Integrate all TODO.md items into README TODO section

Add all 14 design questions (7 were missing: atime removal, path
normalization, outer SHA-256 scope, signatureString format, detached
signatures, deterministic-by-default, scanner/checker consolidation).

Add all missing implementation tasks from TODO.md phases 1-4:
- Phase 1 foundation: consolidate internal packages, deterministic
  ordering, decompression size limit, errors.Is fix, AddFile size
  verification, path invariants
- Phase 2 CLI: flag naming, URL construction, progress rate-limiting,
  deterministic flag
- Phase 3: subprocess timeouts
- Phase 4: atime deprecation

Organize design questions with sub-headers (Format Design, Signature
Design, Implementation Design) matching original TODO.md structure.

README.md

@@ -216,6 +216,8 @@ desired username for an account on this Gitea instance.
 These require @sneak's input before implementation. Answers should be added
 inline below each question.
 
+### Format Design
+
 **1. Should `MFFileChecksum` be simplified?** Currently it's a separate
 message wrapping a single `bytes multiHash` field. Since multihash
 already self-describes the algorithm, `repeated bytes hashes` directly on
@@ -233,27 +235,23 @@ even if we don't populate it yet?
 
 > _answer:_
 
-**3. Should the `manifest` type be exported?** Currently unexported with
-exported constructors (`NewManifestFromReader`, `NewManifestFromFile`).
-Consumers can't declare `var m *mfer.manifest`. Export the type, or
-define an interface?
+**3. Should `atime` be removed from the schema?** Access time is
+volatile, non-deterministic, and often disabled (`noatime`). Including it
+means two manifests of the same directory at different times will differ,
+which conflicts with the determinism goal. Remove it, or document it as
+"never set by default"?
 
 > _answer:_
 
-**4. What should the Go module path be for 1.0?** Currently
-`sneak.berlin/go/mfer` in `go.mod` but `git.eeqj.de/sneak/mfer/mfer` in
-the proto `go_package` option. Which is canonical?
+**4. What are the path normalization rules?** The proto has `string path`
+with no specification about: always forward-slash? Must be relative? No
+`..` components allowed? UTF-8 NFC vs NFD normalization (macOS vs
+Linux)? Max path length? This is a security issue (path traversal) and a
+cross-platform compatibility issue. What rules should the spec mandate?
 
 > _answer:_
 
-**5. GPG vs pure-Go crypto for signatures?** Shelling out to `gpg` is
-fragile (may not be installed, version-dependent output).
-`github.com/ProtonMail/go-crypto` provides pure-Go OpenPGP, or we could
-use Ed25519/signify (simpler, no key management). Which direction?
-
-> _answer:_
-
-**6. Should we add a version byte after the magic?** Currently
+**5. Should we add a version byte after the magic?** Currently
 `ZNAVSRFG` is followed immediately by protobuf. Adding a version byte
 (`ZNAVSRFG\x01`) would allow future framing changes without requiring
 protobuf parsing to detect the version. `MFFileOuter.Version` serves
@@ -262,13 +260,75 @@ extra byte?
 
 > _answer:_
 
-**7. Should we add a length-prefix after the magic?** Protobuf is not
+**6. Should we add a length-prefix after the magic?** Protobuf is not
 self-delimiting. If we ever want to concatenate manifests or append data
 after the protobuf, the current framing is insufficient. Add a varint or
 fixed-width length-prefix?
 
 > _answer:_
 
+### Signature Design
+
+**7. What does the outer SHA-256 hash cover — compressed or uncompressed
+data?** The code currently hashes compressed data (good for verifying
+before decompression), but this should be explicitly documented. Which is
+the intended behavior?
+
+> _answer:_
+
+**8. Should `signatureString()` sign raw bytes instead of a hex-encoded
+string?** Currently the canonical string is `MAGIC-UUID-MULTIHASH` with
+hex encoding, which adds a transformation layer. Signing the raw `sha256`
+bytes (or compressed `innerMessage` directly) would be simpler. Keep the
+string format or switch to raw bytes?
+
+> _answer:_
+
+**9. Should we support detached signature files (`.mf.sig`)?** Embedded
+signatures are better for single-file distribution. Detached `.mf.sig`
+files follow the familiar `SHASUMS`/`SHASUMS.asc` pattern and are
+simpler for HTTP serving. Support both modes?
+
+> _answer:_
+
+**10. GPG vs pure-Go crypto for signatures?** Shelling out to `gpg` is
+fragile (may not be installed, version-dependent output).
+`github.com/ProtonMail/go-crypto` provides pure-Go OpenPGP, or we could
+use Ed25519/signify (simpler, no key management). Which direction?
+
+> _answer:_
+
+### Implementation Design
+
+**11. Should manifests be deterministic by default?** This means: sort
+file entries by path, omit `createdAt` timestamp (or make it opt-in), no
+`atime`. Should determinism be the default, with a
+`--include-timestamps` flag to opt in?
+
+> _answer:_
+
+**12. Should we consolidate or keep both scanner/checker
+implementations?** There are two parallel implementations:
+`mfer/scanner.go` + `mfer/checker.go` (typed with `FileSize`,
+`RelFilePath`) and `internal/scanner/` + `internal/checker/` (raw
+`int64`, `string`). The `mfer/` versions are superior. Delete the
+`internal/` versions?
+
+> _answer:_
+
+**13. Should the `manifest` type be exported?** Currently unexported with
+exported constructors (`NewManifestFromReader`, `NewManifestFromFile`).
+Consumers can't declare `var m *mfer.manifest`. Export the type, or
+define an interface?
+
+> _answer:_
+
+**14. What should the Go module path be for 1.0?** Currently
+`sneak.berlin/go/mfer` in `go.mod` but `git.eeqj.de/sneak/mfer/mfer` in
+the proto `go_package` option. Which is canonical?
+
+> _answer:_
+
 ## Implementation Tasks
 
 ### Repo Infrastructure
@@ -282,27 +342,55 @@ fixed-width length-prefix?
 
 - [ ] Resolve proto `go_package` path inconsistency
       (`git.eeqj.de/sneak/mfer/mfer` vs `sneak.berlin/go/mfer`)
+- [ ] Specify path invariants — add proto comments requiring UTF-8,
+      forward-slash, relative paths, no `..`, no leading `/`; validate
+      in `Builder.AddFile` and `Builder.AddFileWithHash` (pending design
+      question answer)
+- [ ] Remove or deprecate `atime` from proto (pending design question
+      answer)
 - [ ] Reserve `optional uint32 mode = 305` in `MFFilePath` for future
       file permissions (pending design question answer)
 - [ ] Add version byte after magic — `ZNAVSRFG\x01` for format version
       1 (pending design question answer)
+- [ ] Write format specification document — separate from README:
+      magic, outer structure, compression, inner structure, path
+      invariants, signature scheme, canonical serialization
 
 ### Library
 
+- [ ] Delete `internal/scanner/` and `internal/checker/` — consolidate
+      on `mfer/` package versions; update CLI code (pending design
+      question answer)
+- [ ] Add deterministic file ordering — sort entries by path
+      (lexicographic, byte-order) in `Builder.Build()`; add test
+      asserting byte-identical output from two runs
+- [ ] Add decompression size limit — `io.LimitReader` in
+      `deserializeInner()` with `m.pbOuter.Size` as bound
+- [ ] Fix `errors.Is` dead code in checker — replace with
+      `os.IsNotExist(err)` or `errors.Is(err, fs.ErrNotExist)`
+- [ ] Fix `AddFile` to verify size — check `totalRead == size` after
+      reading, return error on mismatch
 - [ ] Export the `manifest` type or define a public interface (pending
       design question answer) — currently consumers cannot hold a reference
       to a loaded manifest in their own type declarations
 - [ ] Replace GPG subprocess calls with pure-Go crypto (pending design
       question answer) — current implementation shells out to `gpg` which
       may not be installed
+- [ ] Add timeout to any remaining subprocess calls
 
 ### CLI
 
+- [ ] Fix flag naming — all CLI flags should use kebab-case as primary
+      (`--include-dotfiles`, `--follow-symlinks`)
+- [ ] Fix URL construction in fetch — use `BaseURL.JoinPath()` or
+      `url.JoinPath()` instead of string concatenation
+- [ ] Add progress rate-limiting to Checker — throttle to once per
+      second, matching Scanner
+- [ ] Add `--deterministic` flag or make it default — omit `createdAt`,
+      sort files (pending design question answer)
 - [ ] Wire `--version` flag properly (currently only a `version`
       subcommand exists; top-level `--version` shows urfave/cli generic
       output)
-- [ ] Add `--deterministic` flag documentation — deterministic output is
-      the default, but this isn't obvious from CLI help
 - [ ] Add retry logic to `fetch` — currently no retries on transient
       HTTP errors; needs exponential backoff
 - [ ] `fetch` command uses bare `http.Get` with no timeout — needs
@@ -319,9 +407,8 @@ fixed-width length-prefix?
 
 ### Documentation
 
-- [ ] Write standalone format specification document — `FORMAT.md`
-      exists but should be promoted to the primary spec reference; README
-      should link to it more prominently
+- [ ] Promote `FORMAT.md` as primary spec reference; README should link
+      to it more prominently
 - [ ] Audit and update all error messages for consistency and
       helpfulness
 - [ ] Document the signature scheme more thoroughly (canonical string