refactor(javascript): bind application links only at graph finish

Remove the empty application-node index from incremental projection state. The completed application graph now owns the only binding pass, and indexing returns the map directly instead of a wrapper.

Validation: 76 builder/composition tests and 19 filesystem, CLI-output, and SDK MCP trace boundary tests pass. Identity budgets and streaming/full-projection parity remain covered; no throughput improvement is claimed.

src/application/javascript/JavaScriptSemanticGraphBuilder.test.ts

@@ -355,7 +355,7 @@ const semanticNodeFor = (roleKey: string) => {
     unpacked: false,
     text: { included: true, value: "" },
   };
-  const state = createSemanticGraphProjectionState({ nodes: [] });
+  const state = createSemanticGraphProjectionState();
   return constructSemanticGraphNode(
     file,
     {
@@ -565,7 +565,7 @@ it("does not mark a file truncated when it exactly fills its budget", () => {
 it("only records node loss when the budget rejects a new identity", () => {
   // The truncation signal must record blocked node creation, not a zero
   // remaining budget: a file using exactly its share drops nothing.
-  const state = createSemanticGraphProjectionState({ nodes: [] });
+  const state = createSemanticGraphProjectionState();
   state.fileNodeBudget = 2;
   state.fileNodesDropped = false;
   const first = addSemanticGraphNode(state, semanticNodeFor("first"));

src/application/javascript/JavaScriptSemanticGraphBuilder.ts

@@ -148,7 +148,7 @@ export interface JavaScriptSemanticGraphProjection {
 /** Accumulate semantic nodes while each source IR is still file-local. */
 export const createJavaScriptSemanticGraphProjection =
   (): JavaScriptSemanticGraphProjection => {
-    const state = emptyState({ nodes: [] });
+    const state = emptyState();
     const fingerprints: JavaScriptSemanticFingerprint[] = [];
     let truncatedFiles = 0;
     const projectSourceSteps = function* (

src/application/javascript/JavaScriptSemanticGraphConstruction.ts

@@ -28,7 +28,6 @@ export interface SemanticGraphProjectionState {
   readonly unknowns: Map<string, JavaScriptSemanticGraphUnknown>;
   readonly evidenceContexts: JavaScriptSemanticEvidenceContextRegistry;
   readonly roots: Set<string>;
-  readonly applicationNodeIdsByLocation: ReadonlyMap<string, readonly string[]>;
   /**
    * Remaining node budget for the file currently being projected.
    *
@@ -69,32 +68,29 @@ export interface SemanticRelationConstructionInput {
   readonly properties?: Readonly<Record<string, JsonValue>>;
 }
 
-/** Create empty projection state with structural application-node mappings. */
-export const createSemanticGraphProjectionState = (
-  applicationGraph: Pick<JavaScriptApplicationGraph, "nodes">,
-): SemanticGraphProjectionState => {
-  const index = indexApplicationNodes(applicationGraph.nodes);
-  return {
+/** Create empty projection state; application-node links are bound at finish. */
+export const createSemanticGraphProjectionState =
+  (): SemanticGraphProjectionState => ({
     nodes: new Map(),
     relations: new Map(),
     unknowns: new Map(),
     evidenceContexts: new JavaScriptSemanticEvidenceContextRegistry(),
     roots: new Set(),
-    applicationNodeIdsByLocation: index.identifiers,
-  };
-};
+  });
 
 /** Bind retained semantic identities after all application observations exist. */
 export const bindSemanticGraphApplicationNodes = (
   state: SemanticGraphProjectionState,
   applicationGraph: Pick<JavaScriptApplicationGraph, "nodes">,
 ): void => {
-  const index = indexApplicationNodes(applicationGraph.nodes).identifiers;
+  const applicationNodeIdsByLocation = indexApplicationNodes(
+    applicationGraph.nodes,
+  );
   for (const [identifier, node] of state.nodes) {
     state.nodes.set(identifier, {
       ...node,
       application_node_ids: [
-        ...(index.get(
+        ...(applicationNodeIdsByLocation.get(
           applicationLocationKey(
             node.identity.artifact_sha256,
             node.identity.module_path,
@@ -122,7 +118,7 @@ export const constructSemanticGraphNode = (
         role_key: input.roleKey,
       },
       function_node_id: input.functionNodeId,
-      application_node_ids: matchingApplicationNodeIds(file, input, state),
+      application_node_ids: [],
       label: input.label === null ? null : javascriptDisplayText(input.label),
       properties: input.properties ?? {},
       evidence: observedSemanticEvidence(file, input.location),
@@ -247,9 +243,7 @@ export const addSemanticFallbackRoot = (
 
 const indexApplicationNodes = (
   nodes: JavaScriptApplicationGraph["nodes"],
-): {
-  readonly identifiers: ReadonlyMap<string, readonly string[]>;
-} => {
+): ReadonlyMap<string, readonly string[]> => {
   const identifiers = new Map<string, Set<string>>();
   for (const node of nodes) {
     for (const observation of node.observations) {
@@ -280,19 +274,9 @@ const indexApplicationNodes = (
       return [key, sorted];
     }),
   );
-  return { identifiers: indexed };
+  return indexed;
 };
 
-const matchingApplicationNodeIds = (
-  file: JavaScriptArtifactFile,
-  input: SemanticNodeConstructionInput,
-  state: SemanticGraphProjectionState,
-): string[] => [
-  ...(state.applicationNodeIdsByLocation.get(
-    applicationLocationKey(file.sha256, file.path, input.location),
-  ) ?? []),
-];
-
 const addApplicationNodeIdentifier = (
   identifiers: Map<string, Set<string>>,
   key: string,