diff --git a/cue/build.go b/cue/build.go
index 44730dd..9c603af 100644
--- a/cue/build.go
+++ b/cue/build.go
@@ -33,14 +33,16 @@
 // Deprecated: use Context.
 type Runtime runtime.Runtime
 
-func (r *Runtime) index() *runtime.Runtime {
+func (r *Runtime) runtime() *runtime.Runtime {
 	rt := (*runtime.Runtime)(r)
 	rt.Init()
 	return rt
 }
 
+type hiddenRuntime = Runtime
+
 func (r *Runtime) complete(p *build.Instance, v *adt.Vertex) (*Instance, error) {
-	idx := r.index()
+	idx := r.runtime()
 	inst := getImportFromBuild(idx, p, v)
 	inst.ImportPath = p.ImportPath
 	if inst.Err != nil {
@@ -55,9 +57,9 @@
 // Build to allow importing non-builtin packages.
 //
 // Deprecated: use Parse or ParseBytes. The use of Instance is being phased out.
-func (r *Runtime) Compile(filename string, source interface{}) (*Instance, error) {
+func (r *hiddenRuntime) Compile(filename string, source interface{}) (*Instance, error) {
 	cfg := &runtime.Config{Filename: filename}
-	v, p := r.index().Compile(cfg, source)
+	v, p := r.runtime().Compile(cfg, source)
 	return r.complete(p, v)
 }
 
@@ -65,8 +67,8 @@
 // import builtin packages. Use Build to allow importing non-builtin packages.
 //
 // Deprecated: use BuildFile. The use of Instance is being phased out.
-func (r *Runtime) CompileFile(file *ast.File) (*Instance, error) {
-	v, p := r.index().CompileFile(nil, file)
+func (r *hiddenRuntime) CompileFile(file *ast.File) (*Instance, error) {
+	v, p := r.runtime().CompileFile(nil, file)
 	return r.complete(p, v)
 }
 
@@ -75,8 +77,8 @@
 // packages.
 //
 // Deprecated: use BuildExpr. The use of Instance is being phased out.
-func (r *Runtime) CompileExpr(expr ast.Expr) (*Instance, error) {
-	v, p, err := r.index().CompileExpr(nil, expr)
+func (r *hiddenRuntime) CompileExpr(expr ast.Expr) (*Instance, error) {
+	v, p, err := r.runtime().CompileExpr(nil, expr)
 	if err != nil {
 		return nil, err
 	}
@@ -89,17 +91,17 @@
 //
 // Deprecated: use ParseString or ParseBytes.  The use of Instance is being
 // phased out.
-func (r *Runtime) Parse(name string, source interface{}) (*Instance, error) {
+func (r *hiddenRuntime) Parse(name string, source interface{}) (*Instance, error) {
 	return r.Compile(name, source)
 }
 
 // Build creates an Instance from the given build.Instance. A returned Instance
 // may be incomplete, in which case its Err field is set.
 //
-// Deprecated: use Runtime.BuildInstance. The use of Instance is being phased
+// Deprecated: use Context.BuildInstance. The use of Instance is being phased
 // out.
-func (r *Runtime) Build(p *build.Instance) (*Instance, error) {
-	v, _ := r.index().Build(nil, p)
+func (r *hiddenRuntime) Build(p *build.Instance) (*Instance, error) {
+	v, _ := r.runtime().Build(nil, p)
 	return r.complete(p, v)
 }
 
@@ -109,7 +111,7 @@
 // Example:
 //	inst := cue.Build(load.Instances(args))
 //
-// Deprecated: use Runtime.BuildInstances. The use of Instance is being phased
+// Deprecated: use Context.BuildInstances. The use of Instance is being phased
 // out.
 func Build(instances []*build.Instance) []*Instance {
 	if len(instances) == 0 {
@@ -120,8 +122,8 @@
 	return a
 }
 
-func (r *Runtime) build(instances []*build.Instance) ([]*Instance, error) {
-	index := r.index()
+func (r *hiddenRuntime) build(instances []*build.Instance) ([]*Instance, error) {
+	index := r.runtime()
 
 	loaded := []*Instance{}
 
@@ -142,7 +144,7 @@
 // Any references must be resolved beforehand.
 //
 // Deprecated: use CompileExpr
-func (r *Runtime) FromExpr(expr ast.Expr) (*Instance, error) {
+func (r *hiddenRuntime) FromExpr(expr ast.Expr) (*Instance, error) {
 	return r.CompileFile(&ast.File{
 		Decls: []ast.Decl{&ast.EmbedDecl{Expr: expr}},
 	})
diff --git a/cue/context.go b/cue/context.go
index 1ff8163..63eaa13 100644
--- a/cue/context.go
+++ b/cue/context.go
@@ -38,13 +38,13 @@
 // to create a new Context.
 type Context runtime.Runtime
 
-func (c *Context) index() *runtime.Runtime {
+func (c *Context) runtime() *runtime.Runtime {
 	rt := (*runtime.Runtime)(c)
 	return rt
 }
 
 func (c *Context) ctx() *adt.OpContext {
-	return newContext(c.index())
+	return newContext(c.runtime())
 }
 
 // Context reports the Context with which this value was created.
@@ -92,7 +92,7 @@
 // error occurred.
 func (c *Context) BuildInstance(i *build.Instance, options ...BuildOption) Value {
 	cfg := c.parseOptions(options)
-	v, err := c.index().Build(&cfg, i)
+	v, err := c.runtime().Build(&cfg, i)
 	if err != nil {
 		return c.makeError(err)
 	}
@@ -113,7 +113,7 @@
 	var errs errors.Error
 	var a []Value
 	for _, b := range instances {
-		v, err := c.index().Build(nil, b)
+		v, err := c.runtime().Build(nil, b)
 		if err != nil {
 			errs = errors.Append(errs, err)
 		}
@@ -128,7 +128,7 @@
 // error occurred.
 func (c *Context) BuildFile(f *ast.File, options ...BuildOption) Value {
 	cfg := c.parseOptions(options)
-	return c.compile(c.index().CompileFile(&cfg, f))
+	return c.compile(c.runtime().CompileFile(&cfg, f))
 }
 
 func (c *Context) compile(v *adt.Vertex, p *build.Instance) Value {
@@ -144,7 +144,7 @@
 // error occurred.
 func (c *Context) BuildExpr(x ast.Expr, options ...BuildOption) Value {
 	cfg := c.parseOptions(options)
-	v, p, err := c.index().CompileExpr(&cfg, x)
+	v, p, err := c.runtime().CompileExpr(&cfg, x)
 	if err != nil {
 		return c.makeError(p.Err)
 	}
@@ -157,7 +157,7 @@
 // error occurred.
 func (c *Context) CompileString(src string, options ...BuildOption) Value {
 	cfg := c.parseOptions(options)
-	return c.compile(c.index().Compile(&cfg, src))
+	return c.compile(c.runtime().Compile(&cfg, src))
 }
 
 // ParseString parses and build a Value from the given source bytes.
@@ -166,7 +166,7 @@
 // error occurred.
 func (c *Context) CompileBytes(b []byte, options ...BuildOption) Value {
 	cfg := c.parseOptions(options)
-	return c.compile(c.index().Compile(&cfg, b))
+	return c.compile(c.runtime().Compile(&cfg, b))
 }
 
 // TODO: fs.FS or custom wrapper?
@@ -183,7 +183,7 @@
 // }
 
 func (c *Context) make(v *adt.Vertex) Value {
-	return newValueRoot(c.index(), newContext(c.index()), v)
+	return newValueRoot(c.runtime(), newContext(c.runtime()), v)
 }
 
 // An EncodeOption defines options for the various encoding-related methods of
@@ -214,7 +214,7 @@
 func (c *Context) Encode(x interface{}, option ...EncodeOption) Value {
 	switch v := x.(type) {
 	case adt.Value:
-		return newValueRoot(c.index(), c.ctx(), v)
+		return newValueRoot(c.runtime(), c.ctx(), v)
 	}
 	var options encodeOptions
 	options.process(option)
diff --git a/cue/instance.go b/cue/instance.go
index 02dc82a..df01f0a 100644
--- a/cue/instance.go
+++ b/cue/instance.go
@@ -61,6 +61,8 @@
 	// complete bool // for cycle detection
 }
 
+type hiddenInstance = Instance
+
 func addInst(x *runtime.Runtime, p *Instance) *Instance {
 	if p.inst == nil {
 		p.inst = &build.Instance{
@@ -260,7 +262,7 @@
 // Doc returns the package comments for this instance.
 //
 // Deprecated: use inst.Value().Doc()
-func (inst *Instance) Doc() []*ast.CommentGroup {
+func (inst *hiddenInstance) Doc() []*ast.CommentGroup {
 	return inst.Value().Doc()
 }
 
@@ -276,7 +278,7 @@
 // Eval evaluates an expression within an existing instance.
 //
 // Expressions may refer to builtin packages if they can be uniquely identified.
-func (inst *Instance) Eval(expr ast.Expr) Value {
+func (inst *hiddenInstance) Eval(expr ast.Expr) Value {
 	ctx := newContext(inst.index)
 	v := inst.root
 	v.Finalize(ctx)
@@ -311,7 +313,9 @@
 // Build creates a new instance from the build instances, allowing unbound
 // identifier to bind to the top-level field in inst. The top-level fields in
 // inst take precedence over predeclared identifier and builtin functions.
-func (inst *Instance) Build(p *build.Instance) *Instance {
+//
+// Deprecated: use Context.Build
+func (inst *hiddenInstance) Build(p *build.Instance) *Instance {
 	p.Complete()
 
 	idx := inst.index
@@ -350,14 +354,18 @@
 // exist. The Err method reports if any error occurred during evaluation. The
 // empty path returns the top-level configuration struct. Use LookupDef for definitions or LookupField for
 // any kind of field.
-func (inst *Instance) Lookup(path ...string) Value {
+//
+// Deprecated: use Value.LookupPath
+func (inst *hiddenInstance) Lookup(path ...string) Value {
 	return inst.value().Lookup(path...)
 }
 
 // LookupDef reports the definition with the given name within struct v. The
 // Exists method of the returned value will report false if the definition did
 // not exist. The Err method reports if any error occurred during evaluation.
-func (inst *Instance) LookupDef(path string) Value {
+//
+// Deprecated: use Value.LookupPath
+func (inst *hiddenInstance) LookupDef(path string) Value {
 	return inst.value().LookupDef(path)
 }
 
@@ -368,7 +376,9 @@
 //
 // Deprecated: this API does not work with new-style definitions. Use
 // FieldByName defined on inst.Value().
-func (inst *Instance) LookupField(path ...string) (f FieldInfo, err error) {
+//
+// Deprecated: use Value.LookupPath
+func (inst *hiddenInstance) LookupField(path ...string) (f FieldInfo, err error) {
 	v := inst.value()
 	for _, k := range path {
 		s, err := v.Struct()
@@ -396,7 +406,7 @@
 // Runtime.
 //
 // Deprecated: use Value.FillPath()
-func (inst *Instance) Fill(x interface{}, path ...string) (*Instance, error) {
+func (inst *hiddenInstance) Fill(x interface{}, path ...string) (*Instance, error) {
 	v := inst.Value().Fill(x, path...)
 
 	inst = addInst(inst.index, &Instance{
diff --git a/cue/marshal.go b/cue/marshal.go
index f877b77..43ca6d4 100644
--- a/cue/marshal.go
+++ b/cue/marshal.go
@@ -140,7 +140,7 @@
 			return p
 		}
 		// TODO: support exporting instance
-		file, _ := export.Def(r.index(), i.inst.ID(), i.root)
+		file, _ := export.Def(r.runtime(), i.inst.ID(), i.root)
 		imports := []string{}
 		file.VisitImports(func(i *ast.ImportDecl) {
 			for _, spec := range i.Specs {
@@ -190,7 +190,7 @@
 		p := len(staged) - 1
 
 		for _, imp := range imports {
-			i := getImportFromPath(r.index(), imp)
+			i := getImportFromPath(r.runtime(), imp)
 			if i == nil || !strings.Contains(imp, ".") {
 				continue // a builtin package.
 			}
diff --git a/cue/types.go b/cue/types.go
index 86ac88e..e06cef0 100644
--- a/cue/types.go
+++ b/cue/types.go
@@ -94,8 +94,10 @@
 	features []adt.Feature
 }
 
+type hiddenStructValue = structValue
+
 // Len reports the number of fields in this struct.
-func (o *structValue) Len() int {
+func (o *hiddenStructValue) Len() int {
 	if o.obj == nil {
 		return 0
 	}
@@ -103,12 +105,12 @@
 }
 
 // At reports the key and value of the ith field, i < o.Len().
-func (o *structValue) At(i int) (key string, v Value) {
+func (o *hiddenStructValue) At(i int) (key string, v Value) {
 	f := o.features[i]
 	return o.v.idx.LabelStr(f), newChildValue(o, i)
 }
 
-func (o *structValue) at(i int) (v *adt.Vertex, isOpt bool) {
+func (o *hiddenStructValue) at(i int) (v *adt.Vertex, isOpt bool) {
 	f := o.features[i]
 	arc := o.obj.Lookup(f)
 	if arc == nil {
@@ -125,7 +127,7 @@
 
 // Lookup reports the field for the given key. The returned Value is invalid
 // if it does not exist.
-func (o *structValue) Lookup(key string) Value {
+func (o *hiddenStructValue) Lookup(key string) Value {
 	f := o.v.idx.StrLabel(key)
 	i := 0
 	len := o.Len()
@@ -336,7 +338,7 @@
 
 // Decimal is for internal use only. The Decimal type that is returned is
 // subject to change.
-func (v Value) Decimal() (d *internal.Decimal, err error) {
+func (v hiddenValue) Decimal() (d *internal.Decimal, err error) {
 	n, err := v.getNum(adt.NumKind)
 	if err != nil {
 		return nil, err
@@ -827,7 +829,7 @@
 //
 // TODO: get rid of this somehow. Probably by including a FieldInfo struct
 // or the like.
-func (v Value) Label() (string, bool) {
+func (v hiddenValue) Label() (string, bool) {
 	if v.v == nil || v.v.Label == 0 {
 		return "", false
 	}
@@ -1037,7 +1039,7 @@
 // Source returns a non-nil value.
 //
 // Deprecated: use Expr.
-func (v Value) Split() []Value {
+func (v hiddenValue) Split() []Value {
 	if v.v == nil {
 		return nil
 	}
@@ -1085,7 +1087,7 @@
 // when the value is not a list or struct.
 //
 // Deprecated: use Allows and Kind/IncompleteKind.
-func (v Value) IsClosed() bool {
+func (v hiddenValue) IsClosed() bool {
 	if v.v == nil {
 		return false
 	}
@@ -1207,7 +1209,7 @@
 // Elem returns the value of undefined element types of lists and structs.
 //
 // Deprecated: use LookupPath in combination with "AnyString" or "AnyIndex".
-func (v Value) Elem() (Value, bool) {
+func (v hiddenValue) Elem() (Value, bool) {
 	sel := AnyString
 	if v.v.IsList() {
 		sel = AnyIndex
@@ -1283,7 +1285,7 @@
 
 // Reader returns a new Reader if v is a string or bytes type and an error
 // otherwise.
-func (v Value) Reader() (io.Reader, error) {
+func (v hiddenValue) Reader() (io.Reader, error) {
 	v, _ = v.Default()
 	ctx := v.ctx()
 	switch x := v.eval(ctx).(type) {
@@ -1358,7 +1360,7 @@
 
 // Struct returns the underlying struct of a value or an error if the value
 // is not a struct.
-func (v Value) Struct() (*Struct, error) {
+func (v hiddenValue) Struct() (*Struct, error) {
 	// TODO: deprecate
 	ctx := v.ctx()
 	obj, err := v.structValOpts(ctx, options{})
@@ -1383,6 +1385,8 @@
 	structValue
 }
 
+type hiddenStruct = Struct
+
 // FieldInfo contains information about a struct field.
 type FieldInfo struct {
 	Selector string
@@ -1395,12 +1399,12 @@
 	IsHidden     bool
 }
 
-func (s *Struct) Len() int {
+func (s *hiddenStruct) Len() int {
 	return s.structValue.Len()
 }
 
 // field reports information about the ith field, i < o.Len().
-func (s *Struct) Field(i int) FieldInfo {
+func (s *hiddenStruct) Field(i int) FieldInfo {
 	a, opt := s.at(i)
 	ctx := s.v.ctx()
 
@@ -1413,7 +1417,7 @@
 // FieldByName looks up a field for the given name. If isIdent is true, it will
 // look up a definition or hidden field (starting with `_` or `_#`). Otherwise
 // it interprets name as an arbitrary string for a regular field.
-func (s *Struct) FieldByName(name string, isIdent bool) (FieldInfo, error) {
+func (s *hiddenStruct) FieldByName(name string, isIdent bool) (FieldInfo, error) {
 	f := s.v.idx.Label(name, isIdent)
 	for i, a := range s.features {
 		if a == f {
@@ -1424,7 +1428,7 @@
 }
 
 // Fields creates an iterator over the Struct's fields.
-func (s *Struct) Fields(opts ...Option) *Iterator {
+func (s *hiddenStruct) Fields(opts ...Option) *Iterator {
 	iter, _ := s.v.Fields(opts...)
 	return iter
 }
@@ -1456,7 +1460,7 @@
 //
 // Deprecated: use LookupPath. At some point before v1.0.0, this method will
 // be removed to be reused eventually for looking up a selector.
-func (v Value) Lookup(path ...string) Value {
+func (v hiddenValue) Lookup(path ...string) Value {
 	ctx := v.ctx()
 	for _, k := range path {
 		// TODO(eval) TODO(error): always search in full data and change error
@@ -1500,7 +1504,7 @@
 // LookupDef is equal to LookupPath(MakePath(Def(name))).
 //
 // Deprecated: use LookupPath.
-func (v Value) LookupDef(name string) Value {
+func (v hiddenValue) LookupDef(name string) Value {
 	return v.LookupPath(MakePath(Def(name)))
 }
 
@@ -1511,7 +1515,7 @@
 // it interprets name as an arbitrary string for a regular field.
 //
 // Deprecated: use LookupPath.
-func (v Value) FieldByName(name string, isIdent bool) (f FieldInfo, err error) {
+func (v hiddenValue) FieldByName(name string, isIdent bool) (f FieldInfo, err error) {
 	s, err := v.Struct()
 	if err != nil {
 		return f, err
@@ -1522,7 +1526,7 @@
 // LookupField reports information about a field of v.
 //
 // Deprecated: use LookupPath
-func (v Value) LookupField(name string) (FieldInfo, error) {
+func (v hiddenValue) LookupField(name string) (FieldInfo, error) {
 	s, err := v.Struct()
 	if err != nil {
 		// TODO: return a Value at the same location and a new error?
@@ -1560,7 +1564,7 @@
 // to x in the newly created value. The resulting value is not validated.
 //
 // Deprecated: use FillPath.
-func (v Value) Fill(x interface{}, path ...string) Value {
+func (v hiddenValue) Fill(x interface{}, path ...string) Value {
 	if v.v == nil {
 		return v
 	}
@@ -1634,7 +1638,7 @@
 // given its name.
 //
 // Deprecated: use LookupPath in combination with using optional selectors.
-func (v Value) Template() func(label string) Value {
+func (v hiddenValue) Template() func(label string) Value {
 	if v.v == nil {
 		return nil
 	}
@@ -1690,7 +1694,7 @@
 // By default, Subsumes tests whether two values are compatible
 // Value v and w must be obtained from the same build.
 // TODO: remove this requirement.
-func (v Value) Subsumes(w Value) bool {
+func (v hiddenValue) Subsumes(w Value) bool {
 	ctx := v.ctx()
 	p := subsume.Profile{Defaults: true}
 	return p.Check(ctx, v.v, w.v)
@@ -1840,7 +1844,7 @@
 // only return a reference if the index resolves to a concrete value.
 //
 // Deprecated: use ReferencePath
-func (v Value) Reference() (inst *Instance, path []string) {
+func (v hiddenValue) Reference() (inst *Instance, path []string) {
 	root, p := v.ReferencePath()
 	if !root.Exists() {
 		return nil, nil
@@ -2032,8 +2036,6 @@
 }
 
 // Hidden indicates that definitions and hidden fields should be included.
-//
-// Deprecated: Hidden fields are deprecated.
 func Hidden(include bool) Option {
 	return func(p *options) {
 		p.hasHidden = true
diff --git a/encoding/json/json.go b/encoding/json/json.go
index a319222..5289b39 100644
--- a/encoding/json/json.go
+++ b/encoding/json/json.go
@@ -55,6 +55,8 @@
 
 // Decode parses JSON-encoded data to a CUE value, using path for position
 // information.
+//
+// Deprecated: use Extract and build using cue.Context.BuildExpr.
 func Decode(r *cue.Runtime, path string, data []byte) (*cue.Instance, error) {
 	expr, err := extract(path, data)
 	if err != nil {
@@ -80,6 +82,8 @@
 // NewDecoder configures a JSON decoder. The path is used to associate position
 // information with each node. The runtime may be nil if the decoder
 // is only used to extract to CUE ast objects.
+//
+// The runtime may be nil if Decode isn't used.
 func NewDecoder(r *cue.Runtime, path string, src io.Reader) *Decoder {
 	return &Decoder{
 		r:      r,
@@ -129,6 +133,8 @@
 
 // Decode converts the current JSON value to a CUE instance. It returns io.EOF
 // if the input has been exhausted.
+//
+// Deprecated: use Extract and build with cue.Context.BuildExpr.
 func (d *Decoder) Decode() (*cue.Instance, error) {
 	expr, err := d.Extract()
 	if err != nil {
diff --git a/encoding/yaml/yaml.go b/encoding/yaml/yaml.go
index 0787077..1e356e0 100644
--- a/encoding/yaml/yaml.go
+++ b/encoding/yaml/yaml.go
@@ -66,6 +66,8 @@
 
 // Decode converts a YAML file to a CUE value. Streams are returned as a list
 // of the streamed values.
+//
+// Deprecate: use Extract and build the File with cue.Context.BuildFile.
 func Decode(r *cue.Runtime, filename string, src interface{}) (*cue.Instance, error) {
 	file, err := Extract(filename, src)
 	if err != nil {