@prometheus-ai/agent 0.5.3 → 0.5.8

package/src/autoresearch/state.ts

@@ -1,4 +1,4 @@
-import type { SessionEntry } from "../session/session-manager";
+import type { SessionEntry } from "../session/session-entries";
 import { inferMetricUnitFromName, isBetter } from "./helpers";
 import type { RunRow, SessionRow } from "./storage";
 import type {

package/src/autoresearch/storage.ts

@@ -194,7 +194,6 @@ const SCHEMA_VERSION = 1;
 const SCHEMA_SQL = `
 PRAGMA journal_mode=WAL;
 PRAGMA synchronous=NORMAL;
-PRAGMA busy_timeout=5000;
 PRAGMA foreign_keys=ON;
 
 CREATE TABLE IF NOT EXISTS sessions (
@@ -263,6 +262,8 @@ export class AutoresearchStorage {
 		this.#projectDir = projectDir;
 		fs.mkdirSync(path.dirname(dbPath), { recursive: true });
 		this.#db = new Database(dbPath);
+		// Install the busy handler BEFORE any lock-taking statement. See #2421.
+		this.#db.run("PRAGMA busy_timeout = 5000");
 		this.#db.run(SCHEMA_SQL);
 		const versionRow = this.#db.query("PRAGMA user_version").get() as { user_version: number } | null;
 		const currentVersion = versionRow?.user_version ?? 0;

package/src/autoresearch/tools/init-experiment.ts

@@ -1,7 +1,7 @@
 import * as path from "node:path";
 
 import { Text } from "@prometheus-ai/tui";
-import * as z from "zod/v4";
+import { z } from "zod/v4";
 import type { ToolDefinition } from "../../extensibility/extensions";
 import type { Theme } from "../../modes/theme/theme";
 import { replaceTabs, truncateToWidth } from "../../tools/render-utils";

package/src/autoresearch/tools/log-experiment.ts

@@ -2,7 +2,7 @@ import * as fs from "node:fs";
 import * as path from "node:path";
 
 import { Text } from "@prometheus-ai/tui";
-import * as z from "zod/v4";
+import { z } from "zod/v4";
 import type { ToolDefinition } from "../../extensibility/extensions";
 import type { Theme } from "../../modes/theme/theme";
 import { replaceTabs, truncateToWidth } from "../../tools/render-utils";

package/src/autoresearch/tools/run-experiment.ts

@@ -2,7 +2,7 @@ import * as fs from "node:fs";
 import * as path from "node:path";
 import { Text } from "@prometheus-ai/tui";
 import { formatBytes } from "@prometheus-ai/utils";
-import * as z from "zod/v4";
+import { z } from "zod/v4";
 import { executeBash } from "../../exec/bash-executor";
 import type { ToolDefinition } from "../../extensibility/extensions";
 import type { Theme } from "../../modes/theme/theme";

package/src/autoresearch/tools/update-notes.ts

@@ -1,5 +1,5 @@
 import { Text } from "@prometheus-ai/tui";
-import * as z from "zod/v4";
+import { z } from "zod/v4";
 import type { ToolDefinition } from "../../extensibility/extensions";
 import type { Theme } from "../../modes/theme/theme";
 import { replaceTabs, truncateToWidth } from "../../tools/render-utils";

package/src/autoresearch/types.ts

@@ -1,6 +1,6 @@
 import type { AgentToolResult } from "@prometheus-ai/agent-core";
 import type { ExtensionAPI, ExtensionContext } from "../extensibility/extensions";
-import type { SessionEntry } from "../session/session-manager";
+import type { SessionEntry } from "../session/session-entries";
 import type { TruncationResult } from "../session/streaming-output";
 
 export type MetricDirection = "lower" | "higher";

package/src/capability/context-file.ts

@@ -8,18 +8,6 @@ import * as path from "node:path";
 import { defineCapability } from ".";
 import type { SourceMeta } from "./types";
 
-/**
- * A concrete file represented by a context file item.
- */
-export interface ContextFileMember {
-	/** File name used for extension IDs and display */
-	name: string;
-	/** Absolute path to the file */
-	path: string;
-	/** File content */
-	content: string;
-}
-
 /**
  * A context file that provides persistent instructions to the agent.
  */
@@ -32,8 +20,6 @@ export interface ContextFile {
 	level: "user" | "project";
 	/** Distance from cwd (0 = in cwd, 1 = parent, etc.) for project files */
 	depth?: number;
-	/** Underlying files represented by a merged context payload */
-	members?: ContextFileMember[];
 	/** Source metadata */
 	_source: SourceMeta;
 }

package/src/capability/fs.ts

@@ -15,6 +15,16 @@ export async function readFile(filePath: string): Promise<string | null> {
 	}
 
 	try {
+		// Gate on the file type first: discovery scans foreign config dirs
+		// (~/.claude, ~/.cursor, project trees), and reading a FIFO/socket/char
+		// device with `.text()` blocks until EOF — i.e. forever — hanging
+		// startup with zero output. `stat` follows symlinks, so symlinked
+		// context files (CLAUDE.md -> AGENTS.md) still resolve.
+		const stats = await fs.promises.stat(abs);
+		if (!stats.isFile()) {
+			contentCache.set(abs, null);
+			return null;
+		}
 		const content = await Bun.file(abs).text();
 		contentCache.set(abs, content);
 		return content;

package/src/capability/index.ts

@@ -110,11 +110,6 @@ async function loadImpl<T>(
 	const disabledExtensionIds = options.includeDisabled
 		? new Set<string>()
 		: new Set<string>(options.disabledExtensions ?? settings?.get("disabledExtensions") ?? []);
-	const providerContext: LoadContext = {
-		...ctx,
-		disabledExtensions: Array.from(disabledExtensionIds),
-		includeDisabled: options.includeDisabled,
-	};
 
 	const results = await Promise.all(
 		providers.map(async provider => {
@@ -122,7 +117,7 @@ async function loadImpl<T>(
 				const result = await logger.time(
 					`capability:${capability.id}:${provider.id}`,
 					provider.load.bind(provider),
-					providerContext,
+					ctx,
 				);
 				return { provider, result };
 			} catch (error) {

package/src/capability/mcp.ts

@@ -36,6 +36,7 @@ export interface MCPServer {
 		tokenUrl?: string;
 		clientId?: string;
 		clientSecret?: string;
+		resource?: string;
 	};
 	/** OAuth configuration (clientId, clientSecret, redirectUri, callbackPort, callbackPath) for servers requiring explicit client credentials */
 	oauth?: {

package/src/capability/rule-buckets.ts

@@ -6,7 +6,7 @@
  * manager, and splits the rest into the always-apply and rulebook buckets.
  *
  * Bucket precedence (matches docs/rulebook-matching-pipeline.md §5):
- *   1. TTSR     — non-empty `condition` that `TtsrManager.addRule` accepts
+ *   1. TTSR     — non-empty `condition`/`astCondition` that `TtsrManager.addRule` accepts
  *   2. always   — `alwaysApply === true`
  *   3. rulebook — has a `description`
  */
@@ -49,7 +49,9 @@ export function bucketRules(
 		if (disabled.has(rule.name)) continue;
 		if (!includeBuiltin && rule._source?.provider === BUILTIN_DEFAULTS_PROVIDER_ID) continue;
 
-		const isTtsrRule = rule.condition && rule.condition.length > 0 ? ttsrManager.addRule(rule) : false;
+		const hasTtsrCondition =
+			(rule.condition && rule.condition.length > 0) || (rule.astCondition && rule.astCondition.length > 0);
+		const isTtsrRule = hasTtsrCondition ? ttsrManager.addRule(rule) : false;
 		if (isTtsrRule) continue;
 		if (rule.alwaysApply === true) {
 			alwaysApplyRules.push(rule);

package/src/capability/rule.ts

@@ -26,6 +26,8 @@ export interface RuleFrontmatter {
 	alwaysApply?: boolean;
 	/** New key for TTSR match conditions. */
 	condition?: string | string[];
+	/** TTSR match condition(s) expressed as ast-grep patterns (edit/write streams only). */
+	astCondition?: string | string[];
 	/** New key for TTSR stream scope. */
 	scope?: string | string[];
 	/** Per-rule TTSR interrupt mode override. */
@@ -51,6 +53,8 @@ export interface Rule {
 	description?: string;
 	/** Regex condition(s) that can trigger TTSR interruption. */
 	condition?: string[];
+	/** ast-grep pattern condition(s) that can trigger TTSR interruption (edit/write streams only). */
+	astCondition?: string[];
 	/** Optional stream scope tokens (for example: text, thinking, tool:edit(*.ts)). */
 	scope?: string[];
 	/** Per-rule TTSR interrupt mode override (falls back to global ttsr.interruptMode). */
@@ -188,10 +192,14 @@ function isLikelyFileGlob(value: string): boolean {
  * - legacy `ttsr_trigger` / `ttsrTrigger` are accepted as a `condition` fallback
  * - condition tokens that look like file globs become scope shorthands:
  *   `*.rs` => `tool:edit(*.rs)`, `tool:write(*.rs)` and a catch-all condition `.*`
+ * - `astCondition` holds ast-grep patterns and is kept verbatim (no glob inference)
  */
-export function parseRuleConditionAndScope(frontmatter: RuleFrontmatter): Pick<Rule, "condition" | "scope"> {
+export function parseRuleConditionAndScope(
+	frontmatter: RuleFrontmatter,
+): Pick<Rule, "condition" | "astCondition" | "scope"> {
 	const rawCondition = frontmatter.condition ?? frontmatter.ttsr_trigger ?? frontmatter.ttsrTrigger;
 	const parsedCondition = normalizeRuleField(rawCondition);
+	const astCondition = normalizeRuleField(frontmatter.astCondition);
 	const parsedScope = normalizeScopeField(frontmatter.scope);
 
 	const inferredScope: string[] = [];
@@ -213,6 +221,7 @@ export function parseRuleConditionAndScope(frontmatter: RuleFrontmatter): Pick<R
 	const scope = [...(parsedScope ?? []), ...inferredScope];
 	return {
 		condition: condition.length > 0 ? Array.from(new Set(condition)) : undefined,
+		astCondition,
 		scope: scope.length > 0 ? Array.from(new Set(scope)) : undefined,
 	};
 }

package/src/capability/types.ts

@@ -16,10 +16,6 @@ export interface LoadContext {
 	home: string;
 	/** Git repository root (directory containing .git), or null if not in a repo */
 	repoRoot: string | null;
-	/** Disabled extension IDs for providers that need to filter before composing items */
-	disabledExtensions?: readonly string[];
-	/** Include disabled items in provider loads. Default: false */
-	includeDisabled?: boolean;
 }
 
 /**

package/src/cli/args.ts

@@ -1,7 +1,7 @@
 /**
  * CLI argument parsing and help display
  */
-import { type Effort, THINKING_EFFORTS } from "@prometheus-ai/ai";
+import { type Effort, THINKING_EFFORTS } from "@prometheus-ai/catalog/effort";
 import { APP_NAME, CONFIG_DIR_NAME, logger } from "@prometheus-ai/utils";
 import chalk from "chalk";
 import { parseEffort } from "../thinking";
@@ -14,6 +14,7 @@ export interface Args {
 	allowHome?: boolean;
 	provider?: string;
 	model?: string;
+	config?: string[];
 	smol?: string;
 	slow?: string;
 	plan?: string;
@@ -31,6 +32,8 @@ export interface Args {
 	sessionDir?: string;
 	providerSessionId?: string;
 	fork?: string;
+	/** Collab link to join at startup (set by the `join` subcommand; no CLI flag). */
+	join?: string;
 	models?: string[];
 	tools?: string[];
 	noTools?: boolean;
@@ -45,14 +48,24 @@ export interface Args {
 	noSkills?: boolean;
 	skills?: string[];
 	noRules?: boolean;
-	listModels?: string | true;
 	noTitle?: boolean;
 	autoApprove?: boolean;
 	approvalMode?: "always-ask" | "write" | "yolo";
 	messages: string[];
 	fileArgs: string[];
-	/** Unknown flags (potentially extension flags) - map of flag name to value */
+	/** Extension-registered flags this parse recognized — name to value. */
 	unknownFlags: Map<string, boolean | string>;
+	/**
+	 * `--`/`-` prefixed tokens this parse could not match against any built-in
+	 * or {@link extensionFlags} entry. The startup parse runs *before*
+	 * extensions load, so it always lists every extension-registered flag here;
+	 * the post-extension reparse in {@link applyExtensionFlags} clears those
+	 * once the real flag set is known. Anything still present after that
+	 * reparse is a genuine typo or stale flag and {@link reportUnrecognizedFlags}
+	 * surfaces it as a hard error so the agent does not silently start a
+	 * session with the misparsed positionals as a prompt (issue #2459).
+	 */
+	unrecognizedFlags: string[];
 }
 
 export function parseArgs(inputArgs: string[], extensionFlags?: Map<string, { type: "boolean" | "string" }>): Args {
@@ -65,12 +78,23 @@ export function parseArgs(inputArgs: string[], extensionFlags?: Map<string, { ty
 		messages: [],
 		fileArgs: [],
 		unknownFlags: new Map(),
+		unrecognizedFlags: [],
 	};
 
+	let sawSeparator = false;
 	for (let i = 0; i < args.length; i++) {
 		let arg = args[i];
 		const flagIndex = i;
 
+		// POSIX positional separator: once `--` lands, every remaining token is
+		// a positional regardless of shape. Without this, a flag-looking message
+		// (`prometheus -p -- --explain-this`) would be re-validated by the loop below
+		// and rejected by the unknown-flag guard (#2461 review).
+		if (sawSeparator) {
+			result.messages.push(arg);
+			continue;
+		}
+
 		// Support --flag=value syntax (e.g. --tools=ask,read). The value is
 		// spliced in as the next token so value-consuming flags pick it up via
 		// `args[++i]`; a non-consuming flag (e.g. a boolean) leaves it behind and
@@ -109,6 +133,10 @@ export function parseArgs(inputArgs: string[], extensionFlags?: Map<string, { ty
 			result.version = true;
 		} else if (arg === "--allow-home") {
 			result.allowHome = true;
+		} else if (arg === "--cwd" && i + 1 < args.length) {
+			result.cwd = args[++i];
+		} else if (arg === "--config" && i + 1 < args.length) {
+			result.config = [...(result.config ?? []), args[++i]];
 		} else if (arg === "--mode" && i + 1 < args.length) {
 			const mode = args[++i];
 			if (mode === "text" || mode === "json" || mode === "rpc" || mode === "acp" || mode === "rpc-ui") {
@@ -221,17 +249,24 @@ export function parseArgs(inputArgs: string[], extensionFlags?: Map<string, { ty
 		} else if (arg === "--skills" && i + 1 < args.length) {
 			// Comma-separated glob patterns for skill filtering
 			result.skills = args[++i].split(",").map(s => s.trim());
-		} else if (arg === "--list-models") {
-			// Check if next arg is a search pattern (not a flag or file arg)
-			if (i + 1 < args.length && !args[i + 1].startsWith("-") && !args[i + 1].startsWith("@")) {
-				result.listModels = args[++i];
-			} else {
-				result.listModels = true;
-			}
 		} else if (arg.startsWith("@")) {
 			result.fileArgs.push(arg.slice(1)); // Remove @ prefix
-		} else if (!arg.startsWith("-")) {
+		} else if (!arg.startsWith("-") || arg === "-") {
+			// Plain positional or lone `-` (stdin marker) — pass through as a
+			// message rather than flagging it.
 			result.messages.push(arg);
+		} else if (arg === "--") {
+			// POSIX positional separator: drop the token and switch the loop
+			// into "everything from here is a positional" mode. The guard at
+			// the top of the loop body handles the remaining tokens.
+			sawSeparator = true;
+		} else {
+			// Flag-shaped (`-x`, `--name`) but unrecognized at this parse. Record
+			// it so the post-extension reparse can decide whether to surface it
+			// as a hard error. `--flag=value` already split `value` into the next
+			// slot; the standard "drop unconsumed equals value" guard below
+			// removes it so it does not leak into messages (issue #2459).
+			result.unrecognizedFlags.push(arg);
 		}
 		// Drop an unconsumed `--flag=value` value (e.g. a boolean flag): when no
 		// branch advanced past the spliced token, remove it so it does not fall
@@ -244,6 +279,24 @@ export function parseArgs(inputArgs: string[], extensionFlags?: Map<string, { ty
 	return result;
 }
 
+/**
+ * Emit a stderr error listing the unrecognized flags and return `true` when
+ * there were any. Caller is expected to exit with a non-zero status. Splitting
+ * the print from the exit keeps the helper unit-testable without forking a
+ * process (issue #2459).
+ */
+export function reportUnrecognizedFlags(
+	args: Pick<Args, "unrecognizedFlags">,
+	write: (text: string) => void = text => process.stderr.write(text),
+): boolean {
+	if (args.unrecognizedFlags.length === 0) return false;
+	const flags = args.unrecognizedFlags;
+	const plural = flags.length === 1 ? "" : "s";
+	write(`${chalk.red(`Error: unknown flag${plural}: ${flags.join(", ")}`)}\n`);
+	write(`Run \`${APP_NAME} --help\` for available flags.\n`);
+	return true;
+}
+
 export function getExtraHelpText(): string {
 	return `${chalk.bold("Environment Variables:")}
   ${chalk.dim("# Core Providers")}
@@ -258,7 +311,7 @@ export function getExtraHelpText(): string {
   NODE_EXTRA_CA_CERTS        - CA bundle path (or inline PEM) for server certificate validation
   OPENAI_API_KEY             - OpenAI GPT models
   GEMINI_API_KEY             - Google Gemini models
-  GITHUB_TOKEN               - GitHub Copilot (or GH_TOKEN, COPILOT_GITHUB_TOKEN)
+  COPILOT_GITHUB_TOKEN      - GitHub Copilot
 
   ${chalk.dim("# Additional LLM Providers")}
   AZURE_OPENAI_API_KEY       - Azure OpenAI models
@@ -284,7 +337,7 @@ export function getExtraHelpText(): string {
   ${chalk.dim("# Search & Tools")}
   EXA_API_KEY                - Exa web search
   BRAVE_API_KEY              - Brave web search
-  PERPLEXITY_API_KEY         - Perplexity web search (API)
+  PERPLEXITY_API_KEY         - Perplexity web search API key (optional; anonymous fallback)
   PERPLEXITY_COOKIES         - Perplexity web search (session cookie)
   TAVILY_API_KEY             - Tavily web search
   ANTHROPIC_SEARCH_API_KEY   - Anthropic web search (override; isolates search from main ANTHROPIC_API_KEY)

package/src/cli/auth-broker-cli.ts

@@ -30,6 +30,7 @@ import {
 	type OAuthCredential,
 	type OAuthProvider,
 	type OAuthProviderInfo,
+	PROVIDER_REGISTRY,
 	SqliteAuthCredentialStore,
 	startAuthBroker,
 } from "@prometheus-ai/ai";
@@ -75,13 +76,11 @@ const ACTIONS: readonly AuthBrokerAction[] = [
 ];
 
 /** Callback ports baked from the per-provider OAuth flow modules. */
-const CALLBACK_PORTS: Record<string, number> = {
-	anthropic: 54545,
-	"openai-codex": 1455,
-	"google-gemini-cli": 8085,
-	"google-antigravity": 51121,
-	"gitlab-duo": 8080,
-};
+const CALLBACK_PORTS: Record<string, number> = Object.fromEntries(
+	PROVIDER_REGISTRY.flatMap(provider =>
+		provider.callbackPort != null ? [[provider.id, provider.callbackPort] as [string, number]] : [],
+	),
+);
 
 function getTokenFilePath(): string {
 	return path.join(getConfigRootDir(), "auth-broker.token");

package/src/cli/auth-gateway-cli.ts

@@ -24,14 +24,12 @@ import {
 	type CredentialCompletionResult,
 	completeSimple,
 	DEFAULT_AUTH_GATEWAY_BIND,
-	type GeneratedProvider,
-	getBundledModels,
-	getBundledProviders,
 	type Model,
 	RemoteAuthCredentialStore,
 	type SnapshotResponse,
 	startAuthGateway,
 } from "@prometheus-ai/ai";
+import { type GeneratedProvider, getBundledModels, getBundledProviders } from "@prometheus-ai/catalog/models";
 import { getConfigRootDir, isEnoent, VERSION } from "@prometheus-ai/utils";
 import chalk from "chalk";
 import { type AuthBrokerClientConfig, resolveAuthBrokerConfig } from "../session/auth-broker-config";
@@ -164,9 +162,9 @@ async function runServe(flags: AuthGatewayCommandArgs["flags"]): Promise<void> {
 	});
 	await storage.reload();
 
-	// Build the model resolver + catalog from Prometheus AI's bundled metadata, scoped
+	// Build the model resolver + catalog from @prometheus-ai/ai's bundled metadata, scoped
 	// to providers we hold credentials for. Format handlers ask `resolveModel`
-	// to translate a client-requested `model` field into a Prometheus AI `Model<Api>`
+	// to translate a client-requested `model` field into an @prometheus-ai/ai `Model<Api>`
 	// before dispatch; `listModels` powers `/v1/models`.
 	const snapshot = storage.exportSnapshot();
 	const providersWithCreds = new Set<string>();
@@ -175,8 +173,9 @@ async function runServe(flags: AuthGatewayCommandArgs["flags"]): Promise<void> {
 	for (const provider of getBundledProviders()) {
 		if (!providersWithCreds.has(provider)) continue;
 		for (const model of getBundledModels(provider as GeneratedProvider)) {
-			// First-write-wins so a canonical model id collisions across providers
-			// stick to the provider listed first by getBundledProviders.
+			// Always set the qualified key (no collision possible)
+			modelById.set(`${model.provider}/${model.id}`, model);
+			// Bare id as fallback for legacy clients (first-write-wins)
 			if (!modelById.has(model.id)) modelById.set(model.id, model);
 		}
 	}
@@ -357,7 +356,7 @@ export async function runAuthGatewayCommand(cmd: AuthGatewayCommandArgs): Promis
 /**
  * Providers whose chat endpoint expects a JSON-serialized credential blob
  * (`{ token, projectId, refreshToken, expiresAt, … }`) rather than the raw
- * access token. Mirrors `getOAuthApiKey` in `packages/ai/src/utils/oauth`.
+ * access token. Mirrors `getOAuthApiKey` in `packages/ai/src/registry/oauth`.
  */
 const STRUCTURED_API_KEY_PROVIDERS: ReadonlySet<string> = new Set([
 	"github-copilot",
@@ -410,7 +409,7 @@ function pickProbeCandidates(provider: string): Model<Api>[] {
 		if (!model.input.includes("text")) return false;
 		const totalCost = (model.cost?.input ?? 0) + (model.cost?.output ?? 0);
 		if (!Number.isFinite(totalCost) || totalCost < 0) return false;
-		if (model.maxTokens <= 0) return false;
+		if (model.maxTokens !== null && model.maxTokens <= 0) return false;
 		return true;
 	});
 	candidates.sort((a, b) => a.cost.input + a.cost.output - (b.cost.input + b.cost.output) || a.id.localeCompare(b.id));