feat: add is_subagent flag to agents, fix all lint/type/test issues

- Add is_subagent checkbox to agent editor; subagents are hidden from Chat Settings
- Add is_subagent field to AgentDefinition type, TOML serialization, and API route
- Filter subagents from ModelSelector agent list
- Fix all biome lint/format errors across codebase (useLiteralKeys, noNonNullAssertion, noExplicitAny, formatting, import sorting)
- Fix svelte-check errors (type narrowing in SkillsBrowser, ToolPermissions, SidebarPanel)
- Fix a11y warnings in App.svelte (label-control associations)
- Fix test mocks missing BackgroundShellStore, BackgroundTranscriptStore, createWebSearchTool, createYoutubeTranscribeTool
- Update stale 409 test to match current message-queuing behavior
- Exclude packaging/ and release/ dirs from biome to avoid linting stale build artifacts

9 files changed, 108 insertions, 100 deletions

diff --git a/packages/core/src/agent/agent.ts b/packages/core/src/agent/agent.ts
index 64a602b..6f1a5a4 100644
--- a/packages/core/src/agent/agent.ts
+++ b/packages/core/src/agent/agent.ts
@@ -188,12 +188,12 @@ export class Agent {
 		}
 
 		try {
-		const execPromise = tool.execute(tc.arguments, {
-			onOutput: (data: string, stream: "stdout" | "stderr") => {
-				shellOutputQueue.push({ data, stream });
-			},
-			queueCallbacks: this.queueCallbacks,
-		});
+			const execPromise = tool.execute(tc.arguments, {
+				onOutput: (data: string, stream: "stdout" | "stderr") => {
+					shellOutputQueue.push({ data, stream });
+				},
+				queueCallbacks: this.queueCallbacks,
+			});
 
 			const rawResult = await execPromise;
 			const resultStr = typeof rawResult === "string" ? rawResult : JSON.stringify(rawResult);
@@ -320,9 +320,7 @@ export class Agent {
 					}
 				} catch (streamErr) {
 					const errMsg = streamErr instanceof Error ? streamErr.message : String(streamErr);
-					const unavailMatch = errMsg.match(
-						/tried to call unavailable tool '([^']+)'/i,
-					);
+					const unavailMatch = errMsg.match(/tried to call unavailable tool '([^']+)'/i);
 					if (!unavailMatch) throw streamErr;
 
 					// Model tried to call an unavailable tool.
@@ -391,8 +389,8 @@ export class Agent {
 					let toolResult: ToolResult | undefined;
 					while (toolResult === undefined) {
 						if (shellOutputQueue.length > 0) {
-							const item = shellOutputQueue.shift()!;
-							yield { type: "shell-output", data: item.data, stream: item.stream };
+							const item = shellOutputQueue.shift();
+							if (item) yield { type: "shell-output", data: item.data, stream: item.stream };
 							continue;
 						}
 						const raceResult = await Promise.race([
@@ -406,30 +404,28 @@ export class Agent {
 						}
 					}
 
-				// Drain any remaining shell output emitted before we read the result
-				while (shellOutputQueue.length > 0) {
-					const item = shellOutputQueue.shift()!;
-					yield { type: "shell-output", data: item.data, stream: item.stream };
-				}
+					// Drain any remaining shell output emitted before we read the result
+					while (shellOutputQueue.length > 0) {
+						const item = shellOutputQueue.shift();
+						if (item) yield { type: "shell-output", data: item.data, stream: item.stream };
+					}
 
-				// Check for queued user messages and append them to the tool result
-				let finalToolResult = toolResult;
-				if (this.queueCallbacks) {
-					const queuedMsgs = this.queueCallbacks.dequeueMessages();
-					if (queuedMsgs.length > 0) {
-						const userMessages = queuedMsgs
-							.map((m) => m.message)
-							.join("\n---\n");
-						finalToolResult = {
-							...toolResult,
-							result: `${toolResult.result}\n\n[USER INTERRUPT]\nThe user has sent you message(s) while you were working. You MUST address these before continuing with your current task:\n\n${userMessages}`,
-						};
+					// Check for queued user messages and append them to the tool result
+					let finalToolResult = toolResult;
+					if (this.queueCallbacks) {
+						const queuedMsgs = this.queueCallbacks.dequeueMessages();
+						if (queuedMsgs.length > 0) {
+							const userMessages = queuedMsgs.map((m) => m.message).join("\n---\n");
+							finalToolResult = {
+								...toolResult,
+								result: `${toolResult.result}\n\n[USER INTERRUPT]\nThe user has sent you message(s) while you were working. You MUST address these before continuing with your current task:\n\n${userMessages}`,
+							};
+						}
 					}
-				}
 
-				stepToolResults.push(finalToolResult);
-				allToolResults.push(finalToolResult);
-				yield { type: "tool-result", toolResult: finalToolResult };
+					stepToolResults.push(finalToolResult);
+					allToolResults.push(finalToolResult);
+					yield { type: "tool-result", toolResult: finalToolResult };
 				}
 
 				// Add tool results back to step messages so LLM can see them
@@ -451,29 +447,29 @@ export class Agent {
 				}
 			}
 
-		const assistantMessage: ChatMessage = {
-			role: "assistant",
-			content: finalText,
-			toolCalls: allToolCalls.length > 0 ? allToolCalls : undefined,
-			toolResults: allToolResults.length > 0 ? allToolResults : undefined,
-		};
-		this.messages.push(assistantMessage);
-
-		// Drain any remaining queued messages that arrived after the last tool call
-		if (this.queueCallbacks) {
-			const remaining = this.queueCallbacks.dequeueMessages();
-			if (remaining.length > 0) {
-				// These messages arrived too late to be injected into a tool result.
-				// Append them as a user message to the conversation so they're not lost.
-				const userMessages = remaining.map(m => m.message).join("\n---\n");
-				this.messages.push({
-					role: "user",
-					content: userMessages,
-				});
+			const assistantMessage: ChatMessage = {
+				role: "assistant",
+				content: finalText,
+				toolCalls: allToolCalls.length > 0 ? allToolCalls : undefined,
+				toolResults: allToolResults.length > 0 ? allToolResults : undefined,
+			};
+			this.messages.push(assistantMessage);
+
+			// Drain any remaining queued messages that arrived after the last tool call
+			if (this.queueCallbacks) {
+				const remaining = this.queueCallbacks.dequeueMessages();
+				if (remaining.length > 0) {
+					// These messages arrived too late to be injected into a tool result.
+					// Append them as a user message to the conversation so they're not lost.
+					const userMessages = remaining.map((m) => m.message).join("\n---\n");
+					this.messages.push({
+						role: "user",
+						content: userMessages,
+					});
+				}
 			}
-		}
 
-		yield { type: "done", message: assistantMessage };
+			yield { type: "done", message: assistantMessage };
 		} catch (err) {
 			const errorMsg = formatError(err, this.config);
 			yield { type: "error", error: errorMsg };
diff --git a/packages/core/src/agents/loader.ts b/packages/core/src/agents/loader.ts
index ec29983..cf84381 100644
--- a/packages/core/src/agents/loader.ts
+++ b/packages/core/src/agents/loader.ts
@@ -112,6 +112,10 @@ export function saveAgent(agent: AgentDefinition): void {
 		tomlContent.cwd = agent.cwd;
 	}
 
+	if (agent.is_subagent) {
+		tomlContent.is_subagent = true;
+	}
+
 	// smol-toml handles [[models]] array-of-tables
 	if (agent.models.length > 0) {
 		tomlContent.models = agent.models.map((m) => ({
@@ -202,6 +206,7 @@ function loadAgentsFromDir(dir: string, scope: string): AgentDefinition[] {
 				scope,
 				slug,
 				...(typeof parsed.cwd === "string" && parsed.cwd ? { cwd: parsed.cwd } : {}),
+				...(parsed.is_subagent === true ? { is_subagent: true } : {}),
 			});
 		} catch {
 			// Skip unparseable files
diff --git a/packages/core/src/config/schema.ts b/packages/core/src/config/schema.ts
index ef10b65..a459a4d 100644
--- a/packages/core/src/config/schema.ts
+++ b/packages/core/src/config/schema.ts
@@ -66,37 +66,37 @@ function validateKey(raw: unknown, path: string, errors: ConfigError[]): KeyDefi
 		errors.push({ path, message: "must be an object" });
 		return null;
 	}
-	if (typeof raw["id"] !== "string") {
+	if (typeof raw.id !== "string") {
 		errors.push({ path: `${path}.id`, message: "must be a string" });
 		return null;
 	}
-	if (typeof raw["provider"] !== "string") {
+	if (typeof raw.provider !== "string") {
 		errors.push({ path: `${path}.provider`, message: "must be a string" });
 		return null;
 	}
-	if (typeof raw["base_url"] !== "string") {
+	if (typeof raw.base_url !== "string") {
 		errors.push({ path: `${path}.base_url`, message: "must be a string" });
 		return null;
 	}
 
 	// "anthropic" provider uses credentials_file instead of env
-	if (raw["provider"] === "anthropic") {
+	if (raw.provider === "anthropic") {
 		return {
-			id: raw["id"] as string,
-			provider: raw["provider"] as string,
-			base_url: raw["base_url"] as string,
-			...(typeof raw["credentials_file"] === "string"
-				? ({ credentials_file: raw["credentials_file"] } as Pick<KeyDefinition, "credentials_file">)
+			id: raw.id as string,
+			provider: raw.provider as string,
+			base_url: raw.base_url as string,
+			...(typeof raw.credentials_file === "string"
+				? ({ credentials_file: raw.credentials_file } as Pick<KeyDefinition, "credentials_file">)
 				: {}),
 		};
 	}
 
 	// Other providers: env is optional (keys can be stored in DB)
 	return {
-		id: raw["id"] as string,
-		provider: raw["provider"] as string,
-		base_url: raw["base_url"] as string,
-		...(typeof raw["env"] === "string" ? { env: raw["env"] } : {}),
+		id: raw.id as string,
+		provider: raw.provider as string,
+		base_url: raw.base_url as string,
+		...(typeof raw.env === "string" ? { env: raw.env } : {}),
 	};
 }
 
@@ -109,17 +109,17 @@ export function validateConfig(raw: unknown): { config: DispatchConfig; errors:
 	}
 
 	// permissions (required, but can be empty)
-	const permissions = validatePermissions(raw["permissions"] ?? {}, "permissions", errors);
+	const permissions = validatePermissions(raw.permissions ?? {}, "permissions", errors);
 
 	// keys (optional)
 	let keys: KeyDefinition[] | undefined;
-	if (raw["keys"] !== undefined) {
-		if (!Array.isArray(raw["keys"])) {
+	if (raw.keys !== undefined) {
+		if (!Array.isArray(raw.keys)) {
 			errors.push({ path: "keys", message: "must be an array" });
 		} else {
 			keys = [];
-			for (let i = 0; i < raw["keys"].length; i++) {
-				const key = validateKey(raw["keys"][i], `keys[${i}]`, errors);
+			for (let i = 0; i < raw.keys.length; i++) {
+				const key = validateKey(raw.keys[i], `keys[${i}]`, errors);
 				if (key) keys.push(key);
 			}
 		}
diff --git a/packages/core/src/index.ts b/packages/core/src/index.ts
index 8d5db16..1e55425 100644
--- a/packages/core/src/index.ts
+++ b/packages/core/src/index.ts
@@ -57,6 +57,9 @@ export { createSummonTool, type SummonCallbacks } from "./tools/summon.js";
 export { createTaskListTool, TaskList } from "./tools/task-list.js";
 export { createWebSearchTool } from "./tools/web-search.js";
 export { createWriteFileTool } from "./tools/write-file.js";
-export { BackgroundTranscriptStore, createYoutubeTranscribeTool } from "./tools/youtube-transcribe.js";
+export {
+	BackgroundTranscriptStore,
+	createYoutubeTranscribeTool,
+} from "./tools/youtube-transcribe.js";
 // Types & Permissions
 export * from "./types/index.js";
diff --git a/packages/core/src/skills/parser.ts b/packages/core/src/skills/parser.ts
index 289073f..bd1205e 100644
--- a/packages/core/src/skills/parser.ts
+++ b/packages/core/src/skills/parser.ts
@@ -30,16 +30,14 @@ export function parseSkillFile(
 			try {
 				const frontmatter = parse(tomlSource);
 
-				if (typeof frontmatter["name"] === "string") {
-					name = frontmatter["name"];
+				if (typeof frontmatter.name === "string") {
+					name = frontmatter.name;
 				}
-				if (typeof frontmatter["description"] === "string") {
-					description = frontmatter["description"];
+				if (typeof frontmatter.description === "string") {
+					description = frontmatter.description;
 				}
-				if (Array.isArray(frontmatter["tags"])) {
-					tags = (frontmatter["tags"] as unknown[]).filter(
-						(t): t is string => typeof t === "string",
-					);
+				if (Array.isArray(frontmatter.tags)) {
+					tags = (frontmatter.tags as unknown[]).filter((t): t is string => typeof t === "string");
 				}
 			} catch {
 				// Malformed TOML — fall through with defaults
diff --git a/packages/core/src/tools/retrieve.ts b/packages/core/src/tools/retrieve.ts
index 021d1b7..80c3715 100644
--- a/packages/core/src/tools/retrieve.ts
+++ b/packages/core/src/tools/retrieve.ts
@@ -28,29 +28,33 @@ export function createRetrieveTool(callbacks: RetrieveCallbacks): ToolDefinition
 		parameters: z.object({
 			agent_id: z.string().describe("The agent_id returned by a previous summon call."),
 		}),
-		execute: async (args: Record<string, unknown>, context?: ToolExecuteContext): Promise<string> => {
+		execute: async (
+			args: Record<string, unknown>,
+			context?: ToolExecuteContext,
+		): Promise<string> => {
 			const agentId = args.agent_id as string;
 			const queueCallbacks = context?.queueCallbacks;
 
 			try {
 				let outcome: { status: "done"; result: string } | { status: "error"; error: string };
 
-			if (queueCallbacks) {
-				const childPromise = callbacks.getResult(agentId);
-				const { promise: queuePromise, cancel: cancelQueueWait } = queueCallbacks.waitForQueuedMessage();
-				const queueSignal = queuePromise.then(() => "QUEUE_INTERRUPT" as const);
+				if (queueCallbacks) {
+					const childPromise = callbacks.getResult(agentId);
+					const { promise: queuePromise, cancel: cancelQueueWait } =
+						queueCallbacks.waitForQueuedMessage();
+					const queueSignal = queuePromise.then(() => "QUEUE_INTERRUPT" as const);
 
-				const raceResult = await Promise.race([childPromise, queueSignal]);
+					const raceResult = await Promise.race([childPromise, queueSignal]);
 
-				if (raceResult === "QUEUE_INTERRUPT") {
-					const queuedMsgs = queueCallbacks.dequeueMessages();
-					const userMessages = queuedMsgs.map((m) => m.message).join("\n---\n");
-					return `The subagent (agent_id: ${agentId}) has not completed its task yet. You will need to call retrieve with this agent_id again later to get the result.\n\n[USER INTERRUPT]\nThe user has sent you message(s) while you were working. You MUST address these before continuing with your current task:\n\n${userMessages}`;
-				}
+					if (raceResult === "QUEUE_INTERRUPT") {
+						const queuedMsgs = queueCallbacks.dequeueMessages();
+						const userMessages = queuedMsgs.map((m) => m.message).join("\n---\n");
+						return `The subagent (agent_id: ${agentId}) has not completed its task yet. You will need to call retrieve with this agent_id again later to get the result.\n\n[USER INTERRUPT]\nThe user has sent you message(s) while you were working. You MUST address these before continuing with your current task:\n\n${userMessages}`;
+					}
 
-				// Child finished first — clean up the queue listener
-				cancelQueueWait();
-				outcome = raceResult;
+					// Child finished first — clean up the queue listener
+					cancelQueueWait();
+					outcome = raceResult;
 				} else {
 					outcome = await callbacks.getResult(agentId);
 				}
diff --git a/packages/core/src/tools/web-search.ts b/packages/core/src/tools/web-search.ts
index 4265aa7..7f061a5 100644
--- a/packages/core/src/tools/web-search.ts
+++ b/packages/core/src/tools/web-search.ts
@@ -70,7 +70,9 @@ export function createWebSearchTool(): ToolDefinition {
 				return `Error: Firecrawl returned HTTP ${response.status} ${response.statusText}${text ? `: ${text}` : ""}`;
 			}
 
-			let json: { data?: Array<{ title?: string; url?: string; description?: string; markdown?: string }> };
+			let json: {
+				data?: Array<{ title?: string; url?: string; description?: string; markdown?: string }>;
+			};
 			try {
 				json = await response.json();
 			} catch {
@@ -96,7 +98,7 @@ export function createWebSearchTool(): ToolDefinition {
 
 			let output = parts.join("\n\n---\n\n");
 			if (output.length > MAX_OUTPUT_CHARS) {
-				output = output.slice(0, MAX_OUTPUT_CHARS) + "\n\n[Output truncated]";
+				output = `${output.slice(0, MAX_OUTPUT_CHARS)}\n\n[Output truncated]`;
 			}
 			return output;
 		},
diff --git a/packages/core/src/tools/youtube-transcribe.ts b/packages/core/src/tools/youtube-transcribe.ts
index cfa006d..ea8ed43 100644
--- a/packages/core/src/tools/youtube-transcribe.ts
+++ b/packages/core/src/tools/youtube-transcribe.ts
@@ -41,9 +41,7 @@ function formatTime(seconds: number): string {
 
 function formatTranscript(data: TranscriptResponse): string {
 	const segments = data.segments ?? [];
-	const segmentsText = segments
-		.map((seg) => `[${formatTime(seg.start)}] ${seg.text}`)
-		.join("\n");
+	const segmentsText = segments.map((seg) => `[${formatTime(seg.start)}] ${seg.text}`).join("\n");
 
 	const output = [
 		`Video ID: ${data.video_id}`,
@@ -58,7 +56,7 @@ function formatTranscript(data: TranscriptResponse): string {
 	].join("\n");
 
 	return output.length > MAX_OUTPUT_CHARS
-		? output.slice(0, MAX_OUTPUT_CHARS) + "\n\n[Transcript truncated]"
+		? `${output.slice(0, MAX_OUTPUT_CHARS)}\n\n[Transcript truncated]`
 		: output;
 }
 
diff --git a/packages/core/src/types/index.ts b/packages/core/src/types/index.ts
index be37674..ff47f49 100644
--- a/packages/core/src/types/index.ts
+++ b/packages/core/src/types/index.ts
@@ -188,4 +188,6 @@ export interface AgentDefinition {
 	slug: string;
 	/** Default working directory for this agent (optional, absolute path) */
 	cwd?: string;
+	/** Whether this agent is a subagent (hidden from Chat Settings) */
+	is_subagent?: boolean;
 }