Remove unused legacy manifest APIs

Removed:
- New(), NewFromPaths(), NewFromFS() - unused constructors
- Scan(), addFile(), addInputPath(), addInputFS() - unused scanning code
- WriteToFile(), Write() - unused output methods (Builder.Build() is used)
- GetFileCount(), GetTotalFileSize() - unused accessors
- pathIsHidden() - duplicated in internal/scanner
- ManifestScanOptions - unused options struct
- HasError(), AddError(), WithContext() - unused error/context handling
- NewFromProto() - deprecated alias
- manifestFile struct - unused internal type

Kept:
- manifest struct (simplified to just pbInner, pbOuter, output)
- NewManifestFromReader(), NewManifestFromFile() - for loading manifests
- Files() - returns files from loaded manifest
- Builder and its methods - for creating manifests

mfer/deserialize.go

@@ -61,7 +61,7 @@ func validateMagic(dat []byte) bool {
 
 // NewManifestFromReader reads a manifest from an io.Reader.
 func NewManifestFromReader(input io.Reader) (*manifest, error) {
-	m := New()
+	m := &manifest{}
 	dat, err := io.ReadAll(input)
 	if err != nil {
 		return nil, err
@@ -102,8 +102,3 @@ func NewManifestFromFile(fs afero.Fs, path string) (*manifest, error) {
 	defer func() { _ = f.Close() }()
 	return NewManifestFromReader(f)
 }
-
-// NewFromProto is deprecated, use NewManifestFromReader instead.
-func NewFromProto(input io.Reader) (*manifest, error) {
-	return NewManifestFromReader(input)
-}