fix(cli): eliminate 5-minute invisible stall on 'codegraph index' by dropping and recreating the DB file instead of row-by-row DELETE

- Add CodeGraph.resetDb(): close DB, unlink the file (including -shm/-wal), then re-initialize a fresh empty database and rebuild all internal components (orchestrator, resolver, graphManager, traverser, contextBuilder)
- Replace both cg.clear() calls in the index subcommand (quiet and normal modes) with cg.resetDb()
- clear() executes DELETE FROM on 4 tables (nodes, edges, files, unresolved_refs) inside a transaction — on a 20GB DB with 10M+ rows this takes 5+ minutes before the progress bar is even created
- resetDb() deletes the DB file in milliseconds, giving the same result (empty DB) without the invisible stall

Author: jischeng

src/bin/codegraph.ts

@@ -628,9 +628,7 @@ program
       const cg = await CodeGraph.open(projectPath);
 
       if (options.quiet) {
-        // Quiet mode: no UI, just run. `index` is a full re-index, so clear the
-        // existing graph and rebuild from scratch (see the note below — #874).
-        cg.clear();
+        cg.resetDb();
         const result = await cg.indexAll();
         if (!result.success) process.exit(1);
         cg.destroy();
@@ -640,12 +638,10 @@ program
       const clack = await importESM('@clack/prompts');
       clack.intro('Indexing project');
 
-      // `index` is a FULL re-index: clear the existing graph and rebuild it from
-      // scratch so the result is identical to a fresh `init`. Without the clear,
-      // indexAll() skips every unchanged file by its content hash and reports
-      // "0 nodes, 0 edges" against the already-populated graph — which reads as
-      // "index wiped my index" (#874). For fast incremental updates use `sync`.
-      cg.clear();
+      // `index` is a FULL re-index: drop and recreate the DB from scratch so
+      // the result is identical to a fresh `init` (much faster than row-by-row
+      // DELETE on a large DB — see #874). For fast incremental updates use `sync`.
+      cg.resetDb();
 
       let result: IndexResult;
 

src/index.ts

@@ -6,6 +6,7 @@
  */
 
 import * as path from 'path';
+import * as fs from 'fs';
 import {
   Node,
   Edge,
@@ -1133,6 +1134,33 @@ export class CodeGraph {
     this.queries.clear();
   }
 
+  /**
+   * Drop and recreate the database (much faster than clear() for large DBs).
+   * Closes the current connection, deletes the DB file, and re-initializes.
+   */
+  resetDb(): void {
+    const dbPath = this.db.getPath();
+    this.db.close();
+    try {
+      fs.unlinkSync(dbPath);
+      for (const ext of ['-shm', '-wal']) {
+        const p = dbPath + ext;
+        try { fs.unlinkSync(p); } catch {}
+      }
+    } catch {}
+    this.db = DatabaseConnection.initialize(dbPath);
+    this.queries = new QueryBuilder(this.db.getDb());
+    this.orchestrator = new ExtractionOrchestrator(this.projectRoot, this.queries);
+    this.resolver = createResolver(this.projectRoot, this.queries);
+    this.graphManager = new GraphQueryManager(this.queries);
+    this.traverser = new GraphTraverser(this.queries);
+    this.contextBuilder = createContextBuilder(
+      this.projectRoot,
+      this.queries,
+      this.traverser
+    );
+  }
+
   /**
    * Alias for close() for backwards compatibility.
    * @deprecated Use close() instead