},
 				),
 			},
 			{
@@ -175,6 +181,12 @@ func (mfa *CLIApp) run(args []string) {
 						Name:  "no-extra-files",
 						Usage: "Fail if files exist in base directory that are not in manifest",
 					},
+					&cli.StringFlag{
+						Name:    "require-signature",
+						Aliases: []string{"S"},
+						Usage:   "Require manifest to be signed by the specified GPG key ID",
+						EnvVars: []string{"MFER_REQUIRE_SIGNATURE"},
+					},
 				),
 			},
 			{
@@ -208,6 +220,12 @@ func (mfa *CLIApp) run(args []string) {
 						Aliases: []string{"P"},
 						Usage:   "Show progress during scanning and hashing",
 					},
+					&cli.StringFlag{
+						Name:    "sign-key",
+						Aliases: []string{"s"},
+						Usage:   "GPG key ID to sign the manifest with",
+						EnvVars: []string{"MFER_SIGN_KEY"},
+					},
 				),
 			},
 			{

mfer/builder.go

@@ -3,13 +3,47 @@ package mfer
 import (
 	"crypto/sha256"
 	"errors"
+	"fmt"
 	"io"
+	"strings"
 	"sync"
 	"time"
+	"unicode/utf8"
 
 	"github.com/multiformats/go-multihash"
 )
 
+// ValidatePath checks that a file path conforms to manifest path invariants:
+//   - Must be valid UTF-8
+//   - Must use forward slashes only (no backslashes)
+//   - Must be relative (no leading /)
+//   - Must not contain ".." segments
+//   - Must not contain empty segments (no "//")
+//   - Must not be empty
+func ValidatePath(p string) error {
+	if p == "" {
+		return errors.New("path cannot be empty")
+	}
+	if !utf8.ValidString(p) {
+		return fmt.Errorf("path %q is not valid UTF-8", p)
+	}
+	if strings.ContainsRune(p, '\\') {
+		return fmt.Errorf("path %q contains backslash; use forward slashes only", p)
+	}
+	if strings.HasPrefix(p, "/") {
+		return fmt.Errorf("path %q is absolute; must be relative", p)
+	}
+	for _, seg := range strings.Split(p, "/") {
+		if seg == "" {
+			return fmt.Errorf("path %q contains empty segment", p)
+		}
+		if seg == ".." {
+			return fmt.Errorf("path %q contains '..' segment", p)
+		}
+	}
+	return nil
+}
+
 // RelFilePath represents a relative file path within a manifest.
 type RelFilePath string
 
@@ -50,9 +84,10 @@ type FileHashProgress struct {
 
 // Builder constructs a manifest by adding files one at a time.
 type Builder struct {
-	mu        sync.Mutex
+	mu             sync.Mutex
-	files     []*MFFilePath
+	files          []*MFFilePath
-	createdAt time.Time
+	createdAt      time.Time
+	signingOptions *SigningOptions
 }
 
 // NewBuilder creates a new Builder.
@@ -73,6 +108,10 @@ func (b *Builder) AddFile(
 	reader io.Reader,
 	progress chan<- FileHashProgress,
 ) (FileSize, error) {
+	if err := ValidatePath(string(path)); err != nil {
+		return 0, err
+	}
+
 	// Create hash writer
 	h := sha256.New()
 
@@ -95,6 +134,11 @@ func (b *Builder) AddFile(
 		}
 	}
 
+	// Verify actual bytes read matches declared size
+	if totalRead != size {
+		return totalRead, fmt.Errorf("size mismatch for %q: declared %d bytes but read %d bytes", path, size, totalRead)
+	}
+
 	// Encode hash as multihash (SHA2-256)
 	mh, err := multihash.Encode(h.Sum(nil), multihash.SHA2_256)
 	if err != nil {
@@ -140,8 +184,8 @@ func (b *Builder) FileCount() int {
 // This is useful when the hash is already known (e.g., from an existing manifest).
 // Returns an error if path is empty, size is negative, or hash is nil/empty.
 func (b *Builder) AddFileWithHash(path RelFilePath, size FileSize, mtime ModTime, hash Multihash) error {
-	if path == "" {
+	if err := ValidatePath(string(path)); err != nil {
-		return errors.New("path cannot be empty")
+		return err
 	}
 	if size < 0 {
 		return errors.New("size cannot be negative")
@@ -165,6 +209,14 @@ func (b *Builder) AddFileWithHash(path RelFilePath, size FileSize, mtime ModTime
 	return nil
 }
 
+// SetSigningOptions sets the GPG signing options for the manifest.
+// If opts is non-nil, the manifest will be signed when Build() is called.
+func (b *Builder) SetSigningOptions(opts *SigningOptions) {
+	b.mu.Lock()
+	defer b.mu.Unlock()
+	b.signingOptions = opts
+}
+
 // Build finalizes the manifest and writes it to the writer.
 func (b *Builder) Build(w io.Writer) error {
 	b.mu.Lock()
@@ -179,7 +231,8 @@ func (b *Builder) Build(w io.Writer) error {
 
 	// Create a temporary manifest to use existing serialization
 	m := &manifest{
-		pbInner: inner,
+		pbInner:        inner,
+		signingOptions: b.signingOptions,
 	}
 
 	// Generate outer wrapper

mfer/builder_test.go

@@ -92,6 +92,29 @@ func TestBuilderBuild(t *testing.T) {
 	assert.True(t, strings.HasPrefix(buf.String(), MAGIC))
 }
 
+func TestNewTimestampFromTimeExtremeDate(t *testing.T) {
+	// Regression test: newTimestampFromTime used UnixNano() which panics
+	// for dates outside ~1678-2262. Now uses Nanosecond() which is safe.
+	tests := []struct {
+		name string
+		time time.Time
+	}{
+		{"zero time", time.Time{}},
+		{"year 1000", time.Date(1000, 1, 1, 0, 0, 0, 0, time.UTC)},
+		{"year 3000", time.Date(3000, 1, 1, 0, 0, 0, 123456789, time.UTC)},
+		{"unix epoch", time.Unix(0, 0)},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			// Should not panic
+			ts := newTimestampFromTime(tt.time)
+			assert.Equal(t, tt.time.Unix(), ts.Seconds)
+			assert.Equal(t, int32(tt.time.Nanosecond()), ts.Nanos)
+		})
+	}
+}
+
 func TestBuilderBuildEmpty(t *testing.T) {
 	b := NewBuilder()
 

mfer/checker.go

@@ -70,6 +70,10 @@ type Checker struct {
 	fs       afero.Fs
 	// manifestPaths is a set of paths in the manifest for quick lookup
 	manifestPaths map[RelFilePath]struct{}
+	// signature info from the manifest
+	signature     []byte
+	signer        []byte
+	signingPubKey []byte
 }
 
 // NewChecker creates a new Checker for the given manifest, base path, and filesystem.
@@ -101,6 +105,9 @@ func NewChecker(manifestPath string, basePath string, fs afero.Fs) (*Checker, er
 		files:         files,
 		fs:            fs,
 		manifestPaths: manifestPaths,
+		signature:     m.pbOuter.Signature,
+		signer:        m.pbOuter.Signer,
+		signingPubKey: m.pbOuter.SigningPubKey,
 	}, nil
 }
 
@@ -118,6 +125,31 @@ func (c *Checker) TotalBytes() FileSize {
 	return total
 }
 
+// IsSigned returns true if the manifest has a signature.
+func (c *Checker) IsSigned() bool {
+	return len(c.signature) > 0
+}
+
+// Signer returns the signer fingerprint if the manifest is signed, nil otherwise.
+func (c *Checker) Signer() []byte {
+	return c.signer
+}
+
+// SigningPubKey returns the signing public key if the manifest is signed, nil otherwise.
+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() (string, error) {
+	if len(c.signingPubKey) == 0 {
+		return "", errors.New("manifest has no signing public key")
+	}
+	return gpgExtractPubKeyFingerprint(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.
@@ -192,12 +224,7 @@ func (c *Checker) checkFile(entry *MFFilePath, checkedBytes *FileSize) Result {
 	// Check if file exists
 	info, err := c.fs.Stat(absPath)
 	if err != nil {
-		if errors.Is(err, afero.ErrFileNotFound) || errors.Is(err, errors.New("file does not exist")) {
+		if errors.Is(err, os.ErrNotExist) || errors.Is(err, afero.ErrFileNotFound) {
-			return Result{Path: relPath, Status: StatusMissing, Message: "file not found"}
-		}
-		// Check for "file does not exist" style errors
-		exists, _ := afero.Exists(c.fs, absPath)
-		if !exists {
 			return Result{Path: relPath, Status: StatusMissing, Message: "file not found"}
 		}
 		return Result{Path: relPath, Status: StatusError, Message: err.Error()}

mfer/checker_test.go

@@ -381,6 +381,39 @@ func TestCheckSubdirectories(t *testing.T) {
 	assert.Equal(t, 3, okCount)
 }
 
+func TestCheckMissingFileDetectedWithoutFallback(t *testing.T) {
+	// Regression test: errors.Is(err, errors.New("...")) never matches because
+	// errors.New creates a new value each time. The fix uses os.ErrNotExist instead.
+	fs := afero.NewMemMapFs()
+	files := map[string][]byte{
+		"exists.txt":  []byte("here"),
+		"missing.txt": []byte("not on disk"),
+	}
+	createTestManifest(t, fs, "/manifest.mf", files)
+	// Only create one file on disk
+	createFilesOnDisk(t, fs, "/data", map[string][]byte{
+		"exists.txt": []byte("here"),
+	})
+
+	chk, err := NewChecker("/manifest.mf", "/data", fs)
+	require.NoError(t, err)
+
+	results := make(chan Result, 10)
+	err = chk.Check(context.Background(), results, nil)
+	require.NoError(t, err)
+
+	statusCounts := map[Status]int{}
+	for r := range results {
+		statusCounts[r.Status]++
+		if r.Status == StatusMissing {
+			assert.Equal(t, RelFilePath("missing.txt"), r.Path)
+		}
+	}
+	assert.Equal(t, 1, statusCounts[StatusOK], "one file should be OK")
+	assert.Equal(t, 1, statusCounts[StatusMissing], "one file should be MISSING")
+	assert.Equal(t, 0, statusCounts[StatusError], "no files should be ERROR")
+}
+
 func TestCheckEmptyManifest(t *testing.T) {
 	fs := afero.NewMemMapFs()
 	// Create manifest with no files

mfer/constants.go

@@ -3,4 +3,9 @@ package mfer
 const (
 	Version     = "0.1.0"
 	ReleaseDate = "2025-12-17"
+
+	// MaxDecompressedSize is the maximum allowed size of decompressed manifest
+	// data (256 MB). This prevents decompression bombs from consuming excessive
+	// memory.
+	MaxDecompressedSize int64 = 256 * 1024 * 1024
 )

mfer/deserialize.go

@@ -2,9 +2,12 @@ package mfer
 
 import (
 	"bytes"
+	"crypto/sha256"
 	"errors"
+	"fmt"
 	"io"
 
+	"github.com/google/uuid"
 	"github.com/klauspost/compress/zstd"
 	"github.com/spf13/afero"
 	"google.golang.org/protobuf/proto"
@@ -12,6 +15,19 @@ import (
 	"sneak.berlin/go/mfer/internal/log"
 )
 
+// validateUUID checks that the byte slice is a valid UUID (16 bytes, parseable).
+func validateUUID(data []byte) error {
+	if len(data) != 16 {
+		return errors.New("invalid UUID length")
+	}
+	// Try to parse as UUID to validate format
+	_, err := uuid.FromBytes(data)
+	if err != nil {
+		return errors.New("invalid UUID format")
+	}
+	return nil
+}
+
 func (m *manifest) deserializeInner() error {
 	if m.pbOuter.Version != MFFileOuter_VERSION_ONE {
 		return errors.New("unknown version")
@@ -20,6 +36,38 @@ func (m *manifest) deserializeInner() error {
 		return errors.New("unknown compression type")
 	}
 
+	// Validate outer UUID before any decompression
+	if err := validateUUID(m.pbOuter.Uuid); err != nil {
+		return errors.New("outer UUID invalid: " + err.Error())
+	}
+
+	// Verify hash of compressed data before decompression
+	h := sha256.New()
+	if _, err := h.Write(m.pbOuter.InnerMessage); err != nil {
+		return err
+	}
+	sha256Hash := h.Sum(nil)
+	if !bytes.Equal(sha256Hash, m.pbOuter.Sha256) {
+		return errors.New("compressed data hash mismatch")
+	}
+
+	// Verify signature if present
+	if len(m.pbOuter.Signature) > 0 {
+		if len(m.pbOuter.SigningPubKey) == 0 {
+			return errors.New("signature present but no public key")
+		}
+
+		sigString, err := m.signatureString()
+		if err != nil {
+			return fmt.Errorf("failed to generate signature string for verification: %w", err)
+		}
+
+		if err := gpgVerify([]byte(sigString), m.pbOuter.Signature, m.pbOuter.SigningPubKey); err != nil {
+			return fmt.Errorf("signature verification failed: %w", err)
+		}
+		log.Infof("signature verified successfully")
+	}
+
 	bb := bytes.NewBuffer(m.pbOuter.InnerMessage)
 
 	zr, err := zstd.NewReader(bb)
@@ -28,10 +76,20 @@ func (m *manifest) deserializeInner() error {
 	}
 	defer zr.Close()
 
-	dat, err := io.ReadAll(zr)
+	// Limit decompressed size to prevent decompression bombs.
+	// Use declared size + 1 byte to detect overflow, capped at MaxDecompressedSize.
+	maxSize := MaxDecompressedSize
+	if m.pbOuter.Size > 0 && m.pbOuter.Size < int64(maxSize) {
+		maxSize = int64(m.pbOuter.Size) + 1
+	}
+	limitedReader := io.LimitReader(zr, maxSize)
+	dat, err := io.ReadAll(limitedReader)
 	if err != nil {
 		return err
 	}
+	if int64(len(dat)) >= MaxDecompressedSize {
+		return fmt.Errorf("decompressed data exceeds maximum allowed size of %d bytes", MaxDecompressedSize)
+	}
 
 	isize := len(dat)
 	if int64(isize) != m.pbOuter.Size {
@@ -45,6 +103,16 @@ func (m *manifest) deserializeInner() error {
 		return err
 	}
 
+	// Validate inner UUID
+	if err := validateUUID(m.pbInner.Uuid); err != nil {
+		return errors.New("inner UUID invalid: " + err.Error())
+	}
+
+	// Verify UUIDs match
+	if !bytes.Equal(m.pbOuter.Uuid, m.pbInner.Uuid) {
+		return errors.New("outer and inner UUID mismatch")
+	}
+
 	log.Infof("loaded manifest with %d files", len(m.pbInner.Files))
 	return nil
 }

mfer/gpg.go

@@ -0,0 +1,212 @@
+package mfer
+
+import (
+	"bytes"
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+)
+
+// GPGKeyID represents a GPG key identifier (fingerprint or key ID).
+type GPGKeyID string
+
+// SigningOptions contains options for GPG signing.
+type SigningOptions struct {
+	KeyID GPGKeyID
+}
+
+// gpgSign creates a detached signature of the data using the specified key.
+// Returns the armored detached signature.
+func gpgSign(data []byte, keyID GPGKeyID) ([]byte, error) {
+	cmd := exec.Command("gpg",
+		"--detach-sign",
+		"--armor",
+		"--local-user", string(keyID),
+	)
+
+	cmd.Stdin = bytes.NewReader(data)
+
+	var stdout, stderr bytes.Buffer
+	cmd.Stdout = &stdout
+	cmd.Stderr = &stderr
+
+	if err := cmd.Run(); 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(keyID GPGKeyID) ([]byte, error) {
+	cmd := exec.Command("gpg",
+		"--export",
+		"--armor",
+		string(keyID),
+	)
+
+	var stdout, stderr bytes.Buffer
+	cmd.Stdout = &stdout
+	cmd.Stderr = &stderr
+
+	if err := cmd.Run(); err != nil {
+		return nil, fmt.Errorf("gpg export failed: %w: %s", err, stderr.String())
+	}
+
+	if stdout.Len() == 0 {
+		return nil, fmt.Errorf("gpg key not found: %s", keyID)
+	}
+
+	return stdout.Bytes(), nil
+}
+
+// gpgGetKeyFingerprint gets the full fingerprint for a key ID.
+func gpgGetKeyFingerprint(keyID GPGKeyID) ([]byte, error) {
+	cmd := exec.Command("gpg",
+		"--with-colons",
+		"--fingerprint",
+		string(keyID),
+	)
+
+	var stdout, stderr bytes.Buffer
+	cmd.Stdout = &stdout
+	cmd.Stderr = &stderr
+
+	if err := cmd.Run(); err != nil {
+		return nil, fmt.Errorf("gpg fingerprint lookup failed: %w: %s", err, stderr.String())
+	}
+
+	// Parse the colon-delimited output to find the fingerprint
+	lines := strings.Split(stdout.String(), "\n")
+	for _, line := range lines {
+		fields := strings.Split(line, ":")
+		if len(fields) >= 10 && fields[0] == "fpr" {
+			return []byte(fields[9]), nil
+		}
+	}
+
+	return nil, fmt.Errorf("fingerprint not found for key: %s", keyID)
+}
+
+// gpgExtractPubKeyFingerprint imports a public key into a temporary keyring
+// and extracts its fingerprint. This verifies the key is valid and returns
+// the actual fingerprint from the key material.
+func gpgExtractPubKeyFingerprint(pubKey []byte) (string, error) {
+	// 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
+	if err := os.Chmod(tmpDir, 0o700); 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")
+	if err := os.WriteFile(pubKeyFile, pubKey, 0o600); err != nil {
+		return "", fmt.Errorf("failed to write public key: %w", err)
+	}
+
+	// Import the public key into the temporary keyring
+	importCmd := exec.Command("gpg",
+		"--homedir", tmpDir,
+		"--import",
+		pubKeyFile,
+	)
+	var importStderr bytes.Buffer
+	importCmd.Stderr = &importStderr
+	if err := importCmd.Run(); err != nil {
+		return "", fmt.Errorf("failed to import public key: %w: %s", err, importStderr.String())
+	}
+
+	// List keys to get fingerprint
+	listCmd := exec.Command("gpg",
+		"--homedir", tmpDir,
+		"--with-colons",
+		"--fingerprint",
+	)
+	var listStdout, listStderr bytes.Buffer
+	listCmd.Stdout = &listStdout
+	listCmd.Stderr = &listStderr
+	if err := listCmd.Run(); err != nil {
+		return "", fmt.Errorf("failed to list keys: %w: %s", err, listStderr.String())
+	}
+
+	// Parse the colon-delimited output to find the fingerprint
+	lines := strings.Split(listStdout.String(), "\n")
+	for _, line := range lines {
+		fields := strings.Split(line, ":")
+		if len(fields) >= 10 && fields[0] == "fpr" {
+			return fields[9], nil
+		}
+	}
+
+	return "", fmt.Errorf("fingerprint not found in imported key")
+}
+
+// gpgVerify verifies a detached signature against data using the provided public key.
+// It creates a temporary keyring to import the public key for verification.
+func gpgVerify(data, signature, pubKey []byte) error {
+	// 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
+	if err := os.Chmod(tmpDir, 0o700); 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")
+	if err := os.WriteFile(pubKeyFile, pubKey, 0o600); err != nil {
+		return fmt.Errorf("failed to write public key: %w", err)
+	}
+
+	// Write signature to temp file
+	sigFile := filepath.Join(tmpDir, "signature.asc")
+	if err := os.WriteFile(sigFile, signature, 0o600); err != nil {
+		return fmt.Errorf("failed to write signature: %w", err)
+	}
+
+	// Write data to temp file
+	dataFile := filepath.Join(tmpDir, "data")
+	if err := os.WriteFile(dataFile, data, 0o600); err != nil {
+		return fmt.Errorf("failed to write data: %w", err)
+	}
+
+	// Import the public key into the temporary keyring
+	importCmd := exec.Command("gpg",
+		"--homedir", tmpDir,
+		"--import",
+		pubKeyFile,
+	)
+	var importStderr bytes.Buffer
+	importCmd.Stderr = &importStderr
+	if err := importCmd.Run(); err != nil {
+		return fmt.Errorf("failed to import public key: %w: %s", err, importStderr.String())
+	}
+
+	// Verify the signature
+	verifyCmd := exec.Command("gpg",
+		"--homedir", tmpDir,
+		"--verify",
+		sigFile,
+		dataFile,
+	)
+	var verifyStderr bytes.Buffer
+	verifyCmd.Stderr = &verifyStderr
+	if err := verifyCmd.Run(); err != nil {
+		return fmt.Errorf("signature verification failed: %w: %s", err, verifyStderr.String())
+	}
+
+	return nil
+}

mfer/gpg_test.go

@@ -0,0 +1,347 @@
+package mfer
+
+import (
+	"bytes"
+	"context"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"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 a cleanup function.
+func testGPGEnv(t *testing.T) (GPGKeyID, func()) {
+	t.Helper()
+
+	// Check if gpg is installed
+	if _, err := exec.LookPath("gpg"); err != nil {
+		t.Skip("gpg not installed, skipping signing test")
+		return "", func() {}
+	}
+
+	// Create temporary GPG home directory
+	gpgHome, err := os.MkdirTemp("", "mfer-gpg-test-*")
+	require.NoError(t, err)
+
+	// Set restrictive permissions on GPG home
+	require.NoError(t, os.Chmod(gpgHome, 0o700))
+
+	// Save original GNUPGHOME and set new one
+	origGPGHome := os.Getenv("GNUPGHOME")
+	require.NoError(t, os.Setenv("GNUPGHOME", gpgHome))
+
+	cleanup := func() {
+		if origGPGHome == "" {
+			_ = os.Unsetenv("GNUPGHOME")
+		} else {
+			_ = os.Setenv("GNUPGHOME", origGPGHome)
+		}
+		_ = os.RemoveAll(gpgHome)
+	}
+
+	// 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))
+
+	cmd := exec.Command("gpg", "--batch", "--gen-key", paramsFile)
+	cmd.Env = append(os.Environ(), "GNUPGHOME="+gpgHome)
+	output, err := cmd.CombinedOutput()
+	if err != nil {
+		cleanup()
+		t.Skipf("failed to generate test GPG key: %v: %s", err, output)
+		return "", func() {}
+	}
+
+	// Get the key fingerprint
+	cmd = exec.Command("gpg", "--list-keys", "--with-colons", "test@mfer.test")
+	cmd.Env = append(os.Environ(), "GNUPGHOME="+gpgHome)
+	output, err = cmd.Output()
+	if err != nil {
+		cleanup()
+		t.Fatalf("failed to list test key: %v", err)
+	}
+
+	// Parse fingerprint from output
+	var keyID string
+	for _, line := range strings.Split(string(output), "\n") {
+		fields := strings.Split(line, ":")
+		if len(fields) >= 10 && fields[0] == "fpr" {
+			keyID = fields[9]
+			break
+		}
+	}
+
+	if keyID == "" {
+		cleanup()
+		t.Fatal("failed to find test key fingerprint")
+	}
+
+	return GPGKeyID(keyID), cleanup
+}
+
+func TestGPGSign(t *testing.T) {
+	keyID, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	data := []byte("test data to sign")
+	sig, err := gpgSign(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, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	pubKey, err := gpgExportPublicKey(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, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	fingerprint, err := gpgGetKeyFingerprint(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")
+}
+
+func TestGPGSignInvalidKey(t *testing.T) {
+	// Set up test environment (we need GNUPGHOME set)
+	_, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	data := []byte("test data")
+	_, err := gpgSign(data, GPGKeyID("NONEXISTENT_KEY_ID_12345"))
+	assert.Error(t, err)
+}
+
+func TestBuilderWithSigning(t *testing.T) {
+	keyID, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	// 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{}, reader, nil)
+	require.NoError(t, err)
+
+	// Build the manifest
+	var buf bytes.Buffer
+	err = b.Build(&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.Signature, "signature should be populated")
+	assert.NotEmpty(t, manifest.pbOuter.Signer, "signer should be populated")
+	assert.NotEmpty(t, manifest.pbOuter.SigningPubKey, "signing public key should be populated")
+
+	// Verify signature is a valid PGP signature
+	assert.Contains(t, string(manifest.pbOuter.Signature), "-----BEGIN PGP SIGNATURE-----")
+
+	// Verify public key is a valid PGP public key block
+	assert.Contains(t, string(manifest.pbOuter.SigningPubKey), "-----BEGIN PGP PUBLIC KEY BLOCK-----")
+}
+
+func TestScannerWithSigning(t *testing.T) {
+	keyID, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	// 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.Signature)
+	assert.NotEmpty(t, manifest.pbOuter.Signer)
+	assert.NotEmpty(t, manifest.pbOuter.SigningPubKey)
+}
+
+func TestGPGVerify(t *testing.T) {
+	keyID, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	data := []byte("test data to sign and verify")
+	sig, err := gpgSign(data, keyID)
+	require.NoError(t, err)
+
+	pubKey, err := gpgExportPublicKey(keyID)
+	require.NoError(t, err)
+
+	// Verify the signature
+	err = gpgVerify(data, sig, pubKey)
+	require.NoError(t, err)
+}
+
+func TestGPGVerifyInvalidSignature(t *testing.T) {
+	keyID, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	data := []byte("test data to sign")
+	sig, err := gpgSign(data, keyID)
+	require.NoError(t, err)
+
+	pubKey, err := gpgExportPublicKey(keyID)
+	require.NoError(t, err)
+
+	// Try to verify with different data - should fail
+	wrongData := []byte("different data")
+	err = gpgVerify(wrongData, sig, pubKey)
+	assert.Error(t, err)
+}
+
+func TestGPGVerifyBadPublicKey(t *testing.T) {
+	keyID, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	data := []byte("test data")
+	sig, err := gpgSign(data, keyID)
+	require.NoError(t, err)
+
+	// Try to verify with invalid public key - should fail
+	badPubKey := []byte("not a valid public key")
+	err = gpgVerify(data, sig, badPubKey)
+	assert.Error(t, err)
+}
+
+func TestManifestSignatureVerification(t *testing.T) {
+	keyID, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	// 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{}, reader, nil)
+	require.NoError(t, err)
+
+	// Build the manifest
+	var buf bytes.Buffer
+	err = b.Build(&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.Signature)
+}
+
+func TestManifestTamperedSignatureFails(t *testing.T) {
+	keyID, cleanup := testGPGEnv(t)
+	defer cleanup()
+
+	// 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{}, reader, nil)
+	require.NoError(t, err)
+
+	var buf bytes.Buffer
+	err = b.Build(&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) {
+	// 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{}, reader, nil)
+	require.NoError(t, err)
+
+	// Build the manifest
+	var buf bytes.Buffer
+	err = b.Build(&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.Signature, "signature should be empty when not signing")
+	assert.Empty(t, manifest.pbOuter.Signer, "signer should be empty when not signing")
+	assert.Empty(t, manifest.pbOuter.SigningPubKey, "signing public key should be empty when not signing")
+}

mfer/manifest.go

@@ -2,16 +2,21 @@ package mfer
 
 import (
 	"bytes"
+	"encoding/hex"
+	"errors"
 	"fmt"
+
+	"github.com/multiformats/go-multihash"
 )
 
 // manifest holds the internal representation of a manifest file.
 // Use NewManifestFromFile or NewManifestFromReader to load an existing manifest,
 // or use Builder to create a new one.
 type manifest struct {
-	pbInner *MFFile
+	pbInner        *MFFile
-	pbOuter *MFFileOuter
+	pbOuter        *MFFileOuter
-	output  *bytes.Buffer
+	output         *bytes.Buffer
+	signingOptions *SigningOptions
 }
 
 func (m *manifest) String() string {
@@ -29,3 +34,26 @@ func (m *manifest) Files() []*MFFilePath {
 	}
 	return m.pbInner.Files
 }
+
+// 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.
+func (m *manifest) signatureString() (string, error) {
+	if m.pbOuter == nil {
+		return "", errors.New("pbOuter not set")
+	}
+	if len(m.pbOuter.Uuid) == 0 {
+		return "", errors.New("UUID not set")
+	}
+	if len(m.pbOuter.Sha256) == 0 {
+		return "", errors.New("SHA256 hash not set")
+	}
+
+	mh, err := multihash.Encode(m.pbOuter.Sha256, multihash.SHA2_256)
+	if err != nil {
+		return "", fmt.Errorf("failed to encode multihash: %w", err)
+	}
+	uuidStr := hex.EncodeToString(m.pbOuter.Uuid)
+	mhStr := hex.EncodeToString(mh)
+	return fmt.Sprintf("%s-%s-%s", MAGIC, uuidStr, mhStr), nil
+}

mfer/mf.pb.go

@@ -218,8 +218,10 @@ type MFFileOuter struct {
 	CompressionType MFFileOuter_CompressionType `protobuf:"varint,102,opt,name=compressionType,proto3,enum=MFFileOuter_CompressionType" json:"compressionType,omitempty"`
 	// these are used solely to detect corruption/truncation
 	// and not for cryptographic integrity.
-	Size         int64  `protobuf:"varint,103,opt,name=size,proto3" json:"size,omitempty"`
+	Size   int64  `protobuf:"varint,103,opt,name=size,proto3" json:"size,omitempty"`
-	Sha256       []byte `protobuf:"bytes,104,opt,name=sha256,proto3" json:"sha256,omitempty"`
+	Sha256 []byte `protobuf:"bytes,104,opt,name=sha256,proto3" json:"sha256,omitempty"`
+	// 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
 	Signature []byte `protobuf:"bytes,201,opt,name=signature,proto3,oneof" json:"signature,omitempty"`
@@ -289,6 +291,13 @@ func (x *MFFileOuter) GetSha256() []byte {
 	return nil
 }
 
+func (x *MFFileOuter) GetUuid() []byte {
+	if x != nil {
+		return x.Uuid
+	}
+	return nil
+}
+
 func (x *MFFileOuter) GetInnerMessage() []byte {
 	if x != nil {
 		return x.InnerMessage
@@ -463,6 +472,9 @@ type MFFile struct {
 	Version MFFile_Version         `protobuf:"varint,100,opt,name=version,proto3,enum=MFFile_Version" json:"version,omitempty"`
 	// required manifest attributes:
 	Files []*MFFilePath `protobuf:"bytes,101,rep,name=files,proto3" json:"files,omitempty"`
+	// uuid is a random v4 UUID generated when creating the manifest
+	// used as part of the signature to prevent replay attacks
+	Uuid []byte `protobuf:"bytes,102,opt,name=uuid,proto3" json:"uuid,omitempty"`
 	// optional manifest attributes 2xx:
 	CreatedAt     *Timestamp `protobuf:"bytes,201,opt,name=createdAt,proto3,oneof" json:"createdAt,omitempty"`
 	unknownFields protoimpl.UnknownFields
@@ -513,6 +525,13 @@ func (x *MFFile) GetFiles() []*MFFilePath {
 	return nil
 }
 
+func (x *MFFile) GetUuid() []byte {
+	if x != nil {
+		return x.Uuid
+	}
+	return nil
+}
+
 func (x *MFFile) GetCreatedAt() *Timestamp {
 	if x != nil {
 		return x.CreatedAt
@@ -527,12 +546,13 @@ const file_mf_proto_rawDesc = "" +
 	"\bmf.proto\";\n" +
 	"\tTimestamp\x12\x18\n" +
 	"\aseconds\x18\x01 \x01(\x03R\aseconds\x12\x14\n" +
-	"\x05nanos\x18\x02 \x01(\x05R\x05nanos\"\xdc\x03\n" +
+	"\x05nanos\x18\x02 \x01(\x05R\x05nanos\"\xf0\x03\n" +
 	"\vMFFileOuter\x12.\n" +
 	"\aversion\x18e \x01(\x0e2\x14.MFFileOuter.VersionR\aversion\x12F\n" +
 	"\x0fcompressionType\x18f \x01(\x0e2\x1c.MFFileOuter.CompressionTypeR\x0fcompressionType\x12\x12\n" +
 	"\x04size\x18g \x01(\x03R\x04size\x12\x16\n" +
-	"\x06sha256\x18h \x01(\fR\x06sha256\x12#\n" +
+	"\x06sha256\x18h \x01(\fR\x06sha256\x12\x12\n" +
+	"\x04uuid\x18i \x01(\fR\x04uuid\x12#\n" +
 	"\finnerMessage\x18\xc7\x01 \x01(\fR\finnerMessage\x12\"\n" +
 	"\tsignature\x18\xc9\x01 \x01(\fH\x00R\tsignature\x88\x01\x01\x12\x1c\n" +
 	"\x06signer\x18\xca\x01 \x01(\fH\x01R\x06signer\x88\x01\x01\x12*\n" +
@@ -564,10 +584,11 @@ const file_mf_proto_rawDesc = "" +
 	"\x06_ctimeB\b\n" +
 	"\x06_atime\".\n" +
 	"\x0eMFFileChecksum\x12\x1c\n" +
-	"\tmultiHash\x18\x01 \x01(\fR\tmultiHash\"\xc2\x01\n" +
+	"\tmultiHash\x18\x01 \x01(\fR\tmultiHash\"\xd6\x01\n" +
 	"\x06MFFile\x12)\n" +
 	"\aversion\x18d \x01(\x0e2\x0f.MFFile.VersionR\aversion\x12!\n" +
-	"\x05files\x18e \x03(\v2\v.MFFilePathR\x05files\x12.\n" +
+	"\x05files\x18e \x03(\v2\v.MFFilePathR\x05files\x12\x12\n" +
+	"\x04uuid\x18f \x01(\fR\x04uuid\x12.\n" +
 	"\tcreatedAt\x18\xc9\x01 \x01(\v2\n" +
 	".TimestampH\x00R\tcreatedAt\x88\x01\x01\",\n" +
 	"\aVersion\x12\x10\n" +

mfer/mf.proto

@@ -28,6 +28,9 @@ message MFFileOuter {
     int64 size = 103;
     bytes sha256 = 104;
 
+    // uuid must match the uuid in the inner message
+    bytes uuid = 105;
+
     bytes innerMessage = 199;
     // 2xx for optional manifest root attributes
     // think we might use gosignify instead of gpg:
@@ -43,6 +46,9 @@ message MFFileOuter {
 
 message MFFilePath {
     // required attributes:
+    // Path invariants: must be valid UTF-8, use forward slashes only,
+    // be relative (no leading /), contain no ".." segments, and no
+    // empty segments (no "//").
     string path = 1;
     int64 size = 2;
 
@@ -72,6 +78,10 @@ message MFFile {
     // required manifest attributes:
     repeated MFFilePath files = 101;
 
+    // uuid is a random v4 UUID generated when creating the manifest
+    // used as part of the signature to prevent replay attacks
+    bytes uuid = 102;
+
     // optional manifest attributes 2xx:
     optional Timestamp createdAt = 201;
 }

mfer/scanner.go

@@ -43,9 +43,10 @@ type ScanStatus struct {
 
 // ScannerOptions configures scanner behavior.
 type ScannerOptions struct {
-	IncludeDotfiles bool     // Include files and directories starting with a dot (default: exclude)
+	IncludeDotfiles bool            // Include files and directories starting with a dot (default: exclude)
-	FollowSymLinks  bool     // Resolve symlinks instead of skipping them
+	FollowSymLinks  bool            // Resolve symlinks instead of skipping them
-	Fs              afero.Fs // Filesystem to use, defaults to OsFs if nil
+	Fs              afero.Fs        // Filesystem to use, defaults to OsFs if nil
+	SigningOptions  *SigningOptions // GPG signing options (nil = no signing)
 }
 
 // FileEntry represents a file that has been enumerated.
@@ -272,6 +273,9 @@ func (s *Scanner) ToManifest(ctx context.Context, w io.Writer, progress chan<- S
 	s.mu.RUnlock()
 
 	builder := NewBuilder()
+	if s.options.SigningOptions != nil {
+		builder.SetSigningOptions(s.options.SigningOptions)
+	}
 
 	var scannedFiles FileCount
 	var scannedBytes FileSize
@@ -381,6 +385,9 @@ func (s *Scanner) ToManifest(ctx context.Context, w io.Writer, progress chan<- S
 // The path should use forward slashes.
 func IsHiddenPath(p string) bool {
 	tp := path.Clean(p)
+	if tp == "." || tp == "/" {
+		return false
+	}
 	if strings.HasPrefix(tp, ".") {
 		return true
 	}

mfer/scanner_test.go

@@ -38,7 +38,7 @@ func TestNewScannerWithOptions(t *testing.T) {
 
 func TestScannerEnumerateFile(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, afero.WriteFile(fs, "/test.txt", []byte("hello world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/test.txt", []byte("hello world"), 0o644))
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
 	err := s.EnumerateFile("/test.txt")
@@ -62,10 +62,10 @@ func TestScannerEnumerateFileMissing(t *testing.T) {
 
 func TestScannerEnumeratePath(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir/subdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir/subdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("one"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("one"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("two"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("two"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/subdir/file3.txt", []byte("three"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/subdir/file3.txt", []byte("three"), 0o644))
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
 	err := s.EnumeratePath("/testdir", nil)
@@ -77,9 +77,9 @@ func TestScannerEnumeratePath(t *testing.T) {
 
 func TestScannerEnumeratePathWithProgress(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("one"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("one"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("two"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("two"), 0o644))
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
 	progress := make(chan EnumerateStatus, 10)
@@ -101,10 +101,10 @@ func TestScannerEnumeratePathWithProgress(t *testing.T) {
 
 func TestScannerEnumeratePaths(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/dir1", 0755))
+	require.NoError(t, fs.MkdirAll("/dir1", 0o755))
-	require.NoError(t, fs.MkdirAll("/dir2", 0755))
+	require.NoError(t, fs.MkdirAll("/dir2", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/dir1/a.txt", []byte("aaa"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/dir1/a.txt", []byte("aaa"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/dir2/b.txt", []byte("bbb"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/dir2/b.txt", []byte("bbb"), 0o644))
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
 	err := s.EnumeratePaths(nil, "/dir1", "/dir2")
@@ -115,10 +115,10 @@ func TestScannerEnumeratePaths(t *testing.T) {
 
 func TestScannerExcludeDotfiles(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir/.hidden", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir/.hidden", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/visible.txt", []byte("visible"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/visible.txt", []byte("visible"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden.txt", []byte("hidden"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden.txt", []byte("hidden"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden/inside.txt", []byte("inside"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/.hidden/inside.txt", []byte("inside"), 0o644))
 
 	t.Run("exclude by default", func(t *testing.T) {
 		s := NewScannerWithOptions(&ScannerOptions{Fs: fs, IncludeDotfiles: false})
@@ -141,9 +141,9 @@ func TestScannerExcludeDotfiles(t *testing.T) {
 
 func TestScannerToManifest(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("content one"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file1.txt", []byte("content one"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("content two"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file2.txt", []byte("content two"), 0o644))
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
 	err := s.EnumeratePath("/testdir", nil)
@@ -160,8 +160,8 @@ func TestScannerToManifest(t *testing.T) {
 
 func TestScannerToManifestWithProgress(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file.txt", bytes.Repeat([]byte("x"), 1000), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file.txt", bytes.Repeat([]byte("x"), 1000), 0o644))
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
 	err := s.EnumeratePath("/testdir", nil)
@@ -189,11 +189,11 @@ func TestScannerToManifestWithProgress(t *testing.T) {
 
 func TestScannerToManifestContextCancellation(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
 	// Create many files to ensure we have time to cancel
 	for i := 0; i < 100; i++ {
 		name := string(rune('a'+i%26)) + string(rune('0'+i/26)) + ".txt"
-		require.NoError(t, afero.WriteFile(fs, "/testdir/"+name, bytes.Repeat([]byte("x"), 100), 0644))
+		require.NoError(t, afero.WriteFile(fs, "/testdir/"+name, bytes.Repeat([]byte("x"), 100), 0o644))
 	}
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
@@ -223,7 +223,7 @@ func TestScannerToManifestEmptyScanner(t *testing.T) {
 
 func TestScannerFilesCopiesSlice(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, afero.WriteFile(fs, "/test.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/test.txt", []byte("hello"), 0o644))
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
 	require.NoError(t, s.EnumerateFile("/test.txt"))
@@ -237,9 +237,9 @@ func TestScannerFilesCopiesSlice(t *testing.T) {
 
 func TestScannerEnumerateFS(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir/sub", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir/sub", 0o755))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/file.txt", []byte("hello"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/file.txt", []byte("hello"), 0o644))
-	require.NoError(t, afero.WriteFile(fs, "/testdir/sub/nested.txt", []byte("world"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/testdir/sub/nested.txt", []byte("world"), 0o644))
 
 	// Create a basepath filesystem
 	baseFs := afero.NewBasePathFs(fs, "/testdir")
@@ -297,7 +297,7 @@ func TestSendStatusNilChannel(t *testing.T) {
 func TestScannerFileEntryFields(t *testing.T) {
 	fs := afero.NewMemMapFs()
 	now := time.Now().Truncate(time.Second)
-	require.NoError(t, afero.WriteFile(fs, "/test.txt", []byte("content"), 0644))
+	require.NoError(t, afero.WriteFile(fs, "/test.txt", []byte("content"), 0o644))
 	require.NoError(t, fs.Chtimes("/test.txt", now, now))
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
@@ -316,12 +316,12 @@ func TestScannerFileEntryFields(t *testing.T) {
 
 func TestScannerLargeFileEnumeration(t *testing.T) {
 	fs := afero.NewMemMapFs()
-	require.NoError(t, fs.MkdirAll("/testdir", 0755))
+	require.NoError(t, fs.MkdirAll("/testdir", 0o755))
 
 	// Create 100 files
 	for i := 0; i < 100; i++ {
 		name := "/testdir/" + string(rune('a'+i%26)) + string(rune('0'+i/26%10)) + ".txt"
-		require.NoError(t, afero.WriteFile(fs, name, []byte("data"), 0644))
+		require.NoError(t, afero.WriteFile(fs, name, []byte("data"), 0o644))
 	}
 
 	s := NewScannerWithOptions(&ScannerOptions{Fs: fs})
@@ -352,6 +352,8 @@ func TestIsHiddenPath(t *testing.T) {
 		{"/absolute/.hidden", true},
 		{"./relative", false}, // path.Clean removes leading ./
 		{"a/b/c/.d/e", true},
+		{".", false}, // current directory is not hidden
+		{"/", false}, // root is not hidden
 	}
 
 	for _, tt := range tests {

mfer/serialize.go

@@ -4,8 +4,10 @@ import (
 	"bytes"
 	"crypto/sha256"
 	"errors"
+	"fmt"
 	"time"
 
+	"github.com/google/uuid"
 	"github.com/klauspost/compress/zstd"
 	"google.golang.org/protobuf/proto"
 )
@@ -14,11 +16,10 @@ import (
 const MAGIC string = "ZNAVSRFG"
 
 func newTimestampFromTime(t time.Time) *Timestamp {
-	out := &Timestamp{
+	return &Timestamp{
 		Seconds: t.Unix(),
-		Nanos:   int32(t.UnixNano() - (t.Unix() * 1000000000)),
+		Nanos:   int32(t.Nanosecond()),
 	}
-	return out
 }
 
 func (m *manifest) generate() error {
@@ -47,14 +48,17 @@ func (m *manifest) generateOuter() error {
 	if m.pbInner == nil {
 		return errors.New("internal error")
 	}
+
+	// Generate UUID and set on inner message
+	manifestUUID := uuid.New()
+	m.pbInner.Uuid = manifestUUID[:]
+
 	innerData, err := proto.MarshalOptions{Deterministic: true}.Marshal(m.pbInner)
 	if err != nil {
 		return err
 	}
 
-	h := sha256.New()
+	// Compress the inner data
-	h.Write(innerData)
-
 	idc := new(bytes.Buffer)
 	zw, err := zstd.NewWriter(idc, zstd.WithEncoderLevel(zstd.SpeedBestCompression))
 	if err != nil {
@@ -64,16 +68,51 @@ func (m *manifest) generateOuter() error {
 	if err != nil {
 		return err
 	}
-
 	_ = zw.Close()
 
-	o := &MFFileOuter{
+	compressedData := idc.Bytes()
-		InnerMessage:    idc.Bytes(),
+
+	// Hash the compressed data for integrity verification before decompression
+	h := sha256.New()
+	if _, err := h.Write(compressedData); err != nil {
+		return err
+	}
+	sha256Hash := h.Sum(nil)
+
+	m.pbOuter = &MFFileOuter{
+		InnerMessage:    compressedData,
 		Size:            int64(len(innerData)),
-		Sha256:          h.Sum(nil),
+		Sha256:          sha256Hash,
+		Uuid:            manifestUUID[:],
 		Version:         MFFileOuter_VERSION_ONE,
 		CompressionType: MFFileOuter_COMPRESSION_ZSTD,
 	}
-	m.pbOuter = o
+
+	// Sign the manifest if signing options are provided
+	if m.signingOptions != nil && m.signingOptions.KeyID != "" {
+		sigString, err := m.signatureString()
+		if err != nil {
+			return fmt.Errorf("failed to generate signature string: %w", err)
+		}
+
+		sig, err := gpgSign([]byte(sigString), m.signingOptions.KeyID)
+		if err != nil {
+			return fmt.Errorf("failed to sign manifest: %w", err)
+		}
+		m.pbOuter.Signature = sig
+
+		fingerprint, err := gpgGetKeyFingerprint(m.signingOptions.KeyID)
+		if err != nil {
+			return fmt.Errorf("failed to get key fingerprint: %w", err)
+		}
+		m.pbOuter.Signer = fingerprint
+
+		pubKey, err := gpgExportPublicKey(m.signingOptions.KeyID)
+		if err != nil {
+			return fmt.Errorf("failed to export public key: %w", err)
+		}
+		m.pbOuter.SigningPubKey = pubKey
+	}
+
 	return nil
 }