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/ai/CHANGELOG.md

@@ -6,6 +6,7 @@
 
 - Fixed OpenAI-compatible provider feature detection to use `model.provider` in addition to URL, allowing custom base URLs (e.g., proxies) to work correctly with provider-specific settings ([#774](https://github.com/badlogic/pi-mono/issues/774))
 - Fixed Bedrock tool call IDs to use only alphanumeric characters, avoiding API errors from invalid characters ([#781](https://github.com/badlogic/pi-mono/pull/781) by [@pjtf93](https://github.com/pjtf93))
+- Fixed empty error assistant messages (from 429/500 errors) breaking the tool_use to tool_result chain by filtering them in `transformMessages`
 
 ## [0.47.0] - 2026-01-16
 

packages/ai/src/providers/transform-messages.ts

@@ -118,6 +118,14 @@ export function transformMessages<TApi extends Api>(messages: Message[], model:
 				existingToolResultIds = new Set();
 			}
 
+			// Skip empty assistant messages (no content and no tool calls)
+			// This handles error responses (e.g., 429/500) that produced no content
+			// All providers already filter these in convertMessages, but we do it here
+			// centrally to prevent issues with the tool_use -> tool_result chain
+			if (assistantMsg.content.length === 0 && toolCalls.length === 0) {
+				continue;
+			}
+
 			result.push(msg);
 		} else if (msg.role === "toolResult") {
 			existingToolResultIds.add(msg.toolCallId);

packages/coding-agent/CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### Added
 
+- Added `shellCommandPrefix` setting to prepend commands to every bash execution, enabling alias expansion in non-interactive shells (e.g., `"shellCommandPrefix": "shopt -s expand_aliases"`) ([#790](https://github.com/badlogic/pi-mono/pull/790) by [@richardgill](https://github.com/richardgill))
 - Added bash-style argument slicing for prompt templates ([#770](https://github.com/badlogic/pi-mono/pull/770) by [@airtonix](https://github.com/airtonix))
 - Extension commands can provide argument auto-completions via `getArgumentCompletions` in `pi.registerCommand()` ([#775](https://github.com/badlogic/pi-mono/pull/775) by [@ribelo](https://github.com/ribelo))
 - Bash tool now displays the timeout value in the UI when a timeout is set ([#780](https://github.com/badlogic/pi-mono/pull/780) by [@dannote](https://github.com/dannote))

packages/coding-agent/README.md

@@ -116,6 +116,17 @@ For most users, [Git for Windows](https://git-scm.com/download/win) is sufficien
 }
 ```
 
+**Alias expansion:** Pi runs bash in non-interactive mode (`bash -c`), which doesn't expand aliases by default. To enable your shell aliases:
+
+```json
+// ~/.pi/agent/settings.json
+{
+  "shellCommandPrefix": "shopt -s expand_aliases\neval \"$(grep '^alias ' ~/.zshrc)\""
+}
+```
+
+Adjust the path (`~/.zshrc`, `~/.bashrc`, etc.) to match your shell config.
+
 ### Terminal Setup
 
 Pi uses the [Kitty keyboard protocol](https://sw.kovidgoyal.net/kitty/keyboard-protocol/) for reliable modifier key detection. Most modern terminals support this protocol, but some require configuration.
@@ -742,6 +753,7 @@ Global `~/.pi/agent/settings.json` stores persistent preferences:
   "steeringMode": "one-at-a-time",
   "followUpMode": "one-at-a-time",
   "shellPath": "C:\\path\\to\\bash.exe",
+  "shellCommandPrefix": "shopt -s expand_aliases",
   "hideThinkingBlock": false,
   "collapseChangelog": false,
   "compaction": {
@@ -778,6 +790,7 @@ Global `~/.pi/agent/settings.json` stores persistent preferences:
 | `steeringMode` | Steering message delivery: `all` or `one-at-a-time` | `one-at-a-time` |
 | `followUpMode` | Follow-up message delivery: `all` or `one-at-a-time` | `one-at-a-time` |
 | `shellPath` | Custom bash path (Windows) | auto-detected |
+| `shellCommandPrefix` | Command prefix for bash (e.g., `shopt -s expand_aliases` for alias support) | - |
 | `hideThinkingBlock` | Hide thinking blocks in output (Ctrl+T to toggle) | `false` |
 | `collapseChangelog` | Show condensed changelog after update | `false` |
 | `compaction.enabled` | Enable auto-compaction | `true` |

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),

packages/coding-agent/test/settings-manager.test.ts

@@ -105,4 +105,36 @@ describe("SettingsManager", () => {
 			expect(savedSettings.defaultThinkingLevel).toBe("high");
 		});
 	});
+
+	describe("shellCommandPrefix", () => {
+		it("should load shellCommandPrefix from settings", () => {
+			const settingsPath = join(agentDir, "settings.json");
+			writeFileSync(settingsPath, JSON.stringify({ shellCommandPrefix: "shopt -s expand_aliases" }));
+
+			const manager = SettingsManager.create(projectDir, agentDir);
+
+			expect(manager.getShellCommandPrefix()).toBe("shopt -s expand_aliases");
+		});
+
+		it("should return undefined when shellCommandPrefix is not set", () => {
+			const settingsPath = join(agentDir, "settings.json");
+			writeFileSync(settingsPath, JSON.stringify({ theme: "dark" }));
+
+			const manager = SettingsManager.create(projectDir, agentDir);
+
+			expect(manager.getShellCommandPrefix()).toBeUndefined();
+		});
+
+		it("should preserve shellCommandPrefix when saving unrelated settings", () => {
+			const settingsPath = join(agentDir, "settings.json");
+			writeFileSync(settingsPath, JSON.stringify({ shellCommandPrefix: "shopt -s expand_aliases" }));
+
+			const manager = SettingsManager.create(projectDir, agentDir);
+			manager.setTheme("light");
+
+			const savedSettings = JSON.parse(readFileSync(settingsPath, "utf-8"));
+			expect(savedSettings.shellCommandPrefix).toBe("shopt -s expand_aliases");
+			expect(savedSettings.theme).toBe("light");
+		});
+	});
 });

packages/coding-agent/test/tools.test.ts

@@ -299,6 +299,31 @@ describe("Coding Agent Tools", () => {
 
 			await expect(bashWithBadShell.execute("test-call-12", { command: "echo test" })).rejects.toThrow(/ENOENT/);
 		});
+
+		it("should prepend command prefix when configured", async () => {
+			const bashWithPrefix = createBashTool(testDir, {
+				commandPrefix: "export TEST_VAR=hello",
+			});
+
+			const result = await bashWithPrefix.execute("test-prefix-1", { command: "echo $TEST_VAR" });
+			expect(getTextOutput(result).trim()).toBe("hello");
+		});
+
+		it("should include output from both prefix and command", async () => {
+			const bashWithPrefix = createBashTool(testDir, {
+				commandPrefix: "echo prefix-output",
+			});
+
+			const result = await bashWithPrefix.execute("test-prefix-2", { command: "echo command-output" });
+			expect(getTextOutput(result).trim()).toBe("prefix-output\ncommand-output");
+		});
+
+		it("should work without command prefix", async () => {
+			const bashWithoutPrefix = createBashTool(testDir, {});
+
+			const result = await bashWithoutPrefix.execute("test-prefix-3", { command: "echo no-prefix" });
+			expect(getTextOutput(result).trim()).toBe("no-prefix");
+		});
 	});
 
 	describe("grep tool", () => {