fix(ai): filter empty error assistant messages in transformMessages

When 429/500 errors occur during tool execution, empty assistant messages
with stopReason='error' get persisted. These break the tool_use -> tool_result
chain for Claude/Gemini APIs.

Added centralized filtering in transformMessages to skip assistant messages
with empty content and no tool calls. Provider-level filters remain for
defense-in-depth.

packages/coding-agent/src/core/tools/bash.ts

@@ -135,10 +135,13 @@ const defaultBashOperations: BashOperations = {
 export interface BashToolOptions {
 	/** Custom operations for command execution. Default: local shell */
 	operations?: BashOperations;
+	/** Command prefix prepended to every command (e.g., "shopt -s expand_aliases" for alias support) */
+	commandPrefix?: string;
 }
 
 export function createBashTool(cwd: string, options?: BashToolOptions): AgentTool<typeof bashSchema> {
 	const ops = options?.operations ?? defaultBashOperations;
+	const commandPrefix = options?.commandPrefix;
 
 	return {
 		name: "bash",
@@ -151,6 +154,9 @@ export function createBashTool(cwd: string, options?: BashToolOptions): AgentToo
 			signal?: AbortSignal,
 			onUpdate?,
 		) => {
+			// Apply command prefix if configured (e.g., "shopt -s expand_aliases" for alias support)
+			const resolvedCommand = commandPrefix ? `${commandPrefix}\n${command}` : command;
+
 			return new Promise((resolve, reject) => {
 				// We'll stream to a temp file if output gets large
 				let tempFilePath: string | undefined;
@@ -206,7 +212,7 @@ export function createBashTool(cwd: string, options?: BashToolOptions): AgentToo
 					}
 				};
 
-				ops.exec(command, cwd, { onData: handleData, signal, timeout })
+				ops.exec(resolvedCommand, cwd, { onData: handleData, signal, timeout })
 					.then(({ exitCode }) => {
 						// Close temp file stream
 						if (tempFileStream) {