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/agent-session.ts

@@ -1740,13 +1740,17 @@ export class AgentSession {
 	): Promise<BashResult> {
 		this._bashAbortController = new AbortController();
 
+		// Apply command prefix if configured (e.g., "shopt -s expand_aliases" for alias support)
+		const prefix = this.settingsManager.getShellCommandPrefix();
+		const resolvedCommand = prefix ? `${prefix}\n${command}` : command;
+
 		try {
 			const result = options?.operations
-				? await executeBashWithOperations(command, process.cwd(), options.operations, {
+				? await executeBashWithOperations(resolvedCommand, process.cwd(), options.operations, {
 						onChunk,
 						signal: this._bashAbortController.signal,
 					})
-				: await executeBashCommand(command, {
+				: await executeBashCommand(resolvedCommand, {
 						onChunk,
 						signal: this._bashAbortController.signal,
 					});

packages/coding-agent/src/core/sdk.ts

@@ -438,8 +438,12 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 	time("discoverContextFiles");
 
 	const autoResizeImages = settingsManager.getImageAutoResize();
+	const shellCommandPrefix = settingsManager.getShellCommandPrefix();
 	// Create ALL built-in tools for the registry (extensions can enable any of them)
-	const allBuiltInToolsMap = createAllTools(cwd, { read: { autoResizeImages } });
+	const allBuiltInToolsMap = createAllTools(cwd, {
+		read: { autoResizeImages },
+		bash: { commandPrefix: shellCommandPrefix },
+	});
 	// Determine initially active built-in tools (default: read, bash, edit, write)
 	const defaultActiveToolNames: ToolName[] = ["read", "bash", "edit", "write"];
 	const initialActiveToolNames: ToolName[] = options.tools

packages/coding-agent/src/core/settings-manager.ts

@@ -61,6 +61,7 @@ export interface Settings {
 	hideThinkingBlock?: boolean;
 	shellPath?: string; // Custom shell path (e.g., for Cygwin users on Windows)
 	quietStartup?: boolean;
+	shellCommandPrefix?: string; // Prefix prepended to every bash command (e.g., "shopt -s expand_aliases" for alias support)
 	collapseChangelog?: boolean; // Show condensed changelog after update (use /changelog for full)
 	extensions?: string[]; // Array of extension file paths
 	skills?: SkillsSettings;
@@ -356,6 +357,15 @@ export class SettingsManager {
 		this.save();
 	}
 
+	getShellCommandPrefix(): string | undefined {
+		return this.settings.shellCommandPrefix;
+	}
+
+	setShellCommandPrefix(prefix: string | undefined): void {
+		this.globalSettings.shellCommandPrefix = prefix;
+		this.save();
+	}
+
 	getCollapseChangelog(): boolean {
 		return this.settings.collapseChangelog ?? false;
 	}

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) {

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

@@ -1,4 +1,10 @@
-export { type BashOperations, type BashToolDetails, type BashToolOptions, bashTool, createBashTool } from "./bash.js";
+export {
+	type BashOperations,
+	type BashToolDetails,
+	type BashToolOptions,
+	bashTool,
+	createBashTool,
+} from "./bash.js";
 export { createEditTool, type EditOperations, type EditToolDetails, type EditToolOptions, editTool } from "./edit.js";
 export { createFindTool, type FindOperations, type FindToolDetails, type FindToolOptions, findTool } from "./find.js";
 export { createGrepTool, type GrepOperations, type GrepToolDetails, type GrepToolOptions, grepTool } from "./grep.js";
@@ -23,7 +29,7 @@ export {
 export { createWriteTool, type WriteOperations, type WriteToolOptions, writeTool } from "./write.js";
 
 import type { AgentTool } from "@mariozechner/pi-agent-core";
-import { bashTool, createBashTool } from "./bash.js";
+import { type BashToolOptions, bashTool, createBashTool } from "./bash.js";
 import { createEditTool, editTool } from "./edit.js";
 import { createFindTool, findTool } from "./find.js";
 import { createGrepTool, grepTool } from "./grep.js";
@@ -56,13 +62,20 @@ export type ToolName = keyof typeof allTools;
 export interface ToolsOptions {
 	/** Options for the read tool */
 	read?: ReadToolOptions;
+	/** Options for the bash tool */
+	bash?: BashToolOptions;
 }
 
 /**
  * Create coding tools configured for a specific working directory.
  */
 export function createCodingTools(cwd: string, options?: ToolsOptions): Tool[] {
-	return [createReadTool(cwd, options?.read), createBashTool(cwd), createEditTool(cwd), createWriteTool(cwd)];
+	return [
+		createReadTool(cwd, options?.read),
+		createBashTool(cwd, options?.bash),
+		createEditTool(cwd),
+		createWriteTool(cwd),
+	];
 }
 
 /**
@@ -78,7 +91,7 @@ export function createReadOnlyTools(cwd: string, options?: ToolsOptions): Tool[]
 export function createAllTools(cwd: string, options?: ToolsOptions): Record<ToolName, Tool> {
 	return {
 		read: createReadTool(cwd, options?.read),
-		bash: createBashTool(cwd),
+		bash: createBashTool(cwd, options?.bash),
 		edit: createEditTool(cwd),
 		write: createWriteTool(cwd),
 		grep: createGrepTool(cwd),