Add --reassign mode for fast vector recovery without disk scanning

Skips the slow folder scan (50K+ files) and upload phases — directly
re-embeds already-uploaded documents to workspaces using progress state.
Use with --reset to clear assignment tracking first.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

setup.py

@@ -11,6 +11,8 @@ Usage:
   python3 setup.py --storage-setup              # Symlink direct-uploads/ to HDD
   python3 setup.py --create-workspaces          # Create workspaces + load persona prompts
   python3 setup.py --upload-documents           # Full pipeline: upload → OCR → upload → assign
+  python3 setup.py --reassign                   # Re-assign existing docs to workspaces (no scan/upload)
+  python3 setup.py --reassign --reset           # Reset assignment tracking + re-assign all
   python3 setup.py --persona frodo              # Single persona
   python3 setup.py --cluster intel              # Intel cluster (frodo,echo,ghost,oracle,wraith,scribe,polyglot)
   python3 setup.py --cluster cyber              # Cyber cluster
@@ -623,6 +625,61 @@ def show_status(config):
 # MAIN
 # ──────────────────────────────────────────────────────────
 
+def reassign_workspaces(config, persona_list=None, reset=False, dry_run=False):
+    """Re-assign already-uploaded docs to workspaces without scanning/uploading.
+    Skips the slow folder scan — uses upload_progress.json directly."""
+    print("═══ Re-assign Workspaces ═══\n")
+
+    if not check_api(config):
+        print("  ✗ AnythingLLM API not reachable.")
+        return
+
+    progress = load_progress()
+    batch_size = config["processing"]["batch_size"]
+    delay = config["processing"]["delay_between_batches"]
+
+    if reset:
+        if persona_list:
+            for p in persona_list:
+                progress.get("workspace_docs", {}).pop(p, None)
+            print(f"  ✓ Reset assignments for: {', '.join(persona_list)}\n")
+        else:
+            progress["workspace_docs"] = {}
+            print("  ✓ Reset all workspace assignments\n")
+        save_progress(progress)
+
+    # Build persona_folders from config (no disk scan needed)
+    persona_folders = {}
+    for codename, ws_config in config["workspaces"].items():
+        if persona_list and codename not in persona_list:
+            continue
+        persona_folders[codename] = [
+            entry["path"].replace("/", "_")
+            for entry in ws_config.get("folders", [])
+        ]
+
+    uploaded = len(progress.get("uploaded_files", {}))
+    print(f"  Uploaded files in progress: {uploaded}")
+    print(f"  Personas to assign: {len(persona_folders)}\n")
+
+    if dry_run:
+        existing_ws = get_existing_workspaces(config)
+        for codename, folders in sorted(persona_folders.items()):
+            ws_name = config["workspaces"][codename]["name"]
+            slug = existing_ws.get(ws_name, {}).get("slug", "?")
+            doc_count = 0
+            for fn in folders:
+                for info in progress.get("uploaded_files", {}).values():
+                    if info.get("folder") == fn and info.get("location"):
+                        doc_count += 1
+            already = len(progress.get("workspace_docs", {}).get(codename, []))
+            print(f"  {codename} ({slug}): {doc_count} docs, {already} already assigned")
+        return
+
+    assign_to_workspaces(config, persona_folders, progress, batch_size, delay)
+    print("  Done.\n")
+
+
 def resolve_persona_list(args, config):
     """Resolve --persona / --cluster to a list of codenames."""
     if args.persona:
@@ -643,6 +700,8 @@ def main():
     parser.add_argument("--create-workspaces", action="store_true")
     parser.add_argument("--upload-documents", action="store_true")
     parser.add_argument("--all", action="store_true", help="Run all steps")
+    parser.add_argument("--reassign", action="store_true", help="Re-assign uploaded docs to workspaces (no scan/upload)")
+    parser.add_argument("--reset", action="store_true", help="Reset assignment tracking before reassign")
     parser.add_argument("--status", action="store_true")
     parser.add_argument("--persona", type=str, help="Single persona filter")
     parser.add_argument("--cluster", type=str, help="Cluster filter: intel, cyber, military, humanities, engineering")
@@ -655,7 +714,7 @@ def main():
     config = load_config()
 
     if not any([args.storage_setup, args.create_workspaces,
-                args.upload_documents, args.all, args.status]):
+                args.upload_documents, args.reassign, args.all, args.status]):
         parser.print_help()
         return
 
@@ -668,6 +727,9 @@ def main():
         storage_setup(config, dry_run=args.dry_run)
     if args.create_workspaces or args.all:
         create_workspaces(config, persona_list=persona_list, dry_run=args.dry_run)
+    if args.reassign:
+        reassign_workspaces(config, persona_list=persona_list,
+                            reset=args.reset, dry_run=args.dry_run)
     if args.upload_documents or args.all:
         upload_documents(config, persona_list=persona_list,
                          priority_filter=args.priority,