From 7191ae9e62c5b2a96d2f6482baf72197b52139fc Mon Sep 17 00:00:00 2001
From: Research Assistant <research@example.com>
Date: Tue, 21 Apr 2026 23:44:45 +0800
Subject: [PATCH] feat(setup): add safety harness - never overwrite user files

- Add safe_copy() function: checks if file exists, skips if true
- Auto-backup existing files before any modification
- Safety notice at install start
- Protects Zotero DB, existing notes, and configs
---
 scripts/setup.py | 57 +++++++++++++++++++++++++++++++++---------------
 1 file changed, 40 insertions(+), 17 deletions(-)

diff --git a/scripts/setup.py b/scripts/setup.py
index 0c24c550..94ea017f 100644
--- a/scripts/setup.py
+++ b/scripts/setup.py
@@ -429,6 +429,26 @@ Generated by PaperForge setup.py on {platform.system()}
     print_success(f"AGENTS.md created at {agents_path}")
 
 
+def safe_copy(src: Path, dst: Path, backup: bool = True) -> bool:
+    """Safely copy file, never overwrite without consent.
+    
+    Returns True if copied, False if skipped.
+    """
+    if dst.exists():
+        if backup:
+            backup_path = dst.with_suffix(dst.suffix + ".backup")
+            shutil.copy2(dst, backup_path)
+            print(f"{Colors.YELLOW}[BACKUP]{Colors.ENDC} Existing file saved to {backup_path.name}")
+        
+        print(f"{Colors.YELLOW}[SKIP]{Colors.ENDC} File exists: {dst}")
+        print(f"    To update, manually delete or rename the existing file.")
+        return False
+    
+    dst.parent.mkdir(parents=True, exist_ok=True)
+    shutil.copy2(src, dst)
+    return True
+
+
 def deploy_workflow_scripts(vault_path: Path, agent_key: str, agent_config: dict, paths: dict) -> bool:
     """Deploy workflow scripts from repo to vault.
     
@@ -471,13 +491,11 @@ def deploy_workflow_scripts(vault_path: Path, agent_key: str, agent_config: dict
             continue
         
         try:
-            # Ensure parent directory exists
-            dst_path.parent.mkdir(parents=True, exist_ok=True)
-            
-            # Copy file
-            shutil.copy2(src_path, dst_path)
-            print_success(f"Deployed: {dst_rel}")
-            success_count += 1
+            if safe_copy(src_path, dst_path):
+                print_success(f"Deployed: {dst_rel}")
+                success_count += 1
+            else:
+                fail_count += 1
         except Exception as e:
             print_error(f"Failed to deploy {src_rel}: {e}")
             fail_count += 1
@@ -493,8 +511,10 @@ def deploy_workflow_scripts(vault_path: Path, agent_key: str, agent_config: dict
             for chart_file in chart_files:
                 try:
                     dst_file = chart_guide_dst / chart_file.name
-                    shutil.copy2(chart_file, dst_file)
-                    success_count += 1
+                    if safe_copy(chart_file, dst_file):
+                        success_count += 1
+                    else:
+                        fail_count += 1
                 except Exception as e:
                     print_error(f"Failed to deploy chart guide {chart_file.name}: {e}")
                     fail_count += 1
@@ -511,13 +531,10 @@ def deploy_workflow_scripts(vault_path: Path, agent_key: str, agent_config: dict
         dst_path = vault_path / dst_rel
         
         if src_path.exists():
-            try:
-                dst_path.parent.mkdir(parents=True, exist_ok=True)
-                shutil.copy2(src_path, dst_path)
+            if safe_copy(src_path, dst_path):
                 print_success(f"Deployed template: {src_rel}")
                 success_count += 1
-            except Exception as e:
-                print_error(f"Failed to deploy template {src_rel}: {e}")
+            else:
                 fail_count += 1
         else:
             print_warning(f"Template not found (skipping): {src_rel}")
@@ -534,8 +551,10 @@ def deploy_workflow_scripts(vault_path: Path, agent_key: str, agent_config: dict
             for cmd_file in command_files:
                 try:
                     dst_file = command_dst / cmd_file.name
-                    shutil.copy2(cmd_file, dst_file)
-                    success_count += 1
+                    if safe_copy(cmd_file, dst_file):
+                        success_count += 1
+                    else:
+                        fail_count += 1
                 except Exception as e:
                     print_error(f"Failed to deploy command {cmd_file.name}: {e}")
                     fail_count += 1
@@ -595,7 +614,11 @@ def main() -> int:
     except ImportError:
         print_header("Literature Workflow Installer")
     
-    print("This script will help you configure the literature research pipeline.\n")
+    print("This script will help you configure the literature research pipeline.")
+    print(f"\n{Colors.BRIGHT_YELLOW}{Colors.BOLD}[SAFETY NOTICE]{Colors.ENDC}")
+    print(f"  - This installer will NOT modify your Zotero database or existing notes")
+    print(f"  - Existing files will be backed up (.backup) before any change")
+    print(f"  - You can safely re-run this script; it will skip existing files\n")
     
     # Step 0: Select agent platform
     agent_key, agent_config = select_agent()