Delete CLI metadata through the replaced subtree

docs/roadmap/remediation.md

@@ -818,7 +818,14 @@ collection-size limit.
 
 ## 20. Remove Full Metadata Scans Per CLI Replacement Leaf — P2
 
-Status: [ ] Open.
+Status: [x] Complete.
+
+Completion: presence and origin removal now visits only the known replaced
+pre-CLI subtree. Partial mappings still retain omitted fields and their metadata.
+Added broad-mapping coverage with escaped keys, explicit zero/false values,
+empty-list replacement, null pointers, retained siblings, and deleted descendant
+metadata. Existing nested CLI and typed-ownership regressions and
+`./scripts/check.sh` pass.
 
 Owners: `updateOverridePresence`, `deletePresencePathSubtree`, and
 `updateOverrideOrigins` in

internal/engine/override_decode.go

@@ -2,7 +2,6 @@ package engine
 
 import (
 	"reflect"
-	"strings"
 
 	"gitea.maximumdirect.net/eric/ConfigKit/internal/document"
 )
@@ -171,17 +170,16 @@ func updateOverridePresence(presence map[string]inputPresence, existing, incomin
 		return
 	}
 
-	deletePresencePathSubtree(presence, path)
+	deletePresencePathSubtree(presence, existing, path)
 	collectPresence(incoming, path, presence)
 }
 
-func deletePresencePathSubtree(presence map[string]inputPresence, path Path) {
-	pointer := path.String()
-	for candidate := range presence {
-		if candidate == pointer || strings.HasPrefix(candidate, pointer+"/") {
-			delete(presence, candidate)
-		}
-	}
+func deletePresencePathSubtree(presence map[string]inputPresence, existing *document.Node, path Path) {
+	// The typed pre-CLI tree contains every effective descendant. Visit only
+	// the replaced subtree rather than searching unrelated metadata entries.
+	walkDocument(existing, path, func(path Path, _ *document.Node) {
+		delete(presence, path.String())
+	})
 }
 
 func updateOverrideOrigins(origins map[string]Origin, existing, incoming *document.Node, path Path, location document.Location) {
@@ -200,12 +198,9 @@ func updateOverrideOrigins(origins map[string]Origin, existing, incoming *docume
 		return
 	}
 
-	pointer := path.String()
-	for candidate := range origins {
-		if candidate == pointer || strings.HasPrefix(candidate, pointer+"/") {
-			delete(origins, candidate)
-		}
-	}
+	walkDocument(existing, path, func(path Path, _ *document.Node) {
+		delete(origins, path.String())
+	})
 	collectOverlayOrigins(origins, incoming, path, LayerCLI)
 }
 

internal/engine/override_metadata_test.go

@@ -0,0 +1,82 @@
+package engine
+
+import (
+	"fmt"
+	"reflect"
+	"strings"
+	"testing"
+)
+
+func TestBroadPartialCLIOverrideRetainsUnchangedMetadata(t *testing.T) {
+	type child struct {
+		Name string `yaml:"name"`
+	}
+	type record struct {
+		Count   int     `yaml:"count"`
+		Zero    int     `yaml:"zero"`
+		Enabled bool    `yaml:"enabled"`
+		Items   []child `yaml:"items"`
+		Maybe   *child  `yaml:"maybe"`
+	}
+	type config struct {
+		Records map[string]record `yaml:"records"`
+	}
+	var body strings.Builder
+	body.WriteString("records:\n")
+	updates := make(map[string]any)
+	for index := range 96 {
+		name := fmt.Sprintf("key/%d~", index)
+		fmt.Fprintf(&body, "  %s: {count: 9, zero: 0, enabled: false, items: [{name: old}], maybe: {name: old}}\n", name)
+		if index%2 == 0 {
+			updates[name] = map[string]any{"count": 0, "items": []any{}, "maybe": nil}
+		}
+	}
+	input := parseDocumentForDecode(t, body.String())
+	schema := mustSchemaFor[config](t)
+	decoded, issues := decodeConfiguration(schema, reflect.ValueOf(config{}), input)
+	if len(issues) != 0 {
+		t.Fatal(issues)
+	}
+	batch, diagnostics := preparePostStructuralOverrides(overridePreparationInput{root: input}, nil,
+		[]Override{{Path: Keys("records"), Value: updates, Flag: "--records"}}, nil, defaultImportLimits())
+	if len(diagnostics) != 0 {
+		t.Fatal(diagnostics)
+	}
+	result, issues := applyDecodedOverrides(schema, decoded, batch, decodeContext{})
+	if len(issues) != 0 {
+		t.Fatal(issues)
+	}
+	for index := range 96 {
+		name := fmt.Sprintf("key/%d~", index)
+		path := Keys("records", name)
+		value := result.value.Interface().(config).Records[name]
+		for _, key := range []string{"zero", "enabled"} {
+			pointer := path.Key(key).String()
+			if _, explicit := result.presence[pointer]; !explicit || result.origins[pointer].Layer != LayerBase {
+				t.Fatalf("retained explicit field lost metadata at %s", pointer)
+			}
+		}
+		if index%2 != 0 {
+			if value.Count != 9 || len(value.Items) != 1 || value.Maybe == nil || result.origins[path.Key("count").String()].Layer != LayerBase {
+				t.Fatalf("omitted record changed at %s", path)
+			}
+			continue
+		}
+		if value.Count != 0 || len(value.Items) != 0 || value.Maybe != nil {
+			t.Fatalf("CLI replacement failed at %s: %#v", path, value)
+		}
+		for _, removed := range []Path{path.Key("items").Index(0), path.Key("items").Index(0).Key("name"), path.Key("maybe").Key("name")} {
+			_, present := result.presence[removed.String()]
+			_, origin := result.origins[removed.String()]
+			if present || origin {
+				t.Fatalf("removed descendant kept metadata at %s", removed)
+			}
+		}
+		for _, key := range []string{"count", "items", "maybe"} {
+			pointer := path.Key(key).String()
+			if presence, ok := result.presence[pointer]; !ok || presence.location.SourceID != batch.overrides[0].source.ID || result.origins[pointer].Layer != LayerCLI {
+				t.Fatalf("CLI field lost metadata at %s", pointer)
+			}
+		}
+	}
+}