feat: Fix progress bar hanging and improve UI responsiveness during indexing

Adds strategic yield points and direct stdout writes to prevent progress animation from freezing when the main thread is blocked by synchronous operations. Introduces 'finalizing' phase to smooth transition between parsing and resolving steps, ensuring progress reaches 100% completion.

src/index.ts

@@ -390,6 +390,16 @@ export class CodeGraph {
 
         // Resolve references to create call/import/extends edges
         if (result.success && result.filesIndexed > 0) {
+          // Signal transition so progress bar doesn't hang at "Parsing 100%"
+          options.onProgress?.({
+            phase: 'finalizing',
+            current: 0,
+            total: 0,
+          });
+
+          // Yield so shimmer worker can flush the phase transition to stdout
+          await new Promise(resolve => setImmediate(resolve));
+
           // Get count without loading all refs into memory
           const unresolvedCount = this.queries.getUnresolvedReferencesCount();
 
@@ -399,7 +409,7 @@ export class CodeGraph {
             total: unresolvedCount,
           });
 
-          this.resolveReferencesBatched((current, total) => {
+          await this.resolveReferencesBatched((current, total) => {
             options.onProgress?.({
               phase: 'resolving',
               current,
@@ -479,7 +489,7 @@ export class CodeGraph {
               total: unresolvedCount,
             });
 
-            this.resolveReferencesBatched((current, total) => {
+            await this.resolveReferencesBatched((current, total) => {
               options.onProgress?.({
                 phase: 'resolving',
                 current,
@@ -540,7 +550,7 @@ export class CodeGraph {
    * Resolve references in batches to keep memory bounded on large codebases.
    * Processes chunks of unresolved refs, persisting results after each batch.
    */
-  resolveReferencesBatched(onProgress?: (current: number, total: number) => void): ResolutionResult {
+  async resolveReferencesBatched(onProgress?: (current: number, total: number) => void): Promise<ResolutionResult> {
     return this.resolver.resolveAndPersistBatched(onProgress);
   }