Move the CLI to urfave/cli v3 (closes #110)

Ported per the library's v2-to-v3 migration guide: the app is a root
cli.Command, actions take a context and the command, and flag
environment variables become value sources. -v, -q and the version flag
are local so, as before, only the commands defining them accept them.
Every command stops reading flags at its first argument, as v2 did.
ErrWriter is stdout so usage errors print with their help. The action's
context reaches the manifest download in check, export and list.
testify rises to v1.12.1, which v3 requires; the urfave_cli_no_docs
build tag, which v3 lacks, is dropped. v3 accepts a flag given under two
names, so -v --verbose gives debug output, and the test pinning the
refusal becomes a TestVerboseCount case.

Model: opus-5-5

.dockerignore

@@ -59,6 +59,8 @@
 **/.vscode
 **/*.sublime-*
 
-# This repo's own host-built archives (Makefile).
-*.tmp
-*.dockerimage
+# This repo's own host-built binary (make build).
+/bin/mfer
+
+# The protoc script/bootstrap unpacks for script/generate.
+/bin/protoc

.gitignore

@@ -1,11 +1,7 @@
 /bin/mfer
+/bin/protoc/
 /tmp
 /node_modules/
-*.tmp
-*.dockerimage
-/vendor
-vendor.tzst
-modcache.tzst
 
 # Generated manifest files
 /index.mf

.nvmrc

@@ -0,0 +1 @@
+22.17.0

Dockerfile

@@ -9,15 +9,16 @@ RUN go mod download
 COPY . .
 
 # Go half of fmt-check only: this image has no node, so no prettier. The
-# markdown half runs in the mdfmt stage below.
-RUN make fmt-check-go
+# markdown half runs in the mdfmt stage below. The image has no gofumpt
+# either; script/gofumpt builds the version bin/tools/go.mod pins.
+RUN script/gofumpt --check
 # The linter directly, not `make lint`: script/lint builds this stage, and
 # there is no docker inside this build.
 RUN golangci-lint run --config .golangci.yml ./...
 
 # Markdown/JSON format stage — prettier needs node, which the Go images
 # do not have. node:22.17.0-bookworm-slim (2026-08-09); ships node
-# 22.17.0 and yarn 1.22.22, the versions script/bootstrap pins.
+# 22.17.0 and yarn 1.22.22, the versions .nvmrc and script/bootstrap pin.
 FROM node@sha256:b04ce4ae4e95b522112c2e5c52f781471a5cbc3b594527bcddedee9bc48c03a0 AS mdfmt
 
 WORKDIR /src
@@ -30,7 +31,7 @@ COPY . .
 RUN script/prettier --check
 
 # Build stage — tests and compilation
-# golang:1.23 (2026-03-14)
+# golang:1.23.12, 2026-03-14
 FROM golang@sha256:60deed95d3888cc5e4d9ff8a10c54e5edc008c6ae3fba6187be6fb592e19e8c0 AS builder
 
 # Force BuildKit to run the lint and mdfmt stages by creating stage dependencies
@@ -63,7 +64,7 @@ RUN version="${VERSION:-$(git describe --tags --always)}"; \
         exit 1; \
     fi; \
     cd cmd/mfer && \
-    CGO_ENABLED=0 go build -tags urfave_cli_no_docs -ldflags "-X main.Gitrev=$version" -o /mfer .
+    CGO_ENABLED=0 go build -ldflags "-X main.Gitrev=$version" -o /mfer .
 
 # Fail unless /mfer is statically linked: scratch has no C library to run it.
 RUN ldd /mfer 2>&1 | grep -q 'not a dynamic executable'

Makefile

@@ -1,20 +1,8 @@
-export DOCKER_BUILDKIT := 1
-export PROGRESS_NO_TRUNC := 1
-GOPATH := $(shell go env GOPATH)
-export PATH := $(PATH):$(GOPATH)/bin
-SOURCEFILES := mfer/*.go mfer/*.proto internal/*/*.go cmd/*/*.go go.mod go.sum
-ARCH := $(shell uname -m)
-GITREV_BUILD := $(shell bash $(PWD)/bin/gitrev.sh 2>/dev/null || echo unknown)
-APPNAME := mfer
-VERSION := 0.1.0
-export DOCKER_IMAGE_CACHE_DIR := $(HOME)/Library/Caches/Docker/$(APPNAME)-$(ARCH)
-GOLDFLAGS += -X main.Version=$(VERSION)
-GOLDFLAGS += -X main.Gitrev=$(GITREV_BUILD)
-GOFLAGS := -ldflags "$(GOLDFLAGS)"
+.PHONY: bootstrap setup test lint fmt fmt-check check docker hooks build generate fuzz
 
-.PHONY: bootstrap setup docker default run ci test fuzz check lint fmt fmt-check fmt-check-go fmt-check-md hooks fixme generate
-
-default: fmt test
+# Makefile targets are thin shims; the implementations live in script/
+# per the scripts-to-rule-them-all pattern (see the Entrypoints section
+# of README.md).
 
 bootstrap:
 	@script/bootstrap
@@ -22,75 +10,32 @@ bootstrap:
 setup:
 	@script/setup
 
-run: ./bin/mfer
-	./$<
-	./$< gen
-
-ci: test
-
 test:
 	@script/test
 
-fuzz:
-	@script/fuzz
-
-fixme:
-	@grep -nir fixme . | grep -v Makefile
-
-check:
-	@script/check
-
-fmt-check:
-	@script/fmt-check
-
-# Halves of fmt-check, for environments that have only one toolchain:
-# the Docker lint stage has Go but no node, the markdown stage the reverse.
-fmt-check-go:
-	@script/fmt-check-go
-
-fmt-check-md:
-	@script/prettier --check
-
-hooks:
-	@script/install-precommit
-
-generate:
-	@script/generate
-
-bin/mfer: $(SOURCEFILES)
-	cd cmd/mfer && go build -tags urfave_cli_no_docs -o ../../bin/mfer $(GOFLAGS) .
-
-clean:
-	rm -rfv bin/mfer cmd/mfer/mfer *.dockerimage
-
-fmt:
-	@script/fmt
-
 lint:
 	@script/lint
 
+fmt:
+	@script/fmt
+
+fmt-check:
+	@script/fmt-check
+
+check:
+	@script/check
+
 docker:
 	@script/docker
 
-sneak-mfer.$(ARCH).tzst.dockerimage: $(SOURCEFILES) vendor.tzst modcache.tzst
-	docker build --progress plain --build-arg GITREV=$(GITREV_BUILD) -t sneak/mfer .
-	docker save sneak/mfer | pv | zstdmt -19 > $@
-	du -sh $@
+hooks:
+	@script/install-precommit
 
-godoc:
-	open http://127.0.0.1:6060
-	godoc -http=:6060
+build:
+	@script/build
 
-vendor.tzst: go.mod go.sum
-	go mod tidy
-	go mod vendor
-	cd vendor && tar -c . | pv | zstdmt -19 > $(PWD)/$@.tmp
-	rm -rf vendor
-	mv $@.tmp $@
+generate:
+	@script/generate
 
-modcache.tzst: go.mod go.sum
-	go mod tidy
-	cd $(HOME)/go/pkg && chmod -R u+rw . && rm -rf mod sumdb
-	go mod download -x
-	cd $(shell go env GOMODCACHE) && tar -c . | pv | zstdmt -19 > $(PWD)/$@.tmp
-	mv $@.tmp $@
+fuzz:
+	@script/fuzz

README.md

@@ -29,7 +29,7 @@ is committed, so no `protoc` toolchain is required:
 ```sh
 git clone https://git.eeqj.de/sneak/mfer.git
 cd mfer
-go build -o bin/mfer ./cmd/mfer
+make build
 ```
 
 Generate a manifest for a directory tree, verify it later, and fetch a published
@@ -40,12 +40,14 @@ tree by URL:
 bin/mfer gen .
 
 # Verify the files on disk against the manifest. Exits nonzero if any file
-# is missing or corrupted.
+# it lists is missing or corrupted; warns about files it does not list.
 bin/mfer check index.mf
 
-# Download and cryptographically verify a tree published over HTTP: mfer
-# fetches <url>/index.mf, then downloads every file it lists.
-bin/mfer fetch https://example.com/tree/
+# Download and cryptographically verify a tree published over HTTP into
+# ./mirror: mfer fetches <url>/index.mf, downloads every file it lists,
+# skipping any already there with the right hash, then saves the manifest as
+# mirror/index.mf.
+bin/mfer fetch --dest mirror https://example.com/tree/
 ```
 
 Run `bin/mfer help` for the full command list, or `bin/mfer <command> --help`
@@ -65,42 +67,51 @@ standard: normalized scripts in `script/` are the entrypoints for the
 development workflow, and the Makefile targets are thin shims that call them. We
 provide:
 
-- `script/bootstrap` — install all dependencies (Go, Go module download, and
-  node/yarn plus the prettier version pinned in `package.json`/`yarn.lock`),
-  idempotently; golangci-lint is not installed, it runs only in Docker
+- `script/bootstrap` — install all dependencies, idempotently: Go and the
+  modules of both `go.mod` and `bin/tools/go.mod`; node (the version `.nvmrc`
+  names, through nvm when there is no node on `PATH`) and yarn, plus the
+  prettier version pinned in `package.json`/`yarn.lock`; and `protoc` 33.4,
+  unpacked into `bin/protoc` from its release archive once the archive matches
+  the sha256 the script holds for this platform. golangci-lint is not installed,
+  it runs only in Docker
 - `script/setup` — make a fresh clone ready for development: runs
   `script/bootstrap`, then `script/install-precommit`
 - `script/projectname` — output the project name (`mfer`); used by other scripts
   such as `script/docker`
 - `script/test` — run the test suite (`go test`); one test fails when
   `mfer/mf.proto` no longer matches the hash `script/generate` recorded
+- `script/build` (`make build`) — build the `mfer` binary into `bin/mfer`,
+  stamped with the revision `mfer version` prints: the output of
+  `git describe --tags --always --dirty`, as `script/docker` passes it
 - `script/generate` (`make generate`) — regenerate `mfer/mf.pb.go` from
   `mfer/mf.proto` and record the hash of that `mfer/mf.proto` in
   `mfer/mf.proto.sha256`; the only thing that regenerates the committed
-  `mfer/mf.pb.go`. It needs the exact versions that wrote the committed file,
-  and refuses to run with any other: `protoc` 33.4 (unpack
-  `protoc-33.4-<platform>.zip` from
-  [its release](https://github.com/protocolbuffers/protobuf/releases/tag/v33.4)
-  and put its `bin/protoc` on `PATH`) and `protoc-gen-go` v1.36.11
-  (`go install google.golang.org/protobuf/cmd/protoc-gen-go@v1.36.11`, which
-  installs it in `$(go env GOPATH)/bin`; `make generate` adds that directory to
-  `PATH`)
+  `mfer/mf.pb.go`. It runs the `protoc` that `script/bootstrap` unpacks into
+  `bin/protoc`, refusing any version but 33.4, and the `protoc-gen-go` that
+  `bin/tools/go.mod` pins, which `go tool` builds from source checked against
+  the hashes in `bin/tools/go.sum`
 - `script/fuzz` — fuzz the manifest parser for one minute; run by hand
   (`make fuzz`), never by CI, while `script/test` runs its committed seed corpus
   as ordinary tests
 - `script/lint` — run `golangci-lint` in Docker: builds only the `lint` stage of
   the `Dockerfile` (the Go format check, then the linter), uncached so it runs
   every time, then removes the image
-- `script/fmt` — format all code and docs (writes): `gofumpt` and
+- `script/fmt` — format all code and docs (writes): `script/gofumpt --write` and
   `script/prettier --write`
+- `script/gofumpt` — run `gofumpt` over every Go file in the repository in the
+  given mode, `--write` or `--check`, at the version `bin/tools/go.mod` pins
+  (built on demand by `go tool` from source checked against the hashes in
+  `bin/tools/go.sum`, so nothing installs it); `script/fmt`, `script/fmt-check`
+  and the Docker lint stage all go through it, so they cannot disagree about Go
+  formatting
 - `script/prettier` — run prettier over the repository's canonical file set
   (Markdown and JSON, minus `.prettierignore`) in the given mode, `--write` or
-  `--check`; the single definition of that file set, so `script/fmt` and
-  `script/fmt-check` cannot disagree about it
-- `script/fmt-check` — check formatting without writing: `script/fmt-check-go`
-  plus `script/prettier --check`
-- `script/fmt-check-go` — the Go half of `script/fmt-check`, on its own, for the
-  Docker lint stage, whose image has no node
+  `--check`, with the prettier version `yarn.lock` pins, run by the node on
+  `PATH` or else the one `script/bootstrap` installed through nvm; the single
+  definition of that file set, so `script/fmt` and `script/fmt-check` cannot
+  disagree about it
+- `script/fmt-check` — check formatting without writing:
+  `script/gofumpt --check` plus `script/prettier --check`
 - `script/check` — run `script/test`, `script/lint`, and `script/fmt-check`
 - `script/docker` — build the Docker image tagged with the project name
 - `script/cibuild` — CI entrypoint: builds the image with the same command as
@@ -251,10 +262,25 @@ are now tracked only in the [issues](https://git.eeqj.de/sneak/mfer/issues).
 - `mfer check` / `mfer check .`
     - verifies checksums of all files in manifest, displaying error and exiting
       nonzero if any files are missing or corrupted
+    - warns about each file under the base directory that the manifest does not
+      list, hidden files included; with `--no-extra-files` each one is a failure
+      instead
 - `mfer fetch https://example.com/stuff/`
-    - fetches `/stuff/index.mf` and downloads all files listed in manifest,
-      optionally resuming any that already exist locally, and assures
-      cryptographic integrity of downloaded files.
+    - fetches `/stuff/index.mf` and downloads all files listed in manifest into
+      the current directory, or the one given with `--dest`, and assures
+      cryptographic integrity of downloaded files. A file already there with the
+      size and hash the manifest lists is skipped. Once every file is in place,
+      the manifest is saved there as `index.mf`, so `mfer check` can verify the
+      tree later. Each file is downloaded to a temp file beside it, such as
+      `.a.txt.tmp` for `a.txt`, then moved into place. A manifest is refused
+      before any file is downloaded if it lists a file where fetch writes
+      another: at the temp file of a listed file, or at `index.mf` or
+      `.index.mf.tmp` at the top of the tree. Names are compared in any letter
+      case.
+- `mfer fetch --require-signature <fingerprint> https://example.com/stuff/`
+    - as above, but first refuses a manifest not signed by the key with that
+      fingerprint, as `mfer check --require-signature` does, before downloading
+      any file.
 
 # Implementation Plan
 

bin/gitrev.sh

@@ -1,12 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-
-main() {
-    if [[ -n "${GITREV:-}" ]]; then
-        echo "$GITREV"
-    else
-        git describe --tags --always --dirty=-dirty
-    fi
-}
-
-main "$@"

bin/tools/go.mod

@@ -0,0 +1,22 @@
+// The developer tools this repo runs with `go tool`: gofumpt for
+// script/gofumpt and protoc-gen-go for script/generate. Kept out of the mfer
+// module so they add nothing to what mfer's users download. `go tool` builds
+// exactly the source whose hashes go.sum here records.
+module sneak.berlin/go/mfer/bin/tools
+
+go 1.26.0
+
+tool (
+	google.golang.org/protobuf/cmd/protoc-gen-go
+	mvdan.cc/gofumpt
+)
+
+require (
+	golang.org/x/mod v0.40.0 // indirect
+	golang.org/x/sync v0.22.0 // indirect
+	golang.org/x/tools v0.49.0 // indirect
+	// protoc-gen-go v1.36.11, 2026-10-04
+	google.golang.org/protobuf v1.36.11 // indirect
+	// gofumpt v0.12.0, 2026-10-04
+	mvdan.cc/gofumpt v0.12.0 // indirect
+)

bin/tools/go.sum

@@ -0,0 +1,22 @@
+github.com/go-quicktest/qt v1.102.0 h1:HSQxCeh5YZH3EL3W39ixjtyaEhcWSXQHtHnMBzSs474=
+github.com/go-quicktest/qt v1.102.0/go.mod h1:p4lGIVX+8Wa6ZPNDvqcxq36XpUDLh42FLetFU7odllI=
+github.com/google/go-cmp v0.7.0 h1:wk8382ETsv4JYUZwIsn6YpYiWiBsYLSJiTsyBybVuN8=
+github.com/google/go-cmp v0.7.0/go.mod h1:pXiqmnSA92OHEEa9HXL2W4E7lf9JzCmGVUdgjX3N/iU=
+github.com/kr/pretty v0.3.1 h1:flRD4NNwYAUpkphVc1HcthR4KEIFJ65n8Mw5qdRn3LE=
+github.com/kr/pretty v0.3.1/go.mod h1:hoEshYVHaxMs3cyo3Yncou5ZscifuDolrwPKZanG3xk=
+github.com/kr/text v0.2.0 h1:5Nx0Ya0ZqY2ygV366QzturHI13Jq95ApcVaJBhpS+AY=
+github.com/kr/text v0.2.0/go.mod h1:eLer722TekiGuMkidMxC/pM04lWEeraHUUmBw8l2grE=
+github.com/rogpeppe/go-internal v1.16.0 h1:O9DK+vNMDVGLr2BeZqmpLeMjiMNkuXfcqntWbZV6S5g=
+github.com/rogpeppe/go-internal v1.16.0/go.mod h1:DrUVZyrJU+txYW5/1kwtXQSMFio52ZOxX7yM1VHvnxs=
+golang.org/x/mod v0.40.0 h1:hUv+3cXcdRHz08UmSiOob7sadHig73uo5bkXxQ/tvUs=
+golang.org/x/mod v0.40.0/go.mod h1:0/weTWkPWGBikyTWAX3dkjVztMmBA5hM0DH6BElSupE=
+golang.org/x/sync v0.22.0 h1:SZjpbeLmrCk4xhRSZFNZW5gFUeCeFgjekvI/+gfScek=
+golang.org/x/sync v0.22.0/go.mod h1:9xrNwdLfx4jkKbNva9FpL6vEN7evnE43NNNJQ2LF3+0=
+golang.org/x/sys v0.47.0 h1:o7XGOvZQCADBQQ4Y7VNq2dRWQR7JmOUW8Kxx4ZsNgWs=
+golang.org/x/sys v0.47.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
+golang.org/x/tools v0.49.0 h1:3NI7VXzL9+1WZD52Dx2ttoPwD5DWrFGpl9mFZDlmisI=
+golang.org/x/tools v0.49.0/go.mod h1:SJNXV9DBKT0UbdttsQjbfJlAE/q+y36++zo3uL3N0Oo=
+google.golang.org/protobuf v1.36.11 h1:fV6ZwhNocDyBLK0dj+fg8ektcVegBBuEolpbTQyBNVE=
+google.golang.org/protobuf v1.36.11/go.mod h1:HTf+CrKn2C3g5S8VImy6tdcUvCska2kB7j23XfzDpco=
+mvdan.cc/gofumpt v0.12.0 h1:1Lbudkz2kpM9Cjz2pL4M19u7q+GaEhCTNf7N9mfpcho=
+mvdan.cc/gofumpt v0.12.0/go.mod h1:SmBHHrljiZu/uoypeKup3rFzP6eoC9UwCp2iH5E3jZA=

go.mod

@@ -9,27 +9,21 @@ require (
 	github.com/klauspost/compress v1.18.2
 	github.com/multiformats/go-multihash v0.2.3
 	github.com/spf13/afero v1.8.0
-	github.com/stretchr/testify v1.8.1
-	github.com/urfave/cli/v2 v2.27.7
+	github.com/stretchr/testify v1.12.1
+	github.com/urfave/cli/v3 v3.14.0
 	golang.org/x/term v0.0.0-20210927222741-03fcf44c2211
 	google.golang.org/protobuf v1.28.1
 )
 
 require (
-	github.com/cpuguy83/go-md2man/v2 v2.0.7 // indirect
 	github.com/klauspost/cpuid/v2 v2.0.9 // indirect
-	github.com/kr/pretty v0.2.0 // indirect
 	github.com/minio/sha256-simd v1.0.0 // indirect
 	github.com/mr-tron/base58 v1.2.0 // indirect
 	github.com/multiformats/go-varint v0.0.6 // indirect
-	github.com/pmezard/go-difflib v1.0.0 // indirect
-	github.com/russross/blackfriday/v2 v2.1.0 // indirect
 	github.com/spaolacci/murmur3 v1.1.0 // indirect
-	github.com/xrash/smetrics v0.0.0-20240521201337-686a1a2994c1 // indirect
+	go.yaml.in/yaml/v3 v3.0.5 // indirect
 	golang.org/x/crypto v0.0.0-20220525230936-793ad666bf5e // indirect
 	golang.org/x/sys v0.1.0 // indirect
 	golang.org/x/text v0.3.6 // indirect
-	gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 // indirect
-	gopkg.in/yaml.v3 v3.0.1 // indirect
 	lukechampine.com/blake3 v1.1.6 // indirect
 )

go.sum

@@ -46,8 +46,6 @@ github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDk
 github.com/cncf/udpa/go v0.0.0-20191209042840-269d4d468f6f/go.mod h1:M8M6+tZqaGXZJjfX53e64911xZQV5JYwmTeXPW+k8Sc=
 github.com/cncf/udpa/go v0.0.0-20200629203442-efcf912fb354/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk=
 github.com/cncf/udpa/go v0.0.0-20201120205902-5459f2c99403/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk=
-github.com/cpuguy83/go-md2man/v2 v2.0.7 h1:zbFlGlXEAKlwXpmvle3d8Oe3YnkKIK4xSRTd3sHPnBo=
-github.com/cpuguy83/go-md2man/v2 v2.0.7/go.mod h1:oOW0eioCTA6cOiMLiUPZOpcVxMig6NIQQ7OS05n1F4g=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
@@ -134,10 +132,7 @@ github.com/klauspost/cpuid/v2 v2.0.9 h1:lgaqFMSdTdQYdZ04uHyN2d/eKdOMyi2YLSvlQIBF
 github.com/klauspost/cpuid/v2 v2.0.9/go.mod h1:FInQzS24/EEf25PyTYn52gqo7WaD8xa0213Md/qVLRg=
 github.com/kr/fs v0.1.0/go.mod h1:FFnZGqtBN9Gxj7eW1uZ42v5BccTP0vu6NEaFoC2HwRg=
 github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
-github.com/kr/pretty v0.2.0 h1:s5hAObm+yFO5uHYt5dYjxi2rXrsnmRpJx4OYvIWUaQs=
-github.com/kr/pretty v0.2.0/go.mod h1:ipq/a2n7PKx3OHsz4KJII5eveXtPO4qwEXGdVfWzfnI=
 github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
-github.com/kr/text v0.1.0 h1:45sCR5RtlFHMR4UwH9sdQ5TC8v0qDQCHnXt+kaKSTVE=
 github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
 github.com/minio/sha256-simd v1.0.0 h1:v1ta+49hkWZyvaKwrQB8elexRqm6Y0aMLjCNsrYxo6g=
 github.com/minio/sha256-simd v1.0.0/go.mod h1:OuYzVNI5vcoYIAmbIvHPl3N3jUzVedXbKy5RFepssQM=
@@ -149,30 +144,21 @@ github.com/multiformats/go-varint v0.0.6 h1:gk85QWKxh3TazbLxED/NlDVv8+q+ReFJk7Y2
 github.com/multiformats/go-varint v0.0.6/go.mod h1:3Ls8CIEsrijN6+B7PbrXRPxHRPuXSrVKRY101jdMZYE=
 github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
 github.com/pkg/sftp v1.13.1/go.mod h1:3HaPG6Dq1ILlpPZRO0HVMrsydcdLt6HRDccSgb87qRg=
-github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
 github.com/prometheus/client_model v0.0.0-20190812154241-14fe0d1b01d4/go.mod h1:xMI15A0UPsDsEKsMN9yxemIoYk6Tm2C1GtYGdfGttqA=
 github.com/rogpeppe/go-internal v1.3.0/go.mod h1:M8bDsm7K2OlrFYOpmOWEs/qY81heoFRclV5y23lUDJ4=
-github.com/russross/blackfriday/v2 v2.1.0 h1:JIOH55/0cWyOuilr9/qlrm0BSXldqnqwMsf35Ld67mk=
-github.com/russross/blackfriday/v2 v2.1.0/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
 github.com/spaolacci/murmur3 v1.1.0 h1:7c1g84S4BPRrfL5Xrdp6fOJ206sU9y293DDHaoy0bLI=
 github.com/spaolacci/murmur3 v1.1.0/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA=
 github.com/spf13/afero v1.8.0 h1:5MmtuhAgYeU6qpa7w7bP0dv6MBYuup0vekhSpSkoq60=
 github.com/spf13/afero v1.8.0/go.mod h1:CtAatgMJh6bJEIs48Ay/FOnkljP3WeGUG0MC1RfAqwo=
 github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
-github.com/stretchr/objx v0.4.0/go.mod h1:YvHI0jy2hoMjB+UWwv71VJQ9isScKT/TqJzVSSt89Yw=
-github.com/stretchr/objx v0.5.0/go.mod h1:Yh+to48EsGEfYuaHDzXPcE3xhTkx73EhmCGUpEOglKo=
 github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4=
 github.com/stretchr/testify v1.5.1/go.mod h1:5W2xD1RspED5o8YsWQXVCued0rvSQ+mT+I5cxcmMvtA=
 github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
-github.com/stretchr/testify v1.7.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
-github.com/stretchr/testify v1.8.0/go.mod h1:yNjHg4UonilssWZ8iaSj1OCr/vHnekPRkoO+kdMU+MU=
-github.com/stretchr/testify v1.8.1 h1:w7B6lhMri9wdJUVmEZPGGhZzrYTPvgJArz7wNPgYKsk=
-github.com/stretchr/testify v1.8.1/go.mod h1:w2LPCIKwWwSfY2zedu0+kehJoqGctiVI29o6fzry7u4=
-github.com/urfave/cli/v2 v2.27.7 h1:bH59vdhbjLv3LAvIu6gd0usJHgoTTPhCFib8qqOwXYU=
-github.com/urfave/cli/v2 v2.27.7/go.mod h1:CyNAG/xg+iAOg0N4MPGZqVmv2rCoP267496AOXUZjA4=
-github.com/xrash/smetrics v0.0.0-20240521201337-686a1a2994c1 h1:gEOO8jv9F4OT7lGCjxCBTO/36wtF6j2nSip77qHd4x4=
-github.com/xrash/smetrics v0.0.0-20240521201337-686a1a2994c1/go.mod h1:Ohn+xnUBiLI6FVj/9LpzZWtj1/D6lUovWYBkxHVV3aM=
+github.com/stretchr/testify v1.12.1 h1:EuwCh5fleGS7H32xRwO3wRGT7DxrDhLAT6FF8MpWDWE=
+github.com/stretchr/testify v1.12.1/go.mod h1:MDEgiDPPsNp5cuIrHPPCyornHKgEVbtFUmoNlxoYthg=
+github.com/urfave/cli/v3 v3.14.0 h1:a8414NQlHJs0c/iBsulKLzlES0n/lEAskbL2LKpU4/s=
+github.com/urfave/cli/v3 v3.14.0/go.mod h1:vXn6HxPNccJSzQr2QvwVncOKrgYGIHU0HY5h8B2nQj4=
 github.com/yuin/goldmark v1.1.25/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
 github.com/yuin/goldmark v1.1.27/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
 github.com/yuin/goldmark v1.1.32/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
@@ -183,6 +169,8 @@ go.opencensus.io v0.22.2/go.mod h1:yxeiOL68Rb0Xd1ddK5vPZ/oVn4vY4Ynel7k9FzqtOIw=
 go.opencensus.io v0.22.3/go.mod h1:yxeiOL68Rb0Xd1ddK5vPZ/oVn4vY4Ynel7k9FzqtOIw=
 go.opencensus.io v0.22.4/go.mod h1:yxeiOL68Rb0Xd1ddK5vPZ/oVn4vY4Ynel7k9FzqtOIw=
 go.opencensus.io v0.22.5/go.mod h1:5pWMHQbX5EPX2/62yrJeAkowc+lfs/XD7Uxpq3pI6kk=
+go.yaml.in/yaml/v3 v3.0.5 h1:N6y/pJk8buWs9NY5ERU2HSMfm+IuD/OtfdAnq6kESPw=
+go.yaml.in/yaml/v3 v3.0.5/go.mod h1:HVTZu1O7/Vkt2N+BFy8Zza+lnLsABggaTM2ZpNIGuKg=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
 golang.org/x/crypto v0.0.0-20190510104115-cbcb75029529/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
 golang.org/x/crypto v0.0.0-20190605123033-f99c8df09eb5/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
@@ -470,13 +458,9 @@ google.golang.org/protobuf v1.28.1 h1:d0NfwRgPtno5B1Wa6L2DAG+KivqkdutMf1UhdNx175
 google.golang.org/protobuf v1.28.1/go.mod h1:HV8QOd/L58Z+nl8r43ehVNZIU/HEI6OcFqwMG9pJV4I=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo=
-gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI=
 gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
-gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
-gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
 honnef.co/go/tools v0.0.0-20190106161140-3f1c8253044a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
 honnef.co/go/tools v0.0.0-20190418001031-e561f6794a2a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=

internal/cli/check.go

@@ -16,7 +16,7 @@ import (
 
 	"github.com/dustin/go-humanize"
 	"github.com/spf13/afero"
-	"github.com/urfave/cli/v2"
+	"github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/internal/log"
 	"sneak.berlin/go/mfer/mfer"
 )
@@ -96,8 +96,10 @@ func findManifest(fs afero.Fs, dir string) (string, error) {
 
 // fetchManifestToTemp downloads a manifest URL to a temporary file and
 // returns the temp file path. The caller is responsible for removing it.
-func (mfa *CLIApp) fetchManifestToTemp(url string) (string, error) {
-	rc, fetchErr := mfa.openManifestReader(url)
+func (mfa *CLIApp) fetchManifestToTemp(
+	ctx context.Context, url string,
+) (string, error) {
+	rc, fetchErr := mfa.openManifestReader(ctx, url)
 	if fetchErr != nil {
 		return "", fetchErr
 	}
@@ -206,22 +208,29 @@ func countCheckFailures(
 }
 
 // findExtraFiles reports files present on disk but absent from the
-// manifest, counting each as a failure.
-func findExtraFiles(ctx *cli.Context, chk *mfer.Checker, failures *int64) error {
+// manifest, and anything the search cannot read: each is a failure under
+// --no-extra-files, otherwise a warning.
+func findExtraFiles(
+	ctx context.Context, cmd *cli.Command, chk *mfer.Checker, failures *int64,
+) error {
 	extraResults := make(chan mfer.Result, 1)
 	extraDone := make(chan struct{})
 
 	go func() {
 		for result := range extraResults {
-			*failures++
+			if cmd.Bool("no-extra-files") {
+				*failures++
 
-			log.Infof("%s: %s (%s)", result.Status, result.Path, result.Message)
+				log.Infof("%s: %s (%s)", result.Status, result.Path, result.Message)
+			} else {
+				log.Warnf("%s: %s (%s)", result.Status, result.Path, result.Message)
+			}
 		}
 
 		close(extraDone)
 	}()
 
-	err := chk.FindExtraFiles(ctx.Context, extraResults)
+	err := chk.FindExtraFiles(ctx, extraResults)
 	if err != nil {
 		return fmt.Errorf("failed to check for extra files: %w", err)
 	}
@@ -233,7 +242,9 @@ func findExtraFiles(ctx *cli.Context, chk *mfer.Checker, failures *int64) error
 
 // runCheck runs the manifest check with progress and result reporting
 // and returns the number of failures.
-func runCheck(ctx *cli.Context, chk *mfer.Checker, showProgress bool) (int64, error) {
+func runCheck(
+	ctx context.Context, cmd *cli.Command, chk *mfer.Checker, showProgress bool,
+) (int64, error) {
 	// Set up results channel
 	results := make(chan mfer.Result, 1)
 
@@ -259,7 +270,7 @@ func runCheck(ctx *cli.Context, chk *mfer.Checker, showProgress bool) (int64, er
 	go countCheckFailures(results, &failures, done)
 
 	// Run check
-	err := chk.Check(ctx.Context, results, progress)
+	err := chk.Check(ctx, results, progress)
 
 	progressWg.Wait()
 
@@ -270,28 +281,27 @@ func runCheck(ctx *cli.Context, chk *mfer.Checker, showProgress bool) (int64, er
 	// Wait for results processing to complete
 	<-done
 
-	// Check for extra files if requested
-	if ctx.Bool("no-extra-files") {
-		err = findExtraFiles(ctx, chk, &failures)
-		if err != nil {
-			return 0, err
-		}
+	err = findExtraFiles(ctx, cmd, chk, &failures)
+	if err != nil {
+		return 0, err
 	}
 
 	return failures, nil
 }
 
-func (mfa *CLIApp) checkManifestOperation(ctx *cli.Context) error {
+func (mfa *CLIApp) checkManifestOperation(
+	ctx context.Context, cmd *cli.Command,
+) error {
 	log.Debug("checkManifestOperation()")
 
-	manifestPath, err := mfa.resolveManifestArg(ctx)
+	manifestPath, err := mfa.resolveManifestArg(cmd)
 	if err != nil {
 		return fmt.Errorf("check: %w", err)
 	}
 
 	// URL manifests need to be downloaded to a temp file for the checker
 	if isHTTPURL(manifestPath) {
-		tmpPath, tmpErr := mfa.fetchManifestToTemp(manifestPath)
+		tmpPath, tmpErr := mfa.fetchManifestToTemp(ctx, manifestPath)
 		if tmpErr != nil {
 			return fmt.Errorf("check: %w", tmpErr)
 		}
@@ -301,12 +311,13 @@ func (mfa *CLIApp) checkManifestOperation(ctx *cli.Context) error {
 		manifestPath = tmpPath
 	}
 
-	basePath := ctx.String("base")
-	showProgress := ctx.Bool("progress")
+	basePath := cmd.String("base")
+	showProgress := cmd.Bool("progress")
 
 	log.Infof("checking manifest %s with base %s", manifestPath, basePath)
 
 	// Create checker
+	//nolint:contextcheck // mfer loads a manifest without a context
 	chk, err := mfer.NewChecker(&mfer.CheckerOptions{
 		ManifestPath: manifestPath,
 		BasePath:     basePath,
@@ -317,9 +328,9 @@ func (mfa *CLIApp) checkManifestOperation(ctx *cli.Context) error {
 	}
 
 	// Check signature requirement
-	requiredSigner := ctx.String("require-signature")
+	requiredSigner := cmd.String(flagRequireSignature)
 	if requiredSigner != "" {
-		err = verifyRequiredSigner(ctx.Context, chk, requiredSigner)
+		err = verifyRequiredSigner(ctx, chk, requiredSigner)
 		if err != nil {
 			return err
 		}
@@ -328,7 +339,7 @@ func (mfa *CLIApp) checkManifestOperation(ctx *cli.Context) error {
 	log.Infof("manifest contains %d files, %s", chk.FileCount(),
 		humanize.IBytes(safeUint64(int64(chk.TotalBytes()))))
 
-	failures, err := runCheck(ctx, chk, showProgress)
+	failures, err := runCheck(ctx, cmd, chk, showProgress)
 	if err != nil {
 		return err
 	}

internal/cli/entry_test.go

@@ -18,7 +18,7 @@ import (
 	"github.com/spf13/afero"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	urfcli "github.com/urfave/cli/v2"
+	urfcli "github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/internal/log"
 	"sneak.berlin/go/mfer/mfer"
 )
@@ -264,8 +264,9 @@ func commandsTakingVerbose() [][]string {
 }
 
 // TestVerboseCount asserts that one -v or --verbose gives verbose output and
-// two -v give debug output (issue #125). urfave/cli before v2.25.5 counted a
-// flag given by its alias twice, so one -v gave debug output.
+// two -v, or -v and --verbose, give debug output (issue #125). urfave/cli
+// before v2.25.5 counted a flag given by its alias twice, so one -v gave debug
+// output.
 func TestVerboseCount(t *testing.T) {
 	t.Parallel()
 
@@ -276,6 +277,7 @@ func TestVerboseCount(t *testing.T) {
 		{[]string{"-v"}, log.VerboseLevel},
 		{[]string{testFlagVerbose}, log.VerboseLevel},
 		{[]string{"-v", "-v"}, log.DebugLevel},
+		{[]string{"-v", testFlagVerbose}, log.DebugLevel},
 	}
 
 	for _, command := range commandsTakingVerbose() {
@@ -313,28 +315,6 @@ func TestCombinedShortVerboseRefused(t *testing.T) {
 	}
 }
 
-// TestShortAndLongVerboseRefused asserts that -v and --verbose given together
-// are refused (issue #125): urfave/cli v2 refuses a flag given under two of its
-// names, and one flag with an alias keeps help and parsing simple.
-func TestShortAndLongVerboseRefused(t *testing.T) {
-	t.Parallel()
-
-	for _, command := range commandsTakingVerbose() {
-		args := slices.Concat(command, []string{"-v", testFlagVerbose})
-
-		t.Run(strings.Join(args, " "), func(t *testing.T) {
-			t.Parallel()
-
-			opts := testOpts(args, afero.NewMemMapFs())
-			exitCode, level := runCLIWithLevel(opts)
-
-			assert.Equal(t, 1, exitCode)
-			assert.Contains(t, testStderr(t, opts), "Cannot use two forms of the same flag")
-			assert.Equal(t, log.InfoLevel, level)
-		})
-	}
-}
-
 func TestHelpCommand(t *testing.T) {
 	t.Parallel()
 
@@ -705,30 +685,155 @@ func TestNoExtraFilesWithSubdirectory(t *testing.T) {
 		"check should fail when extra files exist in subdirectory")
 }
 
-func TestCheckWithoutNoExtraFilesIgnoresExtra(t *testing.T) {
+// TestCheckWarnsAboutUnlistedFiles adds one file the manifest does not list
+// to a tree that had none: it gets one warning and the check passes, unless
+// --no-extra-files makes it a failure. --quiet hides the warning, not the
+// failure.
+func TestCheckWarnsAboutUnlistedFiles(t *testing.T) {
 	t.Parallel()
 
-	fs := afero.NewMemMapFs()
+	for name, unlisted := range map[string]string{
+		"regular file":             "extra.txt",
+		"dotfile":                  ".hidden",
+		"file in hidden directory": ".git/config",
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
 
-	// Create test file
-	require.NoError(t, fs.MkdirAll(testDir, 0o755))
-	writeTestFile(t, fs, testFile1, "hello")
+			fs := afero.NewMemMapFs()
+			require.NoError(t, fs.MkdirAll(testDir, 0o755))
+			writeTestFile(t, fs, testFile1, "hello")
 
-	// Generate manifest
-	opts := testOpts([]string{testApp, cmdGenerate, "-q", "-o", testManifest, testDir}, fs)
-	exitCode := runCLI(opts)
-	require.Equal(t, 0, exitCode)
+			opts := testOpts([]string{
+				testApp, cmdGenerate, "-q", "-o", testManifest, testDir,
+			}, fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
 
-	// Add extra file
-	writeTestFile(t, fs, "/testdir/extra.txt", "extra")
+			check := func(flags ...string) (int, string) {
+				args := append([]string{testApp, cmdCheck, testFlagBase, testDir}, flags...)
+				opts := testOpts(append(args, testManifest), fs)
+
+				return runCLI(opts), testStderr(t, opts)
+			}
+
+			exitCode, stderr := check()
+			assert.Equal(t, 0, exitCode, "stderr: %s", stderr)
+			assert.NotContains(t, stderr, "not in manifest")
+
+			writeTestFile(t, fs, filepath.Join(testDir, unlisted), "unlisted")
+
+			exitCode, stderr = check()
+			assert.Equal(t, 0, exitCode, "stderr: %s", stderr)
+			assert.Equal(t, 1, strings.Count(stderr, "not in manifest"), stderr)
+			assert.Contains(t, stderr, unlisted)
+
+			exitCode, stderr = check("-q")
+			assert.Equal(t, 0, exitCode, "stderr: %s", stderr)
+			assert.NotContains(t, stderr, "not in manifest")
+
+			exitCode, stderr = check(testFlagNoExtra)
+			assert.Equal(t, 1, exitCode, "stderr: %s", stderr)
+			assert.Contains(t, stderr, unlisted)
+
+			exitCode, _ = check("-q", testFlagNoExtra)
+			assert.Equal(t, 1, exitCode)
+		})
+	}
+}
+
+// TestCheckNeverReportsManifest keeps the manifest inside the checked tree,
+// under several names and path spellings, and names the tree both directly
+// and through a symlink: the manifest is never reported, even under
+// --no-extra-files. The manifest is recognized by file identity, which needs
+// the real filesystem.
+func TestCheckNeverReportsManifest(t *testing.T) {
+	t.Parallel()
+
+	// Manifest paths are relative to the checked tree.
+	for name, manifest := range map[string]string{
+		"default name":                 defaultManifestName,
+		"hidden name":                  ".index.mf",
+		"other name in a subdirectory": "sub/listing.mf",
+		"path spelled through ..":      "sub/../index.mf",
+	} {
+		t.Run(name, func(t *testing.T) {
+			t.Parallel()
+
+			// A temp dir holding data/tree and link, a symlink to data.
+			root := t.TempDir()
+			tree := filepath.Join(root, "data", "tree")
+			// Not filepath.Join, which would clean away a "..".
+			manifestPath := tree + "/" + manifest
+
+			fs := afero.NewOsFs()
+			require.NoError(t, fs.MkdirAll(filepath.Join(tree, "sub"), 0o750))
+			require.NoError(t,
+				os.Symlink(filepath.Join(root, "data"), filepath.Join(root, "link")))
+			writeTestFile(t, fs, filepath.Join(tree, testFileTxt), "hello")
+
+			opts := testOpts([]string{
+				testApp, cmdGenerate, "-q", "-o", manifestPath, tree,
+			}, fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			for _, base := range []string{tree, filepath.Join(root, "link", "tree")} {
+				opts = testOpts([]string{
+					testApp, cmdCheck, testFlagNoExtra, testFlagBase, base, manifestPath,
+				}, fs)
+				assert.Equal(t, 0, runCLI(opts),
+					"base %s, stderr: %s", base, testStderr(t, opts))
+				assert.NotContains(t, testStderr(t, opts), "not in manifest")
+			}
+		})
+	}
+}
+
+// unlistableDirFs is a filesystem on which one directory cannot be listed.
+type unlistableDirFs struct {
+	afero.Fs
+
+	dir string
+}
+
+//nolint:ireturn // Open must return afero.File to satisfy afero.Fs.
+func (f unlistableDirFs) Open(name string) (afero.File, error) {
+	if name == f.dir {
+		return nil, os.ErrPermission
+	}
+
+	return f.Fs.Open(name)
+}
+
+// TestCheckWithUnlistableDirectory has a directory under the base that
+// cannot be listed, followed by an unlisted file: both are warned about and
+// the check still passes, unless --no-extra-files is given.
+func TestCheckWithUnlistableDirectory(t *testing.T) {
+	t.Parallel()
+
+	mem := afero.NewMemMapFs()
+	require.NoError(t, mem.MkdirAll("/testdir/locked", 0o755))
+	writeTestFile(t, mem, testFile1, "hello")
+
+	opts := testOpts([]string{
+		testApp, cmdGenerate, "-q", "-o", testManifest, testDir,
+	}, mem)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	// Directories are searched in name order, so this comes after "locked".
+	writeTestFile(t, mem, "/testdir/unlisted.txt", "unlisted")
+
+	fs := unlistableDirFs{Fs: mem, dir: "/testdir/locked"}
+
+	opts = testOpts([]string{testApp, cmdCheck, testFlagBase, testDir, testManifest}, fs)
+	assert.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+	assert.Contains(t, testStderr(t, opts), os.ErrPermission.Error())
+	assert.Contains(t, testStderr(t, opts), "unlisted.txt")
 
-	// Check WITHOUT --no-extra-files (should pass - extra files ignored)
 	opts = testOpts([]string{
-		testApp, cmdCheck, "-q", testFlagBase, testDir, testManifest,
+		testApp, cmdCheck, testFlagNoExtra, testFlagBase, testDir, testManifest,
 	}, fs)
-	exitCode = runCLI(opts)
-	assert.Equal(t, 0, exitCode,
-		"check without --no-extra-files should ignore extra files")
+	assert.Equal(t, 1, runCLI(opts), "stderr: %s", testStderr(t, opts))
+	assert.Contains(t, testStderr(t, opts), "unlisted.txt")
 }
 
 func TestGenerateAtomicWriteNoTempFileOnSuccess(t *testing.T) {
@@ -1065,6 +1170,22 @@ func TestGenerateValidatesInputPaths(t *testing.T) {
 	})
 }
 
+// TestFlagAfterArgumentIsArgument asserts that flags are read only before a
+// command's first argument: after it, -v is a path, not the verbose flag.
+func TestFlagAfterArgumentIsArgument(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewMemMapFs()
+	require.NoError(t, fs.MkdirAll(testDir, 0o755))
+	writeTestFile(t, fs, testFile1, "content")
+
+	opts := testOpts([]string{testApp, cmdGenerate, testDir, "-v"}, fs)
+	exitCode := runCLI(opts)
+
+	assert.Equal(t, 1, exitCode)
+	assert.Contains(t, testStderr(t, opts), "path does not exist: -v")
+}
+
 func TestCheckDetectsManifestCorruption(t *testing.T) {
 	t.Parallel()
 

internal/cli/errmsg_test.go

@@ -4,7 +4,6 @@ package cli
 import (
 	"bytes"
 	"context"
-	"flag"
 	"net/http"
 	"net/http/httptest"
 	"os"
@@ -15,7 +14,7 @@ import (
 	"github.com/spf13/afero"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	urfcli "github.com/urfave/cli/v2"
+	urfcli "github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/mfer"
 )
 
@@ -111,9 +110,10 @@ func TestVerifyRequiredSignerMessages(t *testing.T) {
 // string; the required signer is a fixed value that cannot match it. Requires
 // gpg and is skipped where it is absent, as the other signing tests are.
 //
-//nolint:paralleltest // signedChecker calls t.Setenv, which bars t.Parallel
+//nolint:paralleltest // signedManifest calls t.Setenv, which bars t.Parallel
 func TestSignerMismatchMessage(t *testing.T) {
-	chk := signedChecker(t)
+	chk := signedChecker(t,
+		signedManifest(t, map[string][]byte{"f.txt": []byte("signed file")}))
 
 	embeddedFP, err := chk.ExtractEmbeddedSigningKeyFP(context.Background())
 	require.NoError(t, err)
@@ -125,9 +125,10 @@ func TestSignerMismatchMessage(t *testing.T) {
 			" does not match required "+msgFpB)
 }
 
-// signedChecker builds a Checker over a manifest signed by a throwaway GPG
-// key generated in a temporary GNUPGHOME.
-func signedChecker(t *testing.T) *mfer.Checker {
+// signedManifest returns a manifest of files signed by a throwaway GPG key
+// generated in a temporary GNUPGHOME, which it leaves set for the rest of
+// the test.
+func signedManifest(t *testing.T, files map[string][]byte) []byte {
 	t.Helper()
 
 	_, err := exec.LookPath("gpg")
@@ -159,17 +160,25 @@ func signedChecker(t *testing.T) *mfer.Checker {
 	b := mfer.NewBuilder()
 	b.SetSigningOptions(&mfer.SigningOptions{KeyID: mfer.GPGKeyID("test@mfer.test")})
 
-	content := []byte("signed file")
-	_, err = b.AddFile("f.txt", mfer.FileSize(len(content)), mfer.ModTime{},
-		bytes.NewReader(content), nil)
-	require.NoError(t, err)
+	for path, content := range files {
+		_, err = b.AddFile(mfer.RelFilePath(path), mfer.FileSize(len(content)),
+			mfer.ModTime{}, bytes.NewReader(content), nil)
+		require.NoError(t, err)
+	}
 
 	var buf bytes.Buffer
 
 	require.NoError(t, b.Build(context.Background(), &buf))
 
+	return buf.Bytes()
+}
+
+// signedChecker builds a Checker over manifest, a signed manifest.
+func signedChecker(t *testing.T, manifest []byte) *mfer.Checker {
+	t.Helper()
+
 	fs := afero.NewMemMapFs()
-	require.NoError(t, afero.WriteFile(fs, "/index.mf", buf.Bytes(), 0o644))
+	require.NoError(t, afero.WriteFile(fs, "/index.mf", manifest, 0o644))
 
 	chk, err := mfer.NewChecker(&mfer.CheckerOptions{
 		ManifestPath: "/index.mf",
@@ -185,13 +194,17 @@ func signedChecker(t *testing.T) *mfer.Checker {
 func TestPathDoesNotExistMessage(t *testing.T) {
 	t.Parallel()
 
-	set := flag.NewFlagSet("gen", flag.ContinueOnError)
-	require.NoError(t, set.Parse([]string{"nope"}))
-
 	mfa := &CLIApp{Fs: afero.NewMemMapFs()}
-	ctx := urfcli.NewContext(nil, set, nil)
+	cmd := &urfcli.Command{
+		Name: cmdGenerate,
+		Action: func(_ context.Context, c *urfcli.Command) error {
+			_, err := mfa.collectInputPaths(c.Args())
 
-	_, err := mfa.collectInputPaths(ctx.Args())
+			return err
+		},
+	}
+
+	err := cmd.Run(context.Background(), []string{cmdGenerate, "nope"})
 	require.ErrorIs(t, err, errPathNotExist)
 	assert.EqualError(t, err, "path does not exist: nope")
 }
@@ -204,18 +217,22 @@ func TestOutputFileExistsMessage(t *testing.T) {
 	require.NoError(t, afero.WriteFile(fs, "/d/f.txt", []byte("hi"), 0o644))
 	require.NoError(t, afero.WriteFile(fs, "/out.mf", []byte("old"), 0o644))
 
-	set := flag.NewFlagSet("gen", flag.ContinueOnError)
-	set.String("output", "", "")
-	set.Bool("force", false, "")
-	require.NoError(t, set.Parse([]string{"/d"}))
-	require.NoError(t, set.Set("output", "/out.mf"))
-
 	mfa := &CLIApp{Fs: fs}
-	ctx := urfcli.NewContext(nil, set, nil)
+	cmd := &urfcli.Command{
+		Name: cmdGenerate,
+		Flags: []urfcli.Flag{
+			&urfcli.StringFlag{Name: "output"},
+			&urfcli.BoolFlag{Name: "force"},
+		},
+		Action: mfa.generateManifestOperation,
+	}
 
 	// generateManifestOperation writes to the process-global logger during
 	// enumeration, so serialize with the other CLI runs.
-	err := runLocked(func() error { return mfa.generateManifestOperation(ctx) })
+	err := runLocked(func() error {
+		return cmd.Run(context.Background(),
+			[]string{cmdGenerate, "--output", "/out.mf", "/d"})
+	})
 	require.ErrorIs(t, err, errOutputExists)
 	assert.EqualError(t, err,
 		"output file /out.mf already exists (use --force to overwrite)")
@@ -240,7 +257,7 @@ func TestUnknownCommandMessage(t *testing.T) {
 	err := runLocked(func() error {
 		mfa.run([]string{testApp})
 
-		return mfa.app.Run([]string{testApp, "bogus"})
+		return mfa.app.Run(context.Background(), []string{testApp, "bogus"})
 	})
 	require.ErrorIs(t, err, errUnknownCommand)
 	assert.EqualError(t, err, `unknown command "bogus"`)
@@ -257,7 +274,7 @@ func TestManifestLoaderHTTPStatusMessage(t *testing.T) {
 
 	mfa := &CLIApp{Fs: afero.NewMemMapFs()}
 
-	_, err := mfa.openManifestReader(server.URL + "/foo.mf")
+	_, err := mfa.openManifestReader(context.Background(), server.URL+"/foo.mf")
 	require.ErrorIs(t, err, errHTTPStatus)
 	assert.EqualError(t, err,
 		"failed to fetch "+server.URL+"/foo.mf: HTTP 404")
@@ -274,17 +291,13 @@ func TestFetchManifestHTTPStatusMessage(t *testing.T) {
 
 	mfa := &CLIApp{Fs: afero.NewMemMapFs()}
 
-	set := flag.NewFlagSet(cmdFetch, flag.ContinueOnError)
-	for _, f := range mfa.fetchCommand().Flags {
-		require.NoError(t, f.Apply(set))
-	}
-
-	require.NoError(t, set.Parse([]string{server.URL}))
-
-	ctx := urfcli.NewContext(nil, set, nil)
+	cmd := mfa.fetchCommand()
+	cmd.Action = mfa.fetchManifestOperation
 
 	// fetchManifestOperation logs to the process-global logger.
-	err := runLocked(func() error { return mfa.fetchManifestOperation(ctx) })
+	err := runLocked(func() error {
+		return cmd.Run(context.Background(), []string{cmdFetch, server.URL})
+	})
 	require.ErrorIs(t, err, errHTTPStatus)
 	assert.EqualError(t, err, "failed to fetch manifest: HTTP 404")
 }
@@ -300,7 +313,7 @@ func TestFetchFileHTTPStatusMessage(t *testing.T) {
 
 	// downloadFile logs each retry of the 500 to the process-global logger.
 	err := runLocked(func() error {
-		return downloadFile(context.Background(), testClient(), server.URL+"/x", "x",
+		return downloadFile(context.Background(), testClient(), server.URL+"/x", ".", "x",
 			&mfer.MFFilePath{}, nil)
 	})
 	require.ErrorIs(t, err, errHTTPStatus)
@@ -310,14 +323,13 @@ func TestFetchFileHTTPStatusMessage(t *testing.T) {
 func TestURLRequiredMessage(t *testing.T) {
 	t.Parallel()
 
-	set := flag.NewFlagSet("fetch", flag.ContinueOnError)
-	require.NoError(t, set.Parse([]string{}))
-
 	mfa := &CLIApp{Fs: afero.NewMemMapFs()}
-	ctx := urfcli.NewContext(nil, set, nil)
+	cmd := &urfcli.Command{Name: cmdFetch, Action: mfa.fetchManifestOperation}
 
 	// fetchManifestOperation logs to the process-global logger.
-	err := runLocked(func() error { return mfa.fetchManifestOperation(ctx) })
+	err := runLocked(func() error {
+		return cmd.Run(context.Background(), []string{cmdFetch})
+	})
 	require.ErrorIs(t, err, errURLRequired)
 	assert.EqualError(t, err, "URL argument required")
 }
@@ -355,7 +367,7 @@ func TestSizeMismatchMessage(t *testing.T) {
 
 	// finishDownload returns the size-mismatch error before it touches the
 	// paths, digest, or entry, so those can be zero here.
-	err := finishDownload("", "", 9, 10, nil, nil, nil, nil)
+	err := finishDownload("", "", "", 9, 10, nil, nil, nil, nil)
 	require.ErrorIs(t, err, errSizeMismatch)
 	assert.EqualError(t, err, "size mismatch: expected 10 bytes, got 9")
 }

internal/cli/export.go

@@ -1,12 +1,13 @@
 package cli
 
 import (
+	"context"
 	"encoding/hex"
 	"encoding/json"
 	"fmt"
 	"time"
 
-	"github.com/urfave/cli/v2"
+	"github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/mfer"
 )
 
@@ -19,19 +20,22 @@ type ExportEntry struct {
 	Ctime  *string  `json:"ctime,omitempty"`
 }
 
-func (mfa *CLIApp) exportManifestOperation(ctx *cli.Context) error {
-	pathOrURL, err := mfa.resolveManifestArg(ctx)
+func (mfa *CLIApp) exportManifestOperation(
+	ctx context.Context, cmd *cli.Command,
+) error {
+	pathOrURL, err := mfa.resolveManifestArg(cmd)
 	if err != nil {
 		return fmt.Errorf("export: %w", err)
 	}
 
-	rc, err := mfa.openManifestReader(pathOrURL)
+	rc, err := mfa.openManifestReader(ctx, pathOrURL)
 	if err != nil {
 		return fmt.Errorf("export: %w", err)
 	}
 
 	defer func() { _ = rc.Close() }()
 
+	//nolint:contextcheck // mfer loads a manifest without a context
 	manifest, err := mfer.NewManifestFromReader(rc)
 	if err != nil {
 		return fmt.Errorf("export: failed to parse manifest: %w", err)

internal/cli/fetch.go

@@ -19,7 +19,8 @@ import (
 
 	"github.com/dustin/go-humanize"
 	"github.com/multiformats/go-multihash"
-	"github.com/urfave/cli/v2"
+	"github.com/spf13/afero"
+	"github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/internal/log"
 	"sneak.berlin/go/mfer/mfer"
 )
@@ -90,6 +91,10 @@ var (
 	// errHashMismatch indicates a downloaded file whose hash matches no
 	// manifest hash.
 	errHashMismatch = errors.New("hash mismatch")
+	// errNameClash indicates a manifest that lists a file where fetch
+	// writes another file.
+	errNameClash = errors.New(
+		"manifest lists a file where fetch writes another file")
 )
 
 // DownloadProgress reports the progress of a single file download.
@@ -239,20 +244,34 @@ func manifestBaseURL(manifestURL string) (*url.URL, error) {
 	return parsed.JoinPath(".."), nil
 }
 
-// downloadManifestFiles downloads every file in the manifest, reporting
-// progress on the progress channel.
+// downloadManifestFiles downloads every file in the manifest into dest,
+// reporting progress on the progress channel. A file already present in
+// dest is skipped. It returns how many files it downloaded and their
+// total size.
 func downloadManifestFiles(
 	ctx context.Context,
 	client retryingClient,
 	baseURL *url.URL,
+	dest string,
 	files []*mfer.MFFilePath,
 	progress chan<- DownloadProgress,
-) error {
+) (int, int64, error) {
+	var (
+		downloaded      int
+		downloadedBytes int64
+	)
+
 	for _, f := range files {
 		// Sanitize the path to prevent path traversal attacks
 		localPath, err := sanitizePath(f.GetPath())
 		if err != nil {
-			return fmt.Errorf("invalid path in manifest: %w", err)
+			return 0, 0, fmt.Errorf("invalid path in manifest: %w", err)
+		}
+
+		if alreadyPresent(dest, localPath, f) {
+			log.Infof("skipping %s: already present", f.GetPath())
+
+			continue
 		}
 
 		// JoinPath takes escaped path text, so a name such as "100%.txt"
@@ -260,28 +279,70 @@ func downloadManifestFiles(
 		fileURL := baseURL.JoinPath(encodeFilePath(f.GetPath())).String()
 		log.Infof("fetching %s", f.GetPath())
 
-		err = downloadFile(ctx, client, fileURL, localPath, f, progress)
+		err = downloadFile(ctx, client, fileURL, dest, localPath, f, progress)
 		if err != nil {
-			return fmt.Errorf("failed to download %s: %w", f.GetPath(), err)
+			return 0, 0, fmt.Errorf("failed to download %s: %w", f.GetPath(), err)
 		}
+
+		downloaded++
+		downloadedBytes += f.GetSize()
 	}
 
-	return nil
+	return downloaded, downloadedBytes, nil
 }
 
-func (mfa *CLIApp) fetchManifestOperation(ctx *cli.Context) error {
+// alreadyPresent reports whether localPath under dest is a regular file
+// with the size and one of the hashes the manifest lists for entry. It
+// hashes the whole file, since a matching size alone would accept a
+// corrupted or partly written one. A file it cannot read, or reaches only
+// through a symlink, is not present: fetch downloads it, and the download
+// reports the problem.
+func alreadyPresent(dest, localPath string, entry *mfer.MFFilePath) bool {
+	if checkNoSymlinks(dest, localPath) != nil {
+		return false
+	}
+
+	path := filepath.Join(dest, localPath)
+
+	info, err := os.Lstat(path)
+	if err != nil || !info.Mode().IsRegular() || info.Size() != entry.GetSize() {
+		return false
+	}
+
+	// G304: localPath is a relative path that sanitizePath keeps inside
+	// dest as text, and checkNoSymlinks just found no symlink in it.
+	f, err := os.Open(path) //nolint:gosec // G304: see comment above
+	if err != nil {
+		return false
+	}
+
+	defer func() { _ = f.Close() }()
+
+	h := sha256.New()
+
+	_, err = io.Copy(h, f)
+	if err != nil {
+		return false
+	}
+
+	return verifyDownloadedHash(h.Sum(nil), entry) == nil
+}
+
+func (mfa *CLIApp) fetchManifestOperation(
+	ctx context.Context, cmd *cli.Command,
+) error {
 	log.Debug("fetchManifestOperation()")
 
-	if ctx.Args().Len() == 0 {
+	if cmd.Args().Len() == 0 {
 		return errURLRequired
 	}
 
-	timeout := ctx.Duration(flagTimeout)
+	timeout := cmd.Duration(flagTimeout)
 	if timeout <= 0 {
 		return errInvalidTimeout
 	}
 
-	manifestURL, err := resolveManifestURL(ctx.Args().Get(0))
+	manifestURL, err := resolveManifestURL(cmd.Args().Get(0))
 	if err != nil {
 		return fmt.Errorf("invalid URL: %w", err)
 	}
@@ -291,43 +352,22 @@ func (mfa *CLIApp) fetchManifestOperation(ctx *cli.Context) error {
 		firstDelay: firstRetryDelay,
 	}
 
-	log.Infof("fetching manifest from %s", manifestURL)
-
-	// Read the whole manifest before parsing it, so that a connection
-	// lost partway through is retried rather than reported as a bad
-	// manifest.
-	var manifestData []byte
-
-	err = client.get(ctx.Context, manifestURL, func(resp *http.Response) error {
-		var readErr error
-
-		manifestData, readErr = io.ReadAll(resp.Body)
-
-		return readErr
-	})
+	manifestData, files, err := fetchManifest(ctx, cmd, client, manifestURL)
 	if err != nil {
-		return fmt.Errorf("failed to fetch manifest: %w", err)
+		return err
 	}
 
-	// Parse manifest
-	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(manifestData))
-	if err != nil {
-		return fmt.Errorf("failed to parse manifest: %w", err)
-	}
-
-	files := manifest.Files()
-	log.Infof("manifest contains %d files", len(files))
-
 	// Compute base URL (directory containing manifest)
 	baseURL, err := manifestBaseURL(manifestURL)
 	if err != nil {
 		return err
 	}
 
-	// Calculate total bytes to download
-	var totalBytes int64
-	for _, f := range files {
-		totalBytes += f.GetSize()
+	dest := cmd.String(flagDest)
+
+	err = os.MkdirAll(dest, dirPerms)
+	if err != nil {
+		return fmt.Errorf("failed to create destination directory %s: %w", dest, err)
 	}
 
 	// Create progress channel and start progress reporter goroutine
@@ -340,7 +380,8 @@ func (mfa *CLIApp) fetchManifestOperation(ctx *cli.Context) error {
 	startTime := time.Now()
 
 	// Download each file
-	dlErr := downloadManifestFiles(ctx.Context, client, baseURL, files, progress)
+	downloaded, downloadedBytes, dlErr := downloadManifestFiles(
+		ctx, client, baseURL, dest, files, progress)
 
 	close(progress)
 	<-done
@@ -349,15 +390,170 @@ func (mfa *CLIApp) fetchManifestOperation(ctx *cli.Context) error {
 		return dlErr
 	}
 
+	// Saved only now that every file is in place and verified, so that
+	// "mfer check" can verify the tree later.
+	err = saveManifest(dest, manifestData)
+	if err != nil {
+		return fmt.Errorf("failed to save manifest: %w", err)
+	}
+
 	// Print summary
 	elapsed := time.Since(startTime)
-	avgBytesPerSec := float64(totalBytes) / elapsed.Seconds()
+	avgBytesPerSec := float64(downloadedBytes) / elapsed.Seconds()
 	avgRate := formatBitrate(avgBytesPerSec * bitsPerByte)
-	log.Infof("downloaded %d files (%s) in %.1fs (%s avg)",
-		len(files),
-		humanize.IBytes(safeUint64(totalBytes)),
+	log.Infof("downloaded %d files (%s) in %.1fs (%s avg), skipped %d already present",
+		downloaded,
+		humanize.IBytes(safeUint64(downloadedBytes)),
 		elapsed.Seconds(),
-		avgRate)
+		avgRate,
+		len(files)-downloaded)
+	log.Infof("saved manifest to %s", filepath.Join(dest, defaultManifestName))
+
+	return nil
+}
+
+// fetchManifest downloads the manifest at manifestURL and parses it,
+// enforcing --require-signature if it is given and refusing a manifest
+// that lists a file where fetch writes another. It returns the manifest as
+// downloaded, to be saved once the files are in place, and the files it
+// lists.
+func fetchManifest(
+	ctx context.Context, cmd *cli.Command, client retryingClient, manifestURL string,
+) ([]byte, []*mfer.MFFilePath, error) {
+	log.Infof("fetching manifest from %s", manifestURL)
+
+	// Read the whole manifest before parsing it, so that a connection
+	// lost partway through is retried rather than reported as a bad
+	// manifest.
+	var manifestData []byte
+
+	err := client.get(ctx, manifestURL, func(resp *http.Response) error {
+		var readErr error
+
+		manifestData, readErr = io.ReadAll(resp.Body)
+
+		return readErr
+	})
+	if err != nil {
+		return nil, nil, fmt.Errorf("failed to fetch manifest: %w", err)
+	}
+
+	// Parse manifest
+	//nolint:contextcheck // mfer loads a manifest without a context
+	manifest, err := mfer.NewManifestFromReader(bytes.NewReader(manifestData))
+	if err != nil {
+		return nil, nil, fmt.Errorf("failed to parse manifest: %w", err)
+	}
+
+	requiredSigner := cmd.String(flagRequireSignature)
+	if requiredSigner != "" {
+		err = verifyFetchedSigner(ctx, manifestData, requiredSigner)
+		if err != nil {
+			return nil, nil, err
+		}
+	}
+
+	files := manifest.Files()
+
+	err = checkNoNameClash(files)
+	if err != nil {
+		return nil, nil, err
+	}
+
+	log.Infof("manifest contains %d files", len(files))
+
+	return manifestData, files, nil
+}
+
+// checkNoNameClash returns an error if files lists a file, or a directory
+// a file is in, under a name where fetch writes another file: the temp
+// file it downloads a listed file to, or, at the top of the tree, the
+// saved manifest or its temp file. fetch would remove or replace what is
+// listed there, or fail partway, leaving a tree check rejects. Names are
+// compared ignoring case, since on a case-insensitive filesystem INDEX.MF
+// and index.mf are one file.
+func checkNoNameClash(files []*mfer.MFFilePath) error {
+	sep := string(filepath.Separator)
+
+	// written maps each name fetch writes, other than the listed files
+	// themselves, in lower case, to the file it writes there.
+	written := map[string]string{
+		defaultManifestName:              "the saved manifest",
+		tempPathFor(defaultManifestName): "the saved manifest's temp file",
+	}
+
+	for _, f := range files {
+		tmpPath := tempPathFor(filepath.Clean(f.GetPath()))
+		written[strings.ToLower(tmpPath)] = "the temp file for " + f.GetPath()
+	}
+
+	for _, f := range files {
+		// Look up each directory on the file's path, then the file itself.
+		parts := strings.Split(strings.ToLower(filepath.Clean(f.GetPath())), sep)
+
+		for i := range parts {
+			what, ok := written[strings.Join(parts[:i+1], sep)]
+			if ok {
+				return fmt.Errorf("%w: %s (%s)", errNameClash, f.GetPath(), what)
+			}
+		}
+	}
+
+	return nil
+}
+
+// verifyFetchedSigner enforces --require-signature on the fetched manifest
+// exactly as check does. verifyRequiredSigner takes a Checker, which loads
+// its manifest from a file, so the manifest is handed to it as a file in
+// memory.
+func verifyFetchedSigner(
+	ctx context.Context, manifestData []byte, requiredSigner string,
+) error {
+	memFs := afero.NewMemMapFs()
+	manifestPath := "/" + defaultManifestName
+
+	err := afero.WriteFile(memFs, manifestPath, manifestData, filePerms)
+	if err != nil {
+		return err
+	}
+
+	//nolint:contextcheck // mfer loads a manifest without a context
+	chk, err := mfer.NewChecker(&mfer.CheckerOptions{
+		ManifestPath: manifestPath,
+		BasePath:     "/",
+		Fs:           memFs,
+	})
+	if err != nil {
+		return fmt.Errorf("failed to load manifest: %w", err)
+	}
+
+	return verifyRequiredSigner(ctx, chk, requiredSigner)
+}
+
+// saveManifest writes the fetched manifest into dest under the default
+// manifest name, the way fetch writes every file: to a new temp file that
+// is then renamed into place.
+func saveManifest(dest string, manifestData []byte) error {
+	tmpPath := tempPathFor(defaultManifestName)
+
+	out, err := createTempFile(dest, tmpPath)
+	if err != nil {
+		return err
+	}
+
+	_, writeErr := out.Write(manifestData)
+	closeErr := out.Close()
+
+	err = errors.Join(writeErr, closeErr)
+	if err == nil {
+		err = moveIntoPlace(dest, tmpPath, defaultManifestName)
+	}
+
+	if err != nil {
+		_ = os.Remove(filepath.Join(dest, tmpPath))
+
+		return err
+	}
 
 	return nil
 }
@@ -401,14 +597,15 @@ func sanitizePath(p string) (string, error) {
 	return cleaned, nil
 }
 
-// checkNoSymlinks returns an error if any part of the relative path p
-// already exists as a symlink. sanitizePath checks p only as text, so
-// without this a symlink inside the target directory could send a write
-// to p outside of it. Parts that do not exist yet are fine: fetch creates
-// them as plain directories and files. Call it immediately before each
-// write: a symlink created after it returns is not caught.
-func checkNoSymlinks(p string) error {
-	current := ""
+// checkNoSymlinks returns an error if any part of p, a path relative to
+// dest, already exists under dest as a symlink. dest itself is the user's
+// choice and may be one. sanitizePath checks p only as text, so without
+// this a symlink inside dest could send a write to p outside of it. Parts
+// that do not exist yet are fine: fetch creates them as plain directories
+// and files. Call it immediately before each write: a symlink created
+// after it returns is not caught.
+func checkNoSymlinks(dest, p string) error {
+	current := dest
 
 	for _, part := range strings.Split(p, string(filepath.Separator)) {
 		current = filepath.Join(current, part)
@@ -548,13 +745,14 @@ func verifyDownloadedHash(digest []byte, entry *mfer.MFFilePath) error {
 	return errHashMismatch
 }
 
-// downloadFile downloads a URL to a local file path with hash verification.
-// It downloads to a temporary file, verifies the hash, then renames to the final path.
-// Progress is reported via the progress channel.
+// downloadFile downloads a URL to localPath, a path relative to dest, with
+// hash verification. It downloads to a temporary file, verifies the hash,
+// then renames to the final path. Progress is reported via the progress
+// channel.
 func downloadFile(
 	ctx context.Context,
 	client retryingClient,
-	fileURL, localPath string,
+	fileURL, dest, localPath string,
 	entry *mfer.MFFilePath,
 	progress chan<- DownloadProgress,
 ) error {
@@ -568,11 +766,13 @@ func downloadFile(
 	// Create parent directories if needed
 	dir := filepath.Dir(localPath)
 	if dir != "" && dir != "." {
-		err = checkNoSymlinks(dir)
+		err = checkNoSymlinks(dest, dir)
 		if err != nil {
 			return err
 		}
 
+		dir = filepath.Join(dest, dir)
+
 		err = os.MkdirAll(dir, dirPerms)
 		if err != nil {
 			return fmt.Errorf("failed to create directory %s: %w", dir, err)
@@ -582,17 +782,61 @@ func downloadFile(
 	tmpPath := tempPathFor(localPath)
 
 	return client.get(ctx, fileURL, func(resp *http.Response) error {
-		return saveResponse(resp, tmpPath, localPath, entry, progress)
+		return saveResponse(resp, dest, tmpPath, localPath, entry, progress)
 	})
 }
 
+// createTempFile creates tmpPath, a path relative to dest, as a new empty
+// file.
+func createTempFile(dest, tmpPath string) (*os.File, error) {
+	err := checkNoSymlinks(dest, tmpPath)
+	if err != nil {
+		return nil, err
+	}
+
+	path := filepath.Join(dest, tmpPath)
+
+	// Remove whatever is at tmpPath, such as a leftover from an
+	// interrupted run, rather than write into it: it may be a hard link
+	// to a file outside dest, and removing a hard link removes only this
+	// name. If the removal fails, O_EXCL below makes the create fail.
+	_ = os.Remove(path)
+
+	// Create the temp file only if nothing is at tmpPath (O_EXCL).
+	//
+	// G304: tmpPath is a relative path that sanitizePath keeps inside dest
+	// as text, and checkNoSymlinks just found no symlink in it.
+	out, err := os.OpenFile( //nolint:gosec // G304: see comment above
+		path, os.O_RDWR|os.O_CREATE|os.O_EXCL, filePerms)
+	if err != nil {
+		return nil, fmt.Errorf("failed to create temp file: %w", err)
+	}
+
+	return out, nil
+}
+
+// moveIntoPlace renames tmpPath to localPath, both relative to dest.
+func moveIntoPlace(dest, tmpPath, localPath string) error {
+	err := checkNoSymlinks(dest, localPath)
+	if err != nil {
+		return err
+	}
+
+	err = os.Rename(filepath.Join(dest, tmpPath), filepath.Join(dest, localPath))
+	if err != nil {
+		return fmt.Errorf("failed to rename temp file: %w", err)
+	}
+
+	return nil
+}
+
 // saveResponse writes resp's body to tmpPath, verifies it against entry,
-// and renames it to localPath. It starts a new temp file each time and
-// removes it on failure, so a retry after a failed try never appends to
-// or keeps a partial file.
+// and renames it to localPath, both paths relative to dest. It starts a
+// new temp file each time and removes it on failure, so a retry after a
+// failed try never appends to or keeps a partial file.
 func saveResponse(
 	resp *http.Response,
-	tmpPath, localPath string,
+	dest, tmpPath, localPath string,
 	entry *mfer.MFFilePath,
 	progress chan<- DownloadProgress,
 ) error {
@@ -604,29 +848,11 @@ func saveResponse(
 		totalBytes = expectedSize
 	}
 
-	err := checkNoSymlinks(tmpPath)
+	out, err := createTempFile(dest, tmpPath)
 	if err != nil {
 		return err
 	}
 
-	// Remove whatever is at tmpPath, such as a leftover from an
-	// interrupted run, rather than write into it: it may be a hard link
-	// to a file outside the target directory, and removing a hard link
-	// removes only this name. If the removal fails, O_EXCL below makes
-	// the create fail.
-	_ = os.Remove(tmpPath)
-
-	// Create the temp file only if nothing is at tmpPath (O_EXCL).
-	//
-	// G304: tmpPath is a relative path that sanitizePath keeps inside the
-	// target directory as text, and checkNoSymlinks just found no symlink
-	// in it.
-	out, err := os.OpenFile( //nolint:gosec // G304: see comment above
-		tmpPath, os.O_RDWR|os.O_CREATE|os.O_EXCL, filePerms)
-	if err != nil {
-		return fmt.Errorf("failed to create temp file: %w", err)
-	}
-
 	// Set up hash computation
 	h := sha256.New()
 
@@ -646,10 +872,10 @@ func saveResponse(
 	closeErr := out.Close()
 
 	err = finishDownload(
-		tmpPath, localPath, written, expectedSize, h.Sum(nil), entry,
+		dest, tmpPath, localPath, written, expectedSize, h.Sum(nil), entry,
 		copyErr, closeErr)
 	if err != nil {
-		_ = os.Remove(tmpPath)
+		_ = os.Remove(filepath.Join(dest, tmpPath))
 
 		return err
 	}
@@ -660,7 +886,7 @@ func saveResponse(
 // finishDownload validates the copy result, verifies size and hash, and
 // moves the temp file into place. On error the caller removes tmpPath.
 func finishDownload(
-	tmpPath, localPath string,
+	dest, tmpPath, localPath string,
 	written, expectedSize int64,
 	digest []byte,
 	entry *mfer.MFFilePath,
@@ -686,16 +912,5 @@ func finishDownload(
 		return err
 	}
 
-	err = checkNoSymlinks(localPath)
-	if err != nil {
-		return err
-	}
-
-	// Rename temp file to final path
-	err = os.Rename(tmpPath, localPath)
-	if err != nil {
-		return fmt.Errorf("failed to rename temp file: %w", err)
-	}
-
-	return nil
+	return moveIntoPlace(dest, tmpPath, localPath)
 }

internal/cli/fetch_test.go

@@ -4,7 +4,6 @@ package cli
 import (
 	"bytes"
 	"context"
-	"flag"
 	"fmt"
 	"io"
 	"maps"
@@ -13,6 +12,7 @@ import (
 	"net/http/httptest"
 	"os"
 	"path/filepath"
+	"slices"
 	"strconv"
 	"sync"
 	"sync/atomic"
@@ -22,7 +22,6 @@ import (
 	"github.com/spf13/afero"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	urfcli "github.com/urfave/cli/v2"
 	"sneak.berlin/go/mfer/mfer"
 )
 
@@ -338,7 +337,7 @@ func TestFetchFromHTTP(t *testing.T) {
 
 		fileURL := baseURL + f.GetPath()
 		err = downloadFile(context.Background(), testClient(),
-			fileURL, localPath, f, progress)
+			fileURL, ".", localPath, f, progress)
 		require.NoError(t, err, "failed to download %s", f.GetPath())
 	}
 
@@ -386,7 +385,7 @@ func TestFetchHashMismatch(t *testing.T) {
 
 	// Try to download - should fail with hash mismatch
 	err = downloadFile(context.Background(), testClient(),
-		server.URL+"/file.txt", testFileTxt, files[0], nil)
+		server.URL+"/file.txt", ".", testFileTxt, files[0], nil)
 	require.Error(t, err)
 	assert.Contains(t, err.Error(), "mismatch")
 
@@ -432,7 +431,7 @@ func TestFetchSizeMismatch(t *testing.T) {
 
 	// Try to download - should fail with size mismatch
 	err = downloadFile(context.Background(), testClient(),
-		server.URL+"/file.txt", testFileTxt, files[0], nil)
+		server.URL+"/file.txt", ".", testFileTxt, files[0], nil)
 	require.Error(t, err)
 	assert.Contains(t, err.Error(), "size mismatch")
 
@@ -490,7 +489,7 @@ func TestFetchProgress(t *testing.T) {
 
 	// Download
 	err = downloadFile(context.Background(), testClient(),
-		server.URL+"/large.txt", "large.txt", files[0], progress)
+		server.URL+"/large.txt", ".", "large.txt", files[0], progress)
 	close(progress)
 	<-done
 
@@ -513,24 +512,51 @@ func TestFetchProgress(t *testing.T) {
 	assert.Equal(t, content, downloaded)
 }
 
-// TestFetchRefusesSymlinks runs fetch into a destination directory that
-// holds a symlink pointing outside it, in each of the three places fetch
-// writes: a parent directory, the temp file, and the file itself, which
-// the temp file is renamed onto; and once as a directory inside a plain
-// directory. The fetch must fail and nothing outside may change.
+// TestFetchRefusesSymlinks runs fetch with --dest naming a directory other
+// than the current one, which holds a symlink pointing outside it, in each
+// place fetch writes: a parent directory, the temp file, the file itself,
+// which the temp file is renamed onto, and the saved manifest's temp file
+// and final name; and once as a directory inside a plain directory. The
+// fetch must fail, and neither the outside directory nor the current one
+// may change.
 //
 //nolint:paralleltest // changes the process-global working directory
 func TestFetchRefusesSymlinks(t *testing.T) {
+	// What a link standing for a file points to: a file outside that does
+	// not exist yet.
+	const newFile = "new.txt"
+
 	tests := []struct {
-		name   string
-		entry  string // the manifest's only file
-		link   string // symlink placed in the destination directory
-		target string // what link points to, relative to the outside directory
+		name    string
+		entry   string // the manifest's only file
+		link    string // symlink placed in the destination directory
+		target  string // what link points to, relative to the outside directory
+		failure string // what fetch reports it was doing when it found link
 	}{
-		{"parent directory", "sub/deeper/file.txt", "sub", "."},
-		{"directory inside a plain directory", "docs/data/passwd", "docs/data", "."},
-		{"temp file", testFileTxt, ".file.txt.tmp", "new.txt"},
-		{"file", testFileTxt, testFileTxt, "new.txt"},
+		{
+			"parent directory", "sub/deeper/file.txt", "sub", ".",
+			"failed to download sub/deeper/file.txt",
+		},
+		{
+			"directory inside a plain directory", "docs/data/passwd", "docs/data", ".",
+			"failed to download docs/data/passwd",
+		},
+		{
+			"temp file", testFileTxt, ".file.txt.tmp", newFile,
+			"failed to download " + testFileTxt,
+		},
+		{
+			"file", testFileTxt, testFileTxt, newFile,
+			"failed to download " + testFileTxt,
+		},
+		{
+			"manifest temp file", testFileTxt, tempPathFor(defaultManifestName), newFile,
+			"failed to save manifest",
+		},
+		{
+			"manifest", testFileTxt, defaultManifestName, newFile,
+			"failed to save manifest",
+		},
 	}
 
 	for _, tt := range tests {
@@ -545,23 +571,61 @@ func TestFetchRefusesSymlinks(t *testing.T) {
 			defer server.Close()
 
 			outside := t.TempDir()
+			cwd := chdirTemp(t)
+			dest := t.TempDir()
+			link := filepath.Join(dest, tt.link)
 
-			chdirTemp(t)
-			require.NoError(t, os.MkdirAll(filepath.Dir(tt.link), 0o750))
-			require.NoError(t, os.Symlink(filepath.Join(outside, tt.target), tt.link))
+			require.NoError(t, os.MkdirAll(filepath.Dir(link), 0o750))
+			require.NoError(t, os.Symlink(filepath.Join(outside, tt.target), link))
 
-			opts := testOpts([]string{testApp, cmdFetch, "-q", server.URL}, afero.NewOsFs())
+			opts := testOpts([]string{
+				testApp, cmdFetch, "-q", "--" + flagDest, dest, server.URL,
+			}, afero.NewOsFs())
 			assert.Equal(t, 1, runCLI(opts))
-			assert.Contains(t, testStderr(t, opts), "failed to download "+tt.entry+
-				": symlink in path not allowed: "+tt.link)
+			assert.Contains(t, testStderr(t, opts),
+				tt.failure+": symlink in path not allowed: "+link)
 
 			written, err := os.ReadDir(outside)
 			require.NoError(t, err)
 			assert.Empty(t, written, "fetch wrote outside the destination")
+
+			written, err = os.ReadDir(cwd)
+			require.NoError(t, err)
+			assert.Empty(t, written, "fetch wrote to the current directory")
 		})
 	}
 }
 
+// TestFetchDoesNotSkipThroughSymlink runs fetch with --dest holding a
+// symlink to a directory outside it, where the file the manifest lists
+// through that symlink already sits with the listed content. fetch must
+// not take that file as already present: it must fail on the symlink, as
+// the download would, and leave the outside file alone.
+func TestFetchDoesNotSkipThroughSymlink(t *testing.T) {
+	t.Parallel()
+
+	content := []byte("fetched")
+	files := map[string][]byte{"sub/" + testFileTxt: content}
+
+	server := httptest.NewServer(fetchTestHandler(manifestOf(t, files), files))
+	defer server.Close()
+
+	outside := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(outside, testFileTxt), content, 0o600))
+
+	dest := t.TempDir()
+	link := filepath.Join(dest, "sub")
+	require.NoError(t, os.Symlink(outside, link))
+
+	opts := testOpts([]string{
+		testApp, cmdFetch, "-q", "--" + flagDest, dest, server.URL,
+	}, afero.NewOsFs())
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts),
+		"failed to download sub/"+testFileTxt+": symlink in path not allowed: "+link)
+	assert.Equal(t, map[string][]byte{testFileTxt: content}, filesUnder(t, outside))
+}
+
 // TestFetchReplacesHardLinkAtTempName runs fetch into a destination
 // directory that holds, at the temp file's name, a hard link to a file
 // outside it. To fetch that is an ordinary leftover from an interrupted
@@ -787,7 +851,7 @@ func TestDownloadFileRetriesToSuccess(t *testing.T) {
 	chdirTemp(t)
 
 	err = downloadFile(context.Background(), testClient(),
-		server.URL+"/"+testFileTxt, testFileTxt, manifest.Files()[0], nil)
+		server.URL+"/"+testFileTxt, ".", testFileTxt, manifest.Files()[0], nil)
 	require.NoError(t, err)
 	assert.Equal(t, int32(3), requests.Load())
 
@@ -878,7 +942,7 @@ func TestFetchEscapedPaths(t *testing.T) {
 
 // TestFetchTree runs fetch on a tree with nested directories. Every file
 // the manifest lists must land under its own path with its own content,
-// and nothing else may be left in the destination.
+// beside the manifest, and nothing else may be left in the destination.
 //
 //nolint:paralleltest // changes the process-global working directory
 func TestFetchTree(t *testing.T) {
@@ -889,7 +953,9 @@ func TestFetchTree(t *testing.T) {
 		"other/deep/est.txt": []byte("in a second directory"),
 	}
 
-	server := httptest.NewServer(fetchTestHandler(manifestOf(t, files), files))
+	manifest := manifestOf(t, files)
+
+	server := httptest.NewServer(fetchTestHandler(manifest, files))
 	defer server.Close()
 
 	dest := chdirTemp(t)
@@ -897,7 +963,9 @@ func TestFetchTree(t *testing.T) {
 	opts := testOpts([]string{testApp, cmdFetch, "-q", server.URL}, afero.NewOsFs())
 	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
 
-	assert.Equal(t, files, filesUnder(t, dest))
+	want := maps.Clone(files)
+	want[defaultManifestName] = manifest
+	assert.Equal(t, want, filesUnder(t, dest))
 }
 
 // TestFetchFailsOnHashMismatch runs fetch against a server that serves a
@@ -922,9 +990,10 @@ func TestFetchFailsOnHashMismatch(t *testing.T) {
 // TestFetchIntoPartlyFilledDestination runs fetch where an interrupted
 // fetch of an older version of the tree left one file current, one file
 // out of date and one half written to its temp file, beside a file the
-// manifest does not list. fetch downloads every file the manifest lists,
-// those already present included, and replaces what is there; the file
-// the manifest does not list is left alone.
+// manifest does not list. fetch skips the current file and downloads the
+// other two. The out-of-date file has the same size as the new version,
+// so only its hash shows that it must be replaced. The file the manifest
+// does not list is left alone, and the manifest is saved beside the files.
 //
 //nolint:paralleltest // changes the process-global working directory
 func TestFetchIntoPartlyFilledDestination(t *testing.T) {
@@ -935,7 +1004,8 @@ func TestFetchIntoPartlyFilledDestination(t *testing.T) {
 	}
 	unlisted := []byte("not in the manifest")
 
-	tree := fetchTestHandler(manifestOf(t, files), files)
+	manifest := manifestOf(t, files)
+	tree := fetchTestHandler(manifest, files)
 
 	var (
 		mu        sync.Mutex
@@ -963,21 +1033,274 @@ func TestFetchIntoPartlyFilledDestination(t *testing.T) {
 		os.WriteFile(tempPathFor("sub/partial.txt"), []byte("cut off"), 0o600))
 	require.NoError(t, os.WriteFile("unlisted.txt", unlisted, 0o600))
 
-	opts := testOpts([]string{testApp, cmdFetch, "-q", server.URL}, afero.NewOsFs())
+	opts := testOpts([]string{testApp, cmdFetch, server.URL}, afero.NewOsFs())
 	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+	assert.Contains(t, testStderr(t, opts), "skipping current.txt: already present")
 
 	want := maps.Clone(files)
 	want["unlisted.txt"] = unlisted
+	want[defaultManifestName] = manifest
 	assert.Equal(t, want, filesUnder(t, dest))
 
 	mu.Lock()
 	defer mu.Unlock()
 
 	assert.ElementsMatch(t, []string{
-		"/" + defaultManifestName, "/current.txt", "/sub/changed.txt", "/sub/partial.txt",
+		"/" + defaultManifestName, "/sub/changed.txt", "/sub/partial.txt",
 	}, requested)
 }
 
+// TestFetchIntoDest fetches a tree with --dest into a directory that does
+// not exist yet. The files and the manifest must land there and nowhere
+// else, and check must pass on the result with no extra files. A second
+// fetch into the same directory must download nothing but the manifest.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestFetchIntoDest(t *testing.T) {
+	files := map[string][]byte{
+		"top.txt":     []byte("at the top"),
+		"sub/one.txt": []byte("one level down"),
+	}
+
+	manifest := manifestOf(t, files)
+	tree := fetchTestHandler(manifest, files)
+
+	var (
+		mu        sync.Mutex
+		requested []string
+	)
+
+	server := httptest.NewServer(
+		http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+			mu.Lock()
+
+			requested = append(requested, r.URL.Path)
+
+			mu.Unlock()
+
+			tree.ServeHTTP(w, r)
+		}))
+	defer server.Close()
+
+	cwd := chdirTemp(t)
+	dest := filepath.Join(t.TempDir(), "mirror")
+	fetch := []string{testApp, cmdFetch, "-q", "--" + flagDest, dest, server.URL}
+
+	opts := testOpts(fetch, afero.NewOsFs())
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+	want := maps.Clone(files)
+	want[defaultManifestName] = manifest
+	assert.Equal(t, want, filesUnder(t, dest))
+	assert.Empty(t, filesUnder(t, cwd), "fetch wrote outside --dest")
+
+	check := testOpts([]string{
+		testApp, cmdCheck, "-q", testFlagBase, dest, testFlagNoExtra,
+		filepath.Join(dest, defaultManifestName),
+	}, afero.NewOsFs())
+	require.Equal(t, 0, runCLI(check), testStderr(t, check))
+
+	mu.Lock()
+	requested = nil
+	mu.Unlock()
+
+	opts = testOpts(fetch, afero.NewOsFs())
+	require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+	assert.Equal(t, want, filesUnder(t, dest))
+
+	mu.Lock()
+	defer mu.Unlock()
+
+	assert.Equal(t, []string{"/" + defaultManifestName}, requested)
+}
+
+// TestFetchRequireSignature runs fetch with --require-signature. A
+// manifest that is unsigned, or signed by another key, must stop fetch
+// with check's message before it downloads or writes anything; the
+// required key lets it through. The signed cases need gpg and are skipped
+// without it, as the other signing tests are.
+//
+//nolint:paralleltest // signedManifest calls t.Setenv, which bars t.Parallel
+func TestFetchRequireSignature(t *testing.T) {
+	files := map[string][]byte{testFileTxt: []byte("signed file")}
+
+	t.Run("unsigned", func(t *testing.T) {
+		assertFetchRefused(t, manifestOf(t, files), files,
+			"manifest is not signed, but signature from "+msgFpA+" is required",
+			"--"+flagRequireSignature, msgFpA)
+	})
+
+	t.Run("signed", func(t *testing.T) {
+		manifest := signedManifest(t, files)
+
+		signer, err := signedChecker(t, manifest).
+			ExtractEmbeddedSigningKeyFP(context.Background())
+		require.NoError(t, err)
+
+		assertFetchRefused(t, manifest, files,
+			"embedded signing key fingerprint "+signer+" does not match required "+msgFpB,
+			"--"+flagRequireSignature, msgFpB)
+
+		server := httptest.NewServer(fetchTestHandler(manifest, files))
+		defer server.Close()
+
+		dest := t.TempDir()
+
+		opts := testOpts([]string{
+			testApp, cmdFetch, "-q", "--" + flagDest, dest,
+			"--" + flagRequireSignature, signer, server.URL,
+		}, afero.NewOsFs())
+		require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+		assert.Equal(t, files[testFileTxt], filesUnder(t, dest)[testFileTxt])
+	})
+}
+
+// TestFetchRefusesListedManifestName fetches manifests that list, at the
+// top of the tree, the name fetch saves the manifest under or that name's
+// temp file: as a file, as a directory, in capitals, and with a leading
+// "./". Saving the manifest would replace or remove what is listed there,
+// so fetch must refuse the manifest before it creates the destination or
+// requests any file.
+func TestFetchRefusesListedManifestName(t *testing.T) {
+	t.Parallel()
+
+	for _, listed := range []string{
+		defaultManifestName,
+		tempPathFor(defaultManifestName),
+		defaultManifestName + "/" + testFileTxt,
+		"INDEX.MF",
+		"./" + defaultManifestName,
+	} {
+		t.Run(listed, func(t *testing.T) {
+			t.Parallel()
+
+			files := map[string][]byte{listed: []byte("listed")}
+
+			assertFetchRefused(t, builtManifest(t, files), files,
+				"manifest lists a file where fetch writes another file: "+listed)
+		})
+	}
+}
+
+// TestFetchRefusesListedTempName fetches manifests that list a.txt and
+// .a.txt.tmp, the temp file fetch downloads a.txt to, at the top of the
+// tree and in a directory. Downloading a.txt would remove .a.txt.tmp, so
+// fetch must refuse the manifest before it creates the destination or
+// requests any file. README with .README.tmp checks that temp names are
+// compared ignoring case. A manifest that lists only one of the two is
+// fetched in full.
+func TestFetchRefusesListedTempName(t *testing.T) {
+	t.Parallel()
+
+	for _, dir := range []string{"", "sub/"} {
+		for file, tmp := range map[string]string{
+			dir + "a.txt":  dir + ".a.txt.tmp",
+			dir + "README": dir + ".README.tmp",
+		} {
+			both := map[string][]byte{
+				file: []byte("a file"),
+				tmp:  []byte("a file at its temp name"),
+			}
+
+			t.Run(file+" and "+tmp, func(t *testing.T) {
+				t.Parallel()
+
+				assertFetchRefused(t, builtManifest(t, both), both,
+					"manifest lists a file where fetch writes another file: "+
+						tmp+" (the temp file for "+file+")")
+			})
+
+			for listed, content := range both {
+				t.Run("only "+listed, func(t *testing.T) {
+					t.Parallel()
+
+					files := map[string][]byte{listed: content}
+					manifest := builtManifest(t, files)
+
+					server := httptest.NewServer(fetchTestHandler(manifest, files))
+					defer server.Close()
+
+					dest := t.TempDir()
+
+					opts := testOpts([]string{
+						testApp, cmdFetch, "-q", "--" + flagDest, dest, server.URL,
+					}, afero.NewOsFs())
+					require.Equal(t, 0, runCLI(opts), testStderr(t, opts))
+
+					want := maps.Clone(files)
+					want[defaultManifestName] = manifest
+					assert.Equal(t, want, filesUnder(t, dest))
+				})
+			}
+		}
+	}
+}
+
+// builtManifest returns a manifest of files, built directly rather than
+// scanned, since a scan lists no hidden files and never a path starting
+// with "./".
+func builtManifest(t *testing.T, files map[string][]byte) []byte {
+	t.Helper()
+
+	builder := mfer.NewBuilder()
+
+	for p, content := range files {
+		_, err := builder.AddFile(mfer.RelFilePath(p), mfer.FileSize(len(content)),
+			mfer.ModTime(time.Now()), bytes.NewReader(content), nil)
+		require.NoError(t, err)
+	}
+
+	var manifest bytes.Buffer
+
+	require.NoError(t, builder.Build(context.Background(), &manifest))
+
+	return manifest.Bytes()
+}
+
+// assertFetchRefused serves manifest, a manifest of files, and fetches it
+// with flags into a directory that does not exist yet. fetch must fail
+// with message after requesting only the manifest, and must not create
+// the directory.
+func assertFetchRefused(
+	t *testing.T, manifest []byte, files map[string][]byte,
+	message string, flags ...string,
+) {
+	t.Helper()
+
+	tree := fetchTestHandler(manifest, files)
+
+	var (
+		mu        sync.Mutex
+		requested []string
+	)
+
+	server := httptest.NewServer(
+		http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+			mu.Lock()
+
+			requested = append(requested, r.URL.Path)
+
+			mu.Unlock()
+
+			tree.ServeHTTP(w, r)
+		}))
+	defer server.Close()
+
+	dest := filepath.Join(t.TempDir(), "mirror")
+
+	opts := testOpts(slices.Concat(
+		[]string{testApp, cmdFetch, "-q", "--" + flagDest, dest}, flags, []string{server.URL},
+	), afero.NewOsFs())
+	assert.Equal(t, 1, runCLI(opts))
+	assert.Contains(t, testStderr(t, opts), message)
+	assert.NoDirExists(t, dest, "fetch created the destination before refusing")
+
+	mu.Lock()
+	defer mu.Unlock()
+
+	assert.Equal(t, []string{"/" + defaultManifestName}, requested)
+}
+
 // TestFetchTimeoutFlag runs fetch with --timeout against a server that
 // never answers. Without the flag's limit the request would wait forever;
 // once fetch gives up on it, the server cancels fetch's context so that
@@ -997,18 +1320,13 @@ func TestFetchTimeoutFlag(t *testing.T) {
 
 	mfa := &CLIApp{Fs: afero.NewMemMapFs()}
 
-	set := flag.NewFlagSet(cmdFetch, flag.ContinueOnError)
-	for _, f := range mfa.fetchCommand().Flags {
-		require.NoError(t, f.Apply(set))
-	}
-
-	require.NoError(t, set.Parse([]string{"--" + flagTimeout, "100ms", server.URL}))
-
-	cliCtx := urfcli.NewContext(nil, set, nil)
-	cliCtx.Context = ctx
+	cmd := mfa.fetchCommand()
+	cmd.Action = mfa.fetchManifestOperation
 
 	// fetchManifestOperation logs to the process-global logger.
-	err := runLocked(func() error { return mfa.fetchManifestOperation(cliCtx) })
+	err := runLocked(func() error {
+		return cmd.Run(ctx, []string{cmdFetch, "--" + flagTimeout, "100ms", server.URL})
+	})
 	require.Error(t, err)
 }
 

internal/cli/freshen.go

@@ -14,7 +14,7 @@ import (
 	"github.com/dustin/go-humanize"
 	"github.com/multiformats/go-multihash"
 	"github.com/spf13/afero"
-	"github.com/urfave/cli/v2"
+	"github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/internal/log"
 	"sneak.berlin/go/mfer/mfer"
 )
@@ -202,12 +202,12 @@ func (s *freshenScanner) walk(path string, info fs.FileInfo, walkErr error) erro
 
 // resolveFreshenManifestPath determines the manifest path from the CLI
 // arguments, searching directories for a manifest where needed.
-func (mfa *CLIApp) resolveFreshenManifestPath(ctx *cli.Context) (string, error) {
-	if ctx.Args().Len() == 0 {
+func (mfa *CLIApp) resolveFreshenManifestPath(cmd *cli.Command) (string, error) {
+	if cmd.Args().Len() == 0 {
 		return findManifest(mfa.Fs, ".")
 	}
 
-	arg := ctx.Args().Get(0)
+	arg := cmd.Args().Get(0)
 
 	info, statErr := mfa.Fs.Stat(arg)
 	if statErr == nil && info.IsDir() {
@@ -338,14 +338,14 @@ func writeFreshenedManifest(
 
 // newFreshenBuilder constructs the manifest builder configured from CLI
 // flags.
-func newFreshenBuilder(ctx *cli.Context) *mfer.Builder {
+func newFreshenBuilder(cmd *cli.Command) *mfer.Builder {
 	builder := mfer.NewBuilder()
-	if ctx.Bool("include-timestamps") {
+	if cmd.Bool("include-timestamps") {
 		builder.SetIncludeTimestamps(true)
 	}
 
 	// Set up signing options if sign-key is provided
-	if signKey := ctx.String("sign-key"); signKey != "" {
+	if signKey := cmd.String("sign-key"); signKey != "" {
 		builder.SetSigningOptions(&mfer.SigningOptions{
 			KeyID: mfer.GPGKeyID(signKey),
 		})
@@ -358,13 +358,13 @@ func newFreshenBuilder(ctx *cli.Context) *mfer.Builder {
 // freshenScan runs the scan phase against the loaded manifest entries
 // and returns the populated scanner and the count of removed files.
 func (mfa *CLIApp) freshenScan(
-	ctx *cli.Context, manifestPath, absBase string,
+	cmd *cli.Command, manifestPath, absBase string,
 	existingByPath map[string]*mfer.MFFilePath,
 ) (*freshenScanner, int64, error) {
 	log.Infof("scanning filesystem...")
 
 	startScan := time.Now()
-	showProgress := ctx.Bool("progress")
+	showProgress := cmd.Bool("progress")
 
 	// Leave out the manifest and a temp file left by an interrupted run,
 	// as gen does. A path that cannot be stat'd, normally because no file
@@ -382,8 +382,8 @@ func (mfa *CLIApp) freshenScan(
 		fs:              mfa.Fs,
 		absBase:         absBase,
 		excluded:        excluded,
-		includeDotfiles: ctx.Bool("include-dotfiles"),
-		followSymlinks:  ctx.Bool("follow-symlinks"),
+		includeDotfiles: cmd.Bool("include-dotfiles"),
+		followSymlinks:  cmd.Bool("follow-symlinks"),
 		showProgress:    showProgress,
 		existingByPath:  existingByPath,
 	}
@@ -433,7 +433,7 @@ func hashTotals(entries []*freshenEntry) (int64, int64) {
 // runFreshenHash processes every entry through the hasher, aborting if
 // the context is canceled.
 func runFreshenHash(
-	ctx *cli.Context, hasher *freshenHasher, entries []*freshenEntry,
+	ctx context.Context, hasher *freshenHasher, entries []*freshenEntry,
 ) error {
 	for _, e := range entries {
 		select {
@@ -479,18 +479,21 @@ func (mfa *CLIApp) loadExistingEntries(
 	return existingByPath, nil
 }
 
-func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
+func (mfa *CLIApp) freshenManifestOperation(
+	ctx context.Context, cmd *cli.Command,
+) error {
 	log.Debug("freshenManifestOperation()")
 
-	basePath := ctx.String("base")
-	showProgress := ctx.Bool("progress")
+	basePath := cmd.String("base")
+	showProgress := cmd.Bool("progress")
 
 	// Find manifest file
-	manifestPath, err := mfa.resolveFreshenManifestPath(ctx)
+	manifestPath, err := mfa.resolveFreshenManifestPath(cmd)
 	if err != nil {
 		return fmt.Errorf("freshen: %w", err)
 	}
 
+	//nolint:contextcheck // mfer loads a manifest without a context
 	existingByPath, err := mfa.loadExistingEntries(manifestPath)
 	if err != nil {
 		return err
@@ -502,7 +505,7 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 	}
 
 	// Phase 1: Scan filesystem
-	scanner, removed, err := mfa.freshenScan(ctx, manifestPath, absBase,
+	scanner, removed, err := mfa.freshenScan(cmd, manifestPath, absBase,
 		existingByPath)
 	if err != nil {
 		return err
@@ -524,7 +527,7 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 		totalHashBytes: totalHashBytes,
 		filesToHash:    filesToHash,
 		startHash:      time.Now(),
-		builder:        newFreshenBuilder(ctx),
+		builder:        newFreshenBuilder(cmd),
 	}
 
 	err = runFreshenHash(ctx, hasher, scanner.entries)
@@ -548,7 +551,7 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 	}
 
 	// Write updated manifest atomically (write to temp, then rename)
-	err = writeFreshenedManifest(ctx.Context, mfa.Fs, hasher.builder, manifestPath)
+	err = writeFreshenedManifest(ctx, mfa.Fs, hasher.builder, manifestPath)
 	if err != nil {
 		return err
 	}

internal/cli/gen.go

@@ -1,6 +1,7 @@
 package cli
 
 import (
+	"context"
 	"errors"
 	"fmt"
 	"os"
@@ -12,7 +13,7 @@ import (
 
 	"github.com/dustin/go-humanize"
 	"github.com/spf13/afero"
-	"github.com/urfave/cli/v2"
+	"github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/internal/log"
 	"sneak.berlin/go/mfer/mfer"
 )
@@ -88,12 +89,12 @@ func (mfa *CLIApp) collectInputPaths(args cli.Args) ([]string, error) {
 }
 
 // buildScannerOptions constructs scanner options from the CLI flags.
-func (mfa *CLIApp) buildScannerOptions(ctx *cli.Context) *mfer.ScannerOptions {
-	output := ctx.String("output")
+func (mfa *CLIApp) buildScannerOptions(cmd *cli.Command) *mfer.ScannerOptions {
+	output := cmd.String("output")
 	opts := &mfer.ScannerOptions{
-		IncludeDotfiles:   ctx.Bool("include-dotfiles"),
-		FollowSymLinks:    ctx.Bool("follow-symlinks"),
-		IncludeTimestamps: ctx.Bool("include-timestamps"),
+		IncludeDotfiles:   cmd.Bool("include-dotfiles"),
+		FollowSymLinks:    cmd.Bool("follow-symlinks"),
+		IncludeTimestamps: cmd.Bool("include-timestamps"),
 		Fs:                mfa.Fs,
 		// Neither a manifest being replaced nor a temp file left by an
 		// interrupted run belongs in the new manifest.
@@ -101,14 +102,14 @@ func (mfa *CLIApp) buildScannerOptions(ctx *cli.Context) *mfer.ScannerOptions {
 	}
 
 	// Set seed for deterministic UUID if provided
-	if seed := ctx.String("seed"); seed != "" {
+	if seed := cmd.String("seed"); seed != "" {
 		opts.Seed = seed
 
 		log.Infof("using deterministic seed for manifest UUID")
 	}
 
 	// Set up signing options if sign-key is provided
-	if signKey := ctx.String("sign-key"); signKey != "" {
+	if signKey := cmd.String("sign-key"); signKey != "" {
 		opts.SigningOptions = &mfer.SigningOptions{
 			KeyID: mfer.GPGKeyID(signKey),
 		}
@@ -173,14 +174,14 @@ func (mfa *CLIApp) cleanupOnSignal(outFile afero.File, tmpPath string) chan os.S
 
 // runEnumeratePhase enumerates all input paths with optional progress
 // reporting and logs the totals.
-func (mfa *CLIApp) runEnumeratePhase(ctx *cli.Context, s *mfer.Scanner) error {
+func (mfa *CLIApp) runEnumeratePhase(cmd *cli.Command, s *mfer.Scanner) error {
 	// Set up enumeration progress reporting
 	var (
 		enumProgress chan mfer.EnumerateStatus
 		enumWg       sync.WaitGroup
 	)
 
-	if ctx.Bool("progress") {
+	if cmd.Bool("progress") {
 		enumProgress = make(chan mfer.EnumerateStatus, 1)
 
 		enumWg.Add(1)
@@ -188,7 +189,7 @@ func (mfa *CLIApp) runEnumeratePhase(ctx *cli.Context, s *mfer.Scanner) error {
 		go reportEnumProgress(enumProgress, &enumWg)
 	}
 
-	err := mfa.enumerateInputs(s, ctx.Args(), enumProgress)
+	err := mfa.enumerateInputs(s, cmd.Args(), enumProgress)
 	if err != nil {
 		return err
 	}
@@ -201,22 +202,24 @@ func (mfa *CLIApp) runEnumeratePhase(ctx *cli.Context, s *mfer.Scanner) error {
 	return nil
 }
 
-func (mfa *CLIApp) generateManifestOperation(ctx *cli.Context) error {
+func (mfa *CLIApp) generateManifestOperation(
+	ctx context.Context, cmd *cli.Command,
+) error {
 	log.Debug("generateManifestOperation()")
 
-	s := mfer.NewScannerWithOptions(mfa.buildScannerOptions(ctx))
+	s := mfer.NewScannerWithOptions(mfa.buildScannerOptions(cmd))
 
 	// Phase 1: Enumeration - collect paths and stat files
-	err := mfa.runEnumeratePhase(ctx, s)
+	err := mfa.runEnumeratePhase(cmd, s)
 	if err != nil {
 		return err
 	}
 
-	showProgress := ctx.Bool("progress")
+	showProgress := cmd.Bool("progress")
 
 	// Check if output file exists
-	outputPath := ctx.String("output")
-	if exists, _ := afero.Exists(mfa.Fs, outputPath); exists && !ctx.Bool("force") {
+	outputPath := cmd.String("output")
+	if exists, _ := afero.Exists(mfa.Fs, outputPath); exists && !cmd.Bool("force") {
 		return fmt.Errorf("output file %s %w", outputPath, errOutputExists)
 	}
 
@@ -259,7 +262,7 @@ func (mfa *CLIApp) generateManifestOperation(ctx *cli.Context) error {
 		go reportScanProgress(scanProgress, &scanWg)
 	}
 
-	err = s.ToManifest(ctx.Context, outFile, scanProgress)
+	err = s.ToManifest(ctx, outFile, scanProgress)
 
 	scanWg.Wait()
 

internal/cli/list.go

@@ -1,33 +1,35 @@
 package cli
 
 import (
+	"context"
 	"fmt"
 	"time"
 
-	"github.com/urfave/cli/v2"
+	"github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/internal/log"
 	"sneak.berlin/go/mfer/mfer"
 )
 
-func (mfa *CLIApp) listManifestOperation(ctx *cli.Context) error {
+func (mfa *CLIApp) listManifestOperation(ctx context.Context, cmd *cli.Command) error {
 	// Default to ErrorLevel for clean output
 	log.SetLevel(log.ErrorLevel)
 
-	longFormat := ctx.Bool("long")
-	print0 := ctx.Bool("print0")
+	longFormat := cmd.Bool("long")
+	print0 := cmd.Bool("print0")
 
-	pathOrURL, err := mfa.resolveManifestArg(ctx)
+	pathOrURL, err := mfa.resolveManifestArg(cmd)
 	if err != nil {
 		return fmt.Errorf("list: %w", err)
 	}
 
-	rc, err := mfa.openManifestReader(pathOrURL)
+	rc, err := mfa.openManifestReader(ctx, pathOrURL)
 	if err != nil {
 		return fmt.Errorf("list: %w", err)
 	}
 
 	defer func() { _ = rc.Close() }()
 
+	//nolint:contextcheck // mfer loads a manifest without a context
 	manifest, err := mfer.NewManifestFromReader(rc)
 	if err != nil {
 		return fmt.Errorf("list: failed to parse manifest: %w", err)

internal/cli/manifest_loader.go

@@ -9,7 +9,7 @@ import (
 	"strings"
 	"time"
 
-	"github.com/urfave/cli/v2"
+	"github.com/urfave/cli/v3"
 )
 
 // manifestFetchTimeout bounds HTTP requests made to fetch a manifest.
@@ -30,13 +30,13 @@ func isHTTPURL(s string) bool {
 
 // openManifestReader opens a manifest from a path or URL and returns a ReadCloser.
 // The caller must close the returned reader.
-func (mfa *CLIApp) openManifestReader(pathOrURL string) (io.ReadCloser, error) {
+func (mfa *CLIApp) openManifestReader(
+	ctx context.Context, pathOrURL string,
+) (io.ReadCloser, error) {
 	if isHTTPURL(pathOrURL) {
 		client := &http.Client{Timeout: manifestFetchTimeout}
 
-		req, err := http.NewRequestWithContext(
-			context.Background(), http.MethodGet, pathOrURL, nil,
-		)
+		req, err := http.NewRequestWithContext(ctx, http.MethodGet, pathOrURL, nil)
 		if err != nil {
 			return nil, fmt.Errorf("failed to fetch %s: %w", pathOrURL, err)
 		}
@@ -67,9 +67,9 @@ func (mfa *CLIApp) openManifestReader(pathOrURL string) (io.ReadCloser, error) {
 // resolveManifestArg resolves the manifest path from CLI arguments.
 // HTTP(S) URLs are returned as-is. Directories are searched for index.mf.
 // If no argument is given, the current directory is searched.
-func (mfa *CLIApp) resolveManifestArg(ctx *cli.Context) (string, error) {
-	if ctx.Args().Len() > 0 {
-		arg := ctx.Args().Get(0)
+func (mfa *CLIApp) resolveManifestArg(cmd *cli.Command) (string, error) {
+	if cmd.Args().Len() > 0 {
+		arg := cmd.Args().Get(0)
 		if isHTTPURL(arg) {
 			return arg, nil
 		}

internal/cli/mfer.go

@@ -1,6 +1,7 @@
 package cli
 
 import (
+	"context"
 	"errors"
 	"fmt"
 	"io"
@@ -8,7 +9,7 @@ import (
 	"time"
 
 	"github.com/spf13/afero"
-	"github.com/urfave/cli/v2"
+	"github.com/urfave/cli/v3"
 	"sneak.berlin/go/mfer/internal/log"
 	"sneak.berlin/go/mfer/mfer"
 )
@@ -22,8 +23,10 @@ const (
 	cmdFetch    = "fetch"
 	cmdVersion  = "version"
 
-	flagProgress = "progress"
-	flagTimeout  = "timeout"
+	flagProgress         = "progress"
+	flagTimeout          = "timeout"
+	flagDest             = "dest"
+	flagRequireSignature = "require-signature"
 
 	manifestArgsUsage = "[manifest file]"
 
@@ -52,7 +55,7 @@ type CLIApp struct {
 	gitrev      string
 	startupTime time.Time
 	exitCode    int
-	app         *cli.App
+	app         *cli.Command
 
 	Stdin  io.Reader // Standard input stream
 	Stdout io.Writer // Standard output stream for normal output
@@ -103,15 +106,15 @@ func (mfa *CLIApp) printBanner() {
 // urfave/cli reads a flag from the nearest command that defines it, so each
 // command in the lineage is asked. The highest -v count wins rather than the
 // sum, because a subcommand without its own copies reads the root's.
-func (mfa *CLIApp) setVerbosity(c *cli.Context) {
+func (mfa *CLIApp) setVerbosity(cmd *cli.Command) {
 	_, present := os.LookupEnv("MFER_DEBUG")
 
 	verbosity := 0
 	quiet := false
 
-	for _, ctx := range c.Lineage() {
-		verbosity = max(verbosity, ctx.Count("verbose"))
-		quiet = quiet || ctx.Bool("quiet")
+	for _, c := range cmd.Lineage() {
+		verbosity = max(verbosity, c.Count("verbose"))
+		quiet = quiet || c.Bool("quiet")
 	}
 
 	switch {
@@ -125,34 +128,57 @@ func (mfa *CLIApp) setVerbosity(c *cli.Context) {
 }
 
 // commonFlags returns the -v and -q flags taken by the root and by the
-// generate, check, freshen and fetch subcommands.
+// generate, check, freshen and fetch subcommands. They are local, so the
+// root's copies are not inherited by the subcommands that do not take them.
 func commonFlags() []cli.Flag {
 	return []cli.Flag{
 		&cli.BoolFlag{
 			Name:    "verbose",
 			Aliases: []string{"v"},
 			Usage:   "Increase verbosity (-v for verbose, -v -v for debug)",
-			Count:   new(int),
+			Local:   true,
 		},
 		&cli.BoolFlag{
 			Name:    "quiet",
 			Aliases: []string{"q"},
 			Usage:   "Suppress output except errors",
+			Local:   true,
 		},
 	}
 }
 
+// stopOnFirstArg returns the StopOnNthArg setting every command uses: flags
+// are read only before the command's first argument, and everything after it
+// is an argument, as with urfave/cli v2. So `mfer gen d -v` names a path "-v".
+func stopOnFirstArg() *int {
+	n := 1
+
+	return &n
+}
+
+// requireSignatureFlag returns the --require-signature flag taken by the
+// check and fetch subcommands.
+func requireSignatureFlag() *cli.StringFlag {
+	return &cli.StringFlag{
+		Name:    flagRequireSignature,
+		Aliases: []string{"S"},
+		Usage:   "Require manifest to be signed by the specified GPG key ID",
+		Sources: cli.EnvVars("MFER_REQUIRE_SIGNATURE"),
+	}
+}
+
 func (mfa *CLIApp) generateCommand() *cli.Command {
 	return &cli.Command{
-		Name:      cmdGenerate,
-		Aliases:   []string{"gen"},
-		Usage:     "Generate manifest file",
-		ArgsUsage: "[path ...]",
-		Action: func(c *cli.Context) error {
-			mfa.setVerbosity(c)
+		Name:         cmdGenerate,
+		Aliases:      []string{"gen"},
+		Usage:        "Generate manifest file",
+		ArgsUsage:    "[path ...]",
+		StopOnNthArg: stopOnFirstArg(),
+		Action: func(ctx context.Context, cmd *cli.Command) error {
+			mfa.setVerbosity(cmd)
 			mfa.printBanner()
 
-			return mfa.generateManifestOperation(c)
+			return mfa.generateManifestOperation(ctx, cmd)
 		},
 		Flags: append(commonFlags(),
 			&cli.BoolFlag{
@@ -186,12 +212,12 @@ func (mfa *CLIApp) generateCommand() *cli.Command {
 				Name:    "sign-key",
 				Aliases: []string{"s"},
 				Usage:   "GPG key ID to sign the manifest with",
-				EnvVars: []string{"MFER_SIGN_KEY"},
+				Sources: cli.EnvVars("MFER_SIGN_KEY"),
 			},
 			&cli.StringFlag{
 				Name:    "seed",
 				Usage:   "Seed value for deterministic manifest UUID",
-				EnvVars: []string{"MFER_SEED"},
+				Sources: cli.EnvVars("MFER_SEED"),
 			},
 			&cli.BoolFlag{
 				Name: "include-timestamps",
@@ -204,14 +230,15 @@ func (mfa *CLIApp) generateCommand() *cli.Command {
 
 func (mfa *CLIApp) checkCommand() *cli.Command {
 	return &cli.Command{
-		Name:      cmdCheck,
-		Usage:     "Validate files using manifest file",
-		ArgsUsage: manifestArgsUsage,
-		Action: func(c *cli.Context) error {
-			mfa.setVerbosity(c)
+		Name:         cmdCheck,
+		Usage:        "Validate files using manifest file",
+		ArgsUsage:    manifestArgsUsage,
+		StopOnNthArg: stopOnFirstArg(),
+		Action: func(ctx context.Context, cmd *cli.Command) error {
+			mfa.setVerbosity(cmd)
 			mfa.printBanner()
 
-			return mfa.checkManifestOperation(c)
+			return mfa.checkManifestOperation(ctx, cmd)
 		},
 		Flags: append(commonFlags(),
 			&cli.StringFlag{
@@ -227,28 +254,24 @@ func (mfa *CLIApp) checkCommand() *cli.Command {
 			},
 			&cli.BoolFlag{
 				Name:  "no-extra-files",
-				Usage: "Fail if files exist in base directory that are not in manifest",
-			},
-			&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"},
+				Usage: "Fail, instead of warning, if files in base directory are not in manifest",
 			},
+			requireSignatureFlag(),
 		),
 	}
 }
 
 func (mfa *CLIApp) freshenCommand() *cli.Command {
 	return &cli.Command{
-		Name:      cmdFreshen,
-		Usage:     "Update manifest with changed, new, and removed files",
-		ArgsUsage: manifestArgsUsage,
-		Action: func(c *cli.Context) error {
-			mfa.setVerbosity(c)
+		Name:         cmdFreshen,
+		Usage:        "Update manifest with changed, new, and removed files",
+		ArgsUsage:    manifestArgsUsage,
+		StopOnNthArg: stopOnFirstArg(),
+		Action: func(ctx context.Context, cmd *cli.Command) error {
+			mfa.setVerbosity(cmd)
 			mfa.printBanner()
 
-			return mfa.freshenManifestOperation(c)
+			return mfa.freshenManifestOperation(ctx, cmd)
 		},
 		Flags: append(commonFlags(),
 			&cli.StringFlag{
@@ -277,7 +300,7 @@ func (mfa *CLIApp) freshenCommand() *cli.Command {
 				Name:    "sign-key",
 				Aliases: []string{"s"},
 				Usage:   "GPG key ID to sign the manifest with",
-				EnvVars: []string{"MFER_SIGN_KEY"},
+				Sources: cli.EnvVars("MFER_SIGN_KEY"),
 			},
 			&cli.BoolFlag{
 				Name: "include-timestamps",
@@ -290,22 +313,24 @@ func (mfa *CLIApp) freshenCommand() *cli.Command {
 
 func (mfa *CLIApp) exportCommand() *cli.Command {
 	return &cli.Command{
-		Name:      cmdExport,
-		Usage:     "Export manifest contents as JSON",
-		ArgsUsage: "[manifest file or URL]",
-		Action: func(c *cli.Context) error {
-			mfa.setVerbosity(c)
+		Name:         cmdExport,
+		Usage:        "Export manifest contents as JSON",
+		ArgsUsage:    "[manifest file or URL]",
+		StopOnNthArg: stopOnFirstArg(),
+		Action: func(ctx context.Context, cmd *cli.Command) error {
+			mfa.setVerbosity(cmd)
 
-			return mfa.exportManifestOperation(c)
+			return mfa.exportManifestOperation(ctx, cmd)
 		},
 	}
 }
 
 func (mfa *CLIApp) versionCommand() *cli.Command {
 	return &cli.Command{
-		Name:  cmdVersion,
-		Usage: "Show version",
-		Action: func(_ *cli.Context) error {
+		Name:         cmdVersion,
+		Usage:        "Show version",
+		StopOnNthArg: stopOnFirstArg(),
+		Action: func(context.Context, *cli.Command) error {
 			mfa.printVersion()
 
 			return nil
@@ -315,13 +340,12 @@ func (mfa *CLIApp) versionCommand() *cli.Command {
 
 func (mfa *CLIApp) listCommand() *cli.Command {
 	return &cli.Command{
-		Name:      "list",
-		Aliases:   []string{"ls"},
-		Usage:     "List files in manifest",
-		ArgsUsage: manifestArgsUsage,
-		Action: func(c *cli.Context) error {
-			return mfa.listManifestOperation(c)
-		},
+		Name:         "list",
+		Aliases:      []string{"ls"},
+		Usage:        "List files in manifest",
+		ArgsUsage:    manifestArgsUsage,
+		StopOnNthArg: stopOnFirstArg(),
+		Action:       mfa.listManifestOperation,
 		Flags: []cli.Flag{
 			&cli.BoolFlag{
 				Name:    "long",
@@ -338,14 +362,15 @@ func (mfa *CLIApp) listCommand() *cli.Command {
 
 func (mfa *CLIApp) fetchCommand() *cli.Command {
 	return &cli.Command{
-		Name:      cmdFetch,
-		Usage:     "fetch manifest and referenced files",
-		ArgsUsage: "URL",
-		Action: func(c *cli.Context) error {
-			mfa.setVerbosity(c)
+		Name:         cmdFetch,
+		Usage:        "fetch manifest and referenced files",
+		ArgsUsage:    "URL",
+		StopOnNthArg: stopOnFirstArg(),
+		Action: func(ctx context.Context, cmd *cli.Command) error {
+			mfa.setVerbosity(cmd)
 			mfa.printBanner()
 
-			return mfa.fetchManifestOperation(c)
+			return mfa.fetchManifestOperation(ctx, cmd)
 		},
 		Flags: append(commonFlags(),
 			&cli.DurationFlag{
@@ -354,6 +379,13 @@ func (mfa *CLIApp) fetchCommand() *cli.Command {
 				Usage: "Time limit for each HTTP request, including the download " +
 					"of its body",
 			},
+			&cli.StringFlag{
+				Name:    flagDest,
+				Aliases: []string{"d"},
+				Value:   ".",
+				Usage:   "Directory to download the files and the manifest into",
+			},
+			requireSignatureFlag(),
 		),
 	}
 }
@@ -370,38 +402,40 @@ func (mfa *CLIApp) run(args []string) {
 	log.SetOutput(mfa.Stdout, mfa.Stderr)
 	log.Init()
 
-	// -v means verbose, not version. urfave/cli's built-in version flag
-	// claims -v by default, which made "mfer -v --version" fail to parse and
-	// gave -v a different meaning at the root than on the generate, check,
-	// freshen and fetch subcommands, where it means verbose. Verbose is the
-	// more common meaning of -v in tools that offer both, so -v means verbose
-	// at the root too and the version flag takes the capital -V.
+	// -v means verbose, not version, at the root as on the generate, check,
+	// freshen and fetch subcommands: verbose is the more common meaning of -v
+	// in tools that offer both. urfave/cli's built-in version flag claims -v
+	// by default, so the version flag takes the capital -V instead.
 	// VersionFlag and VersionPrinter are urfave/cli package globals; run() is
 	// serialized in tests, so assigning them here is safe.
 	cli.VersionFlag = &cli.BoolFlag{
 		Name:    cmdVersion,
 		Aliases: []string{"V"},
 		Usage:   "print the version",
+		Local:   true,
 	}
-	cli.VersionPrinter = func(_ *cli.Context) { mfa.printVersion() }
+	cli.VersionPrinter = func(*cli.Command) { mfa.printVersion() }
 
-	mfa.app = &cli.App{
-		Name:                 mfa.appname,
-		Usage:                "Manifest generator",
-		Version:              mfa.VersionString(),
-		EnableBashCompletion: true,
-		Writer:               mfa.Stdout,
-		ErrWriter:            mfa.Stderr,
-		Flags:                commonFlags(),
-		Action: func(c *cli.Context) error {
-			if c.Args().Len() > 0 {
-				return fmt.Errorf("%w %q", errUnknownCommand, c.Args().First())
+	mfa.app = &cli.Command{
+		Name:                  mfa.appname,
+		Usage:                 "Manifest generator",
+		Version:               mfa.VersionString(),
+		EnableShellCompletion: true,
+		Writer:                mfa.Stdout,
+		// v3 writes its "Incorrect Usage" line to ErrWriter; v2 wrote it to
+		// stdout, before the help, so it stays on stdout.
+		ErrWriter:    mfa.Stdout,
+		Flags:        commonFlags(),
+		StopOnNthArg: stopOnFirstArg(),
+		Action: func(_ context.Context, cmd *cli.Command) error {
+			if cmd.Args().Len() > 0 {
+				return fmt.Errorf("%w %q", errUnknownCommand, cmd.Args().First())
 			}
 
-			mfa.setVerbosity(c)
+			mfa.setVerbosity(cmd)
 			mfa.printBanner()
 
-			return cli.ShowAppHelp(c)
+			return cli.ShowRootCommandHelp(cmd)
 		},
 		Commands: []*cli.Command{
 			mfa.generateCommand(),
@@ -416,7 +450,7 @@ func (mfa *CLIApp) run(args []string) {
 
 	mfa.app.HideVersion = false
 
-	err := mfa.app.Run(args)
+	err := mfa.app.Run(context.Background(), args)
 	if err != nil {
 		mfa.exitCode = 1
 

mfer/checker.go

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

mfer/checker_test.go

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

mfer/mf.go

@@ -1,3 +0,0 @@
-package mfer
-
-//go:generate protoc ./mf.proto --go_out=paths=source_relative:.

package.json

@@ -1,6 +1,5 @@
 {
     "name": "mfer",
-    "version": "0.1.0",
     "private": true,
     "description": "Development tooling for the mfer repository: prettier, used by script/fmt and script/fmt-check to format and verify Markdown and JSON.",
     "license": "WTFPL",

script/bootstrap

@@ -13,11 +13,15 @@ set -eu
 ROOT="$(cd "$(dirname "$0")/.." && pwd -P)"
 
 # Pinned versions, 2026-07-06. Never "latest" or "lts"; exact versions.
-NODE_VERSION="22.17.0"
+# The node version is in .nvmrc, where script/prettier reads it too.
+NODE_VERSION="$(cat "$ROOT/.nvmrc")"
 NVM_VERSION="0.40.3"
 # sha256 of https://github.com/nvm-sh/nvm/archive/refs/tags/v0.40.3.tar.gz
 NVM_SHA256="5f4d6aaa04a177dc93c985e31dbc411ab6b8c6e1e21d8015dbc1372625fcd1d0"
 YARN_VERSION="1.22.22"
+# protoc v33.4, 2026-10-04, for script/generate. The sha256 of each
+# platform's release archive is in ensure_protoc.
+PROTOC_VERSION="33.4"
 
 PKGMGR=""
 SUDO=""
@@ -74,9 +78,11 @@ verify_sha256() {
     fi
 }
 
-# nvm is a bash script; run a command in a bash with nvm loaded
+# nvm is a bash script; run a command in a bash with nvm loaded.
+# --no-use: otherwise loading nvm here switches to the version .nvmrc
+# names, and fails silently while that version is not installed yet.
 nvm_sh() {
-    bash -c ". \"\$HOME/.nvm/nvm.sh\" && $*"
+    bash -c ". \"\$HOME/.nvm/nvm.sh\" --no-use && $*"
 }
 
 ensure_nvm() {
@@ -122,6 +128,48 @@ install_js_deps() {
     fi
 }
 
+# Unpack protoc's release archive for this platform into bin/protoc, after
+# checking the archive's sha256, unless bin/protoc already holds the pinned
+# version.
+ensure_protoc() {
+    dir="$ROOT/bin/protoc"
+    if [ "$("$dir/bin/protoc" --version 2>/dev/null)" = \
+        "libprotoc $PROTOC_VERSION" ]; then
+        return 0
+    fi
+    case "$(uname -s) $(uname -m)" in
+        "Linux x86_64")
+            platform="linux-x86_64"
+            sha256="c0040ea9aef08fdeb2c74ca609b18d5fdbfc44ea0042fcfbfb38860d35f7dd66"
+            ;;
+        "Linux aarch64" | "Linux arm64")
+            platform="linux-aarch_64"
+            sha256="15aa988f4a6090636525ec236a8e4b3aab41eef402751bd5bb2df6afd9b7b5a5"
+            ;;
+        "Darwin x86_64")
+            platform="osx-x86_64"
+            sha256="a49bec10d039e902d3b43e49938c42526f90011467609864fa6386ac4014da58"
+            ;;
+        "Darwin arm64")
+            platform="osx-aarch_64"
+            sha256="726297dcfed58592fd35620a5a6246ae020c39e88f3fd4cb1827df7bcf3dfcf1"
+            ;;
+        *)
+            echo "bootstrap: no protoc archive pinned for $(uname -s) $(uname -m)" >&2
+            exit 1
+            ;;
+    esac
+    if missing curl; then pkg_install curl curl curl curl; fi
+    if missing unzip; then pkg_install unzip unzip unzip unzip; fi
+    tmp="$(mktemp -d)"
+    curl -fsSL -o "$tmp/protoc.zip" \
+        "https://github.com/protocolbuffers/protobuf/releases/download/v${PROTOC_VERSION}/protoc-${PROTOC_VERSION}-${platform}.zip"
+    verify_sha256 "$tmp/protoc.zip" "$sha256"
+    rm -rf "$dir"
+    unzip -q "$tmp/protoc.zip" -d "$dir"
+    rm -rf "$tmp"
+}
+
 main() {
     cd "$ROOT"
 
@@ -132,8 +180,10 @@ main() {
     # ---- JS / docs repos ----
     # This is a Go repo, but node and yarn are required anyway: prettier
     # formats the Markdown and JSON, and script/fmt-check verifies it.
-    # The version is pinned by package.json/yarn.lock, whose integrity
-    # hashes --frozen-lockfile enforces.
+    # The version is pinned by package.json/yarn.lock: yarn checks every
+    # package it fetches against its yarn.lock integrity hash, and
+    # --frozen-lockfile fails instead of rewriting a yarn.lock that no
+    # longer matches package.json.
     ensure_node
     ensure_yarn
     install_js_deps
@@ -142,6 +192,10 @@ main() {
     if missing go; then pkg_install go golang go go; fi
     # No golangci-lint: script/lint runs it in Docker only.
     go mod download
+    # gofumpt and protoc-gen-go: bin/tools/go.mod pins them, and
+    # script/gofumpt and script/generate build them from there.
+    (cd "$ROOT/bin/tools" && go mod download)
+    ensure_protoc
 
     # ---- Python repos ----
     # if missing python3; then pkg_install python3 python3 python3 python3; fi

script/build

@@ -0,0 +1,18 @@
+#!/bin/sh
+# script/build: build the mfer binary into bin/mfer, stamped with the
+# revision `mfer version` prints, derived as script/docker derives it.
+set -eu
+
+ROOT="$(cd "$(dirname "$0")/.." && pwd -P)"
+
+main() {
+    cd "$ROOT"
+    # Own line: a failing command substitution inside an argument does
+    # not trip `set -e`, so the inline form degrades silently to an
+    # empty constant.
+    version="$(git describe --tags --always --dirty 2>/dev/null || true)"
+    [ -n "$version" ] || version="unknown"
+    go build -ldflags "-X main.Gitrev=$version" -o bin/mfer ./cmd/mfer
+}
+
+main "$@"

script/fmt

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

script/fmt-check

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

script/fmt-check-go

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

script/generate

@@ -4,26 +4,17 @@
 # regenerates mf.pb.go: it is committed, so building and checking need no
 # protoc. A test fails while mf.proto no longer matches the recorded hash.
 #
-# Needs exactly the protoc and protoc-gen-go versions named in the header of
-# the committed mf.pb.go (README.md says how to install them). Another
-# version writes a different mf.pb.go, so the script refuses to run.
+# Runs the protoc that script/bootstrap unpacks into bin/protoc, and the
+# protoc-gen-go that bin/tools/go.mod pins. Another version of either
+# writes a different mf.pb.go.
 set -eu
 
 ROOT="$(cd "$(dirname "$0")/.." && pwd -P)"
 
-# protoc 33.4 names itself v6.33.4 in the mf.pb.go header.
+# The protoc version script/bootstrap installs. protoc 33.4 names itself
+# v6.33.4 in the mf.pb.go header.
 PROTOC_VERSION="33.4"
-PROTOC_GEN_GO_VERSION="v1.36.11"
-
-# require_version <command> <its exact --version output>
-require_version() {
-    actual="$("$1" --version 2>/dev/null || true)"
-    if [ "$actual" != "$2" ]; then
-        echo "generate: needs $2 on PATH, found: ${actual:-none}" >&2
-        echo "  README.md says how to install it." >&2
-        exit 1
-    fi
-}
+PROTOC="$ROOT/bin/protoc/bin/protoc"
 
 # sha256 <file>: print "<hash>  <file>", with sha256sum, or with shasum
 # where there is no sha256sum.
@@ -39,13 +30,24 @@ sha256() {
 }
 
 main() {
+    # A bin/protoc left from before the pin moved fails here, until
+    # script/bootstrap replaces it.
+    actual="$("$PROTOC" --version 2>/dev/null || true)"
+    if [ "$actual" != "libprotoc $PROTOC_VERSION" ]; then
+        echo "generate: needs protoc $PROTOC_VERSION in bin/protoc," \
+            "found: ${actual:-none}; run script/bootstrap" >&2
+        exit 1
+    fi
+    # `go tool -n` builds protoc-gen-go from bin/tools and prints where the
+    # binary is, without running it.
+    plugin="$(cd "$ROOT/bin/tools" && go tool -n protoc-gen-go)"
+
     cd "$ROOT/mfer"
-    require_version protoc "libprotoc $PROTOC_VERSION"
-    require_version protoc-gen-go "protoc-gen-go $PROTOC_GEN_GO_VERSION"
     # Hashed before regenerating, so a missing hash tool stops the script
     # before it changes anything. Regenerating leaves mf.proto as it is.
     proto_hash="$(sha256 mf.proto)"
-    go generate .
+    "$PROTOC" --plugin=protoc-gen-go="$plugin" \
+        --go_out=paths=source_relative:. ./mf.proto
     echo "$proto_hash" >mf.proto.sha256
 }
 

script/gofumpt

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

script/prettier

@@ -18,24 +18,9 @@ usage() {
     exit 2
 }
 
-# Prefer the version pinned by package.json/yarn.lock so that CI and
-# developer machines format identically. Fall back to a prettier on PATH,
-# but say so, because a different version formats differently.
-find_prettier() {
-    if [ -x "$ROOT/node_modules/.bin/prettier" ]; then
-        printf '%s\n' "$ROOT/node_modules/.bin/prettier"
-        return 0
-    fi
-    if command -v prettier >/dev/null 2>&1; then
-        echo "prettier: node_modules/.bin/prettier is absent; using the" \
-            "prettier on PATH, which may be a different version than the" \
-            "one pinned in package.json. Run script/bootstrap to install" \
-            "the pinned version." >&2
-        command -v prettier
-        return 0
-    fi
-    return 1
-}
+# Only the prettier yarn installed from yarn.lock, never one on PATH: a
+# different version formats differently.
+PRETTIER="$ROOT/node_modules/.bin/prettier"
 
 main() {
     [ "$#" -eq 1 ] || usage
@@ -46,10 +31,26 @@ main() {
 
     cd "$ROOT"
 
-    if ! prettier_bin="$(find_prettier)"; then
-        echo "prettier: not found." >&2
-        echo "  Install it with: script/bootstrap" >&2
-        echo "  (installs the version pinned in package.json/yarn.lock)" >&2
+    # Where there is no node on PATH, script/bootstrap installs the version
+    # .nvmrc names through nvm, which keeps it in this directory.
+    if ! command -v node >/dev/null 2>&1; then
+        PATH="$HOME/.nvm/versions/node/v$(cat .nvmrc)/bin:$PATH"
+    fi
+    if ! command -v node >/dev/null 2>&1; then
+        echo "prettier: node is missing; run script/bootstrap" >&2
+        exit 1
+    fi
+
+    # node_modules keeps the old prettier after package.json moves to a new
+    # one, until script/bootstrap runs again, so compare the two.
+    if ! installed="$("$PRETTIER" --version 2>/dev/null)"; then
+        echo "prettier: not installed; run script/bootstrap" >&2
+        exit 1
+    fi
+    pinned="$(node -p 'require("./package.json").devDependencies.prettier')"
+    if [ "$installed" != "$pinned" ]; then
+        echo "prettier: package.json pins $pinned but $installed is" \
+            "installed; run script/bootstrap" >&2
         exit 1
     fi
 
@@ -62,8 +63,7 @@ main() {
     # patterns always match at least one tracked file (README.md,
     # package.json), so an empty match means the glob broke, and prettier
     # erroring out is exactly what we want rather than a vacuous pass.
-    "$prettier_bin" "$mode" "**/*.md"
-    "$prettier_bin" "$mode" "**/*.json"
+    "$PRETTIER" "$mode" "**/*.md" "**/*.json"
 }
 
 main "$@"