fix(cli): refine OSError handling and finalize atomic write logic

Author: RbBtSn0w

src/specify_cli/__init__.py

@@ -720,13 +720,13 @@ def merge_json_files(existing_path: Path, new_content: Any, verbose: bool = Fals
                 # Handle comments (JSONC) natively with json5
                 # Note: json5 handles BOM automatically
                 existing_content = json5.load(f)
-        except (FileNotFoundError, OSError):
+        except FileNotFoundError:
             # Handle race condition where file is deleted after exists() check
             exists = False
         except Exception as e:
             if verbose:
-                console.print(f"[yellow]Warning: Could not parse existing JSON in {existing_path.name} ({e}).[/yellow]")
-            # Skip merge to preserve existing file if unparseable
+                console.print(f"[yellow]Warning: Could not read or parse existing JSON in {existing_path.name} ({e}).[/yellow]")
+            # Skip merge to preserve existing file if unparseable or inaccessible (e.g. PermissionError)
             return None
 
     # Validate template content