Add testable CLI with dependency injection and new scanner/checker packages

Major changes:
- Refactor CLI to accept injected I/O streams and filesystem (afero.Fs)
  for testing without touching the real filesystem
- Add RunOptions struct and RunWithOptions() for configurable CLI execution
- Add internal/scanner package with two-phase manifest generation:
  - Phase 1 (Enumeration): walk directories, collect metadata
  - Phase 2 (Scan): read contents, compute hashes, write manifest
- Add internal/checker package for manifest verification with progress
  reporting and channel-based result streaming
- Add mfer/builder.go for incremental manifest construction
- Add --no-extra-files flag to check command to detect files not in manifest
- Add timing summaries showing file count, size, elapsed time, and throughput
- Add comprehensive tests using afero.MemMapFs (no real filesystem access)
- Add contrib/usage.sh integration test script
- Fix banner ASCII art alignment (consistent spacing)
- Fix verbosity levels so summaries display at default log level
- Update internal/log to support configurable output writers

mfer/deserialize.go

@@ -6,12 +6,13 @@ import (
 	"errors"
 	"io"
 
+	"github.com/spf13/afero"
 	"google.golang.org/protobuf/proto"
 	"sneak.berlin/go/mfer/internal/bork"
 	"sneak.berlin/go/mfer/internal/log"
 )
 
-func (m *manifest) validateProtoOuter() error {
+func (m *manifest) deserializeInner() error {
 	if m.pbOuter.Version != MFFileOuter_VERSION_ONE {
 		return errors.New("unknown version")
 	}
@@ -25,10 +26,9 @@ func (m *manifest) validateProtoOuter() error {
 	if err != nil {
 		return err
 	}
-
-	dat, err := io.ReadAll(gzr)
 	defer gzr.Close()
 
+	dat, err := io.ReadAll(gzr)
 	if err != nil {
 		return err
 	}
@@ -38,9 +38,14 @@ func (m *manifest) validateProtoOuter() error {
 		log.Debugf("truncated data, got %d expected %d", isize, m.pbOuter.Size)
 		return bork.ErrFileTruncated
 	}
-	log.Debugf("inner data size is %d", isize)
-	log.Dump(dat)
-	log.Dump(m.pbOuter.Sha256)
+
+	// Deserialize inner message
+	m.pbInner = new(MFFile)
+	if err := proto.Unmarshal(dat, m.pbInner); err != nil {
+		return err
+	}
+
+	log.Debugf("loaded manifest with %d files", len(m.pbInner.Files))
 	return nil
 }
 
@@ -54,7 +59,8 @@ func validateMagic(dat []byte) bool {
 	return bytes.Equal(got, expected)
 }
 
-func NewFromProto(input io.Reader) (*manifest, error) {
+// NewManifestFromReader reads a manifest from an io.Reader.
+func NewManifestFromReader(input io.Reader) (*manifest, error) {
 	m := New()
 	dat, err := io.ReadAll(input)
 	if err != nil {
@@ -69,21 +75,35 @@ func NewFromProto(input io.Reader) (*manifest, error) {
 	bb := bytes.NewBuffer(dat[ml:])
 	dat = bb.Bytes()
 
-	log.Dump(dat)
-
-	// deserialize:
+	// deserialize outer:
 	m.pbOuter = new(MFFileOuter)
-	err = proto.Unmarshal(dat, m.pbOuter)
-
-	if err != nil {
+	if err := proto.Unmarshal(dat, m.pbOuter); err != nil {
 		return nil, err
 	}
 
-	ve := m.validateProtoOuter()
-	if ve != nil {
-		return nil, ve
+	// deserialize inner:
+	if err := m.deserializeInner(); err != nil {
+		return nil, err
 	}
 
-	// FIXME TODO deserialize inner
 	return m, nil
 }
+
+// NewManifestFromFile reads a manifest from a file path using the given filesystem.
+// If fs is nil, the real filesystem (OsFs) is used.
+func NewManifestFromFile(fs afero.Fs, path string) (*manifest, error) {
+	if fs == nil {
+		fs = afero.NewOsFs()
+	}
+	f, err := fs.Open(path)
+	if err != nil {
+		return nil, err
+	}
+	defer f.Close()
+	return NewManifestFromReader(f)
+}
+
+// NewFromProto is deprecated, use NewManifestFromReader instead.
+func NewFromProto(input io.Reader) (*manifest, error) {
+	return NewManifestFromReader(input)
+}