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.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* (