refactor CLI command modules and synchronize docs

src/vlm/executor.py

@@ -93,8 +93,17 @@ class ExecutionEngine:
         transaction_log = None
         if mode == "execute":
             log_path = Path.home() / ".vlm" / "transaction.json"
-            transaction_log = TransactionLog(log_path)
-            transaction_log.start_transaction(plan)
+            try:
+                transaction_log = TransactionLog(log_path)
+                transaction_log.start_transaction(plan)
+            except OSError as exc:
+                log_operation(
+                    self.logger,
+                    logging.WARNING,
+                    f"Transaction log disabled (cannot write {log_path}): {exc}",
+                    operation_type="execute",
+                )
+                transaction_log = None
         
         # Execute all operations
         results = []
@@ -105,9 +114,18 @@ class ExecutionEngine:
             # Update transaction and state logs in execute mode
             if mode == "execute":
                 if transaction_log:
-                    transaction_log.mark_operation_complete(
-                        i, result.success, result.error_message
-                    )
+                    try:
+                        transaction_log.mark_operation_complete(
+                            i, result.success, result.error_message
+                        )
+                    except OSError as exc:
+                        log_operation(
+                            self.logger,
+                            logging.WARNING,
+                            f"Failed to update transaction log: {exc}",
+                            operation_type="execute",
+                        )
+                        transaction_log = None
                 
                 # Update file state if successful and not a no-op
                 if result.success and operation.operation_type != "no-op" and self.state_manager:
@@ -126,7 +144,15 @@ class ExecutionEngine:
         if mode == "execute":
             if transaction_log:
                 status = "completed" if all(r.success for r in results) else "failed"
-                transaction_log.complete_transaction(status=status)
+                try:
+                    transaction_log.complete_transaction(status=status)
+                except OSError as exc:
+                    log_operation(
+                        self.logger,
+                        logging.WARNING,
+                        f"Failed to finalize transaction log: {exc}",
+                        operation_type="execute",
+                    )
             if self.state_manager:
                 self.state_manager.save()
         
@@ -189,6 +215,22 @@ class ExecutionEngine:
                 executed_at=executed_at
             )
 
+        # Handle preserve-directory operations
+        if operation.operation_type == "preserve-directory":
+            log_operation(
+                self.logger,
+                logging.DEBUG,
+                f"Preserving directory: {operation.reason}",
+                operation_type="execute",
+                file_path=operation.source_path
+            )
+            return OperationResult(
+                operation=operation,
+                success=True,
+                error_message=None,
+                executed_at=executed_at
+            )
+
         # Handle quarantine operations (no destination_path; use QuarantineManager)
         if operation.operation_type == "quarantine":
             if not self._quarantine_manager: