import { AuthStorage, createAgentSession, ModelRegistry, SessionManager } from "@bastani/atomic";

// Set up credential storage and model registry
const authStorage = AuthStorage.create();
const modelRegistry = ModelRegistry.create(authStorage);

const { session } = await createAgentSession({
  sessionManager: SessionManager.inMemory(),
  authStorage,
  modelRegistry,
});

session.subscribe((event) => {
  if (event.type === "message_update" && event.assistantMessageEvent.type === "text_delta") {
    process.stdout.write(event.assistantMessageEvent.delta);
  }
});

await session.prompt("What files are in the current directory?");

import { createAgentSession, ModelRuntime, SessionManager } from "@bastani/atomic";

const modelRuntime = await ModelRuntime.create();
const { session } = await createAgentSession({
  sessionManager: SessionManager.inMemory(),
  modelRuntime,
});

npm install @bastani/atomic

pnpm add @bastani/atomic

bun add @bastani/atomic

import { createAgentSession, SessionManager } from "@bastani/atomic";

// Minimal: defaults with DefaultResourceLoader
const { session } = await createAgentSession();

// Custom: override specific options
const { session } = await createAgentSession({
  model: myModel,
  tools: ["read", "bash"],
  // Or keep defaults and remove specific tools:
  // excludedTools: ["ask_user_question"],
  sessionManager: SessionManager.inMemory(),
});

interface AgentSession {
  // Send a prompt and wait for completion
  prompt(text: string, options?: PromptOptions): Promise<void>;

  // Queue messages during streaming
  steer(text: string): Promise<void>;
  followUp(text: string): Promise<void>;

  // Subscribe to events (returns unsubscribe function)
  subscribe(listener: (event: AgentSessionEvent) => void): () => void;

  // Session info
  sessionFile: string | undefined;
  sessionId: string;

  // Model, thinking, and context-window control
  setModel(model: Model): Promise<void>;
  setThinkingLevel(level: ThinkingLevel): void;
  setContextWindow(contextWindow: number, options?: { persistDefault?: boolean }): void;
  cycleModel(): Promise<ModelCycleResult | undefined>;
  cycleThinkingLevel(): ThinkingLevel | undefined;
  getAvailableContextWindows(): number[];
  supportsContextWindowSelection(): boolean;

  // State access
  agent: Agent;
  model: Model | undefined;
  thinkingLevel: ThinkingLevel;
  messages: AgentMessage[];
  isStreaming: boolean;

  // In-place tree navigation within the current session file
  navigateTree(targetId: string, options?: { summarize?: boolean; customInstructions?: string; replaceInstructions?: boolean; label?: string }): Promise<{ editorText?: string; cancelled: boolean; aborted?: boolean; summaryEntry?: BranchSummaryEntry }>;

  // Verbatim line compaction
  compact(options?: Partial<VerbatimCompactionParameters>): Promise<VerbatimCompactionResult>;
  abortCompaction(): void;

  // Abort current operation
  abort(): Promise<void>;

  // Cleanup
  dispose(): void;
}

import {
  type CreateAgentSessionRuntimeFactory,
  createAgentSessionFromServices,
  createAgentSessionRuntime,
  createAgentSessionServices,
  getAgentDir,
  SessionManager,
} from "@bastani/atomic";

const createRuntime: CreateAgentSessionRuntimeFactory = async ({ cwd, sessionManager, sessionStartEvent }) => {
  const services = await createAgentSessionServices({ cwd });
  return {
    ...(await createAgentSessionFromServices({
      services,
      sessionManager,
      sessionStartEvent,
    })),
    services,
    diagnostics: services.diagnostics,
  };
};

const runtime = await createAgentSessionRuntime(createRuntime, {
  cwd: process.cwd(),
  agentDir: getAgentDir(),
  sessionManager: SessionManager.create(process.cwd()),
});

let session = runtime.session;
let unsubscribe = session.subscribe(() => {});

await runtime.newSession();

unsubscribe();
session = runtime.session;
unsubscribe = session.subscribe(() => {});

interface PromptOptions {
  expandPromptTemplates?: boolean;
  images?: ImageContent[];
  streamingBehavior?: "steer" | "followUp";
  source?: InputSource;
  preflightResult?: (success: boolean) => void;
}

// Basic prompt (when not streaming)
await session.prompt("What files are here?");

// With images
await session.prompt("What's in this image?", {
  images: [{ type: "image", source: { type: "base64", mediaType: "image/png", data: "..." } }]
});

// During streaming: must specify how to queue the message
await session.prompt("Stop and do this instead", { streamingBehavior: "steer" });
await session.prompt("After you're done, also check X", { streamingBehavior: "followUp" });

// Queue a steering message for delivery after the current assistant turn finishes its tool calls
await session.steer("New instruction");

// Wait for agent to finish (delivered only when agent stops)
await session.followUp("After you're done, also do this");

// Access current state
const state = session.agent.state;

// state.messages: AgentMessage[] - conversation history
// state.model: Model - current model
// state.thinkingLevel: ThinkingLevel - current thinking level
// state.systemPrompt: string - system prompt
// state.tools: AgentTool[] - available tools
// state.streamingMessage?: AgentMessage - current partial assistant message
// state.errorMessage?: string - latest assistant error

// Replace messages (useful for branching or restoration)
session.agent.state.messages = messages; // copies the top-level array

// Replace tools
session.agent.state.tools = tools; // copies the top-level array

// Wait for agent to finish processing
await session.agent.waitForIdle();

session.subscribe((event) => {
  switch (event.type) {
    // Streaming text from assistant
    case "message_update":
      if (event.assistantMessageEvent.type === "text_delta") {
        process.stdout.write(event.assistantMessageEvent.delta);
      }
      if (event.assistantMessageEvent.type === "thinking_delta") {
        // Thinking output (if thinking enabled)
      }
      break;
    
    // Tool execution
    case "tool_execution_start":
      console.log(`Tool: ${event.toolName}`);
      break;
    case "tool_execution_update":
      // Streaming tool output
      break;
    case "tool_execution_end":
      console.log(`Result: ${event.isError ? "error" : "success"}`);
      break;
    
    // Message lifecycle
    case "message_start":
      // New message starting
      break;
    case "message_end":
      // Message complete
      break;
    
    // Agent lifecycle
    case "agent_start":
      // Agent started processing prompt
      break;
    case "agent_end":
      // Agent finished (event.messages contains new messages)
      break;
    
    // Turn lifecycle (one LLM response + tool calls)
    case "turn_start":
      break;
    case "turn_end":
      // event.message: assistant response
      // event.toolResults: tool results from this turn
      break;
    
    // Session events (queue, context-window, compaction, retry)
    case "queue_update":
      console.log(event.steering, event.followUp);
      break;
    case "context_window_changed":
      console.log(`Context window: ${event.contextWindow}`);
      break;
    case "compaction_start":
    case "compaction_end":
    case "auto_retry_start":
    case "auto_retry_end":
    case "summarization_retry_scheduled":
    case "summarization_retry_attempt_start":
    case "summarization_retry_finished":
      break;
  }
});

const { session } = await createAgentSession({
  // Working directory for DefaultResourceLoader discovery
  cwd: process.cwd(), // default
  
  // Global config directory
  agentDir: "~/.atomic/agent", // default (expands ~)
});

import { getModel } from "@earendil-works/pi-ai/compat";
import { AuthStorage, ModelRegistry } from "@bastani/atomic";

const authStorage = AuthStorage.create();
const modelRegistry = ModelRegistry.create(authStorage);

// Find specific built-in model (doesn't check if API key exists)
const opus = getModel("anthropic", "claude-opus-4-5");
if (!opus) throw new Error("Model not found");

// Find any model by provider/id, including custom models from models.json
// (doesn't check if API key exists)
const customModel = modelRegistry.find("my-provider", "my-model");

// Get only models that have valid API keys configured
const available = await modelRegistry.getAvailable();

const { session } = await createAgentSession({
  model: opus,
  thinkingLevel: "medium", // off, minimal, low, medium, high, xhigh, max (when supported by the model)
  contextWindow: 1_000_000, // optional; must be supported by the selected model unless non-strict fallback is acceptable
  contextWindowStrict: true, // optional; return contextWindowError instead of warning/fallback when unsupported
  
  // Models for cycling (CTRL+P in interactive mode)
  scopedModels: [
    { model: opus, thinkingLevel: "high" },
    { model: haiku, thinkingLevel: "off" },
  ],
  
  authStorage,
  modelRegistry,
});

import { AuthStorage, ModelRegistry } from "@bastani/atomic";

// Default: uses ~/.atomic/agent/auth.json and ~/.atomic/agent/models.json,
// with legacy ~/.pi/agent/* compatibility reads when available.
const authStorage = AuthStorage.create();
const modelRegistry = ModelRegistry.create(authStorage);

const { session } = await createAgentSession({
  sessionManager: SessionManager.inMemory(),
  authStorage,
  modelRegistry,
});

// Runtime API key override (not persisted to disk)
authStorage.setRuntimeApiKey("anthropic", "sk-my-temp-key");

// Custom auth storage location
const customAuth = AuthStorage.create("/my/app/auth.json");
const customRegistry = ModelRegistry.create(customAuth, "/my/app/models.json");

const { session } = await createAgentSession({
  sessionManager: SessionManager.inMemory(),
  authStorage: customAuth,
  modelRegistry: customRegistry,
});

// No custom models.json (built-in models only)
const simpleRegistry = ModelRegistry.inMemory(authStorage);

import { createAgentSession, DefaultResourceLoader } from "@bastani/atomic";

const loader = new DefaultResourceLoader({
  systemPromptOverride: () => "You are a helpful assistant.",
});
await loader.reload();

const { session } = await createAgentSession({ resourceLoader: loader });

import { createAgentSession } from "@bastani/atomic";

// Read-only mode
const { session } = await createAgentSession({
  tools: ["read", "search", "find", "ls"],
});

// Pick specific tools
const { session } = await createAgentSession({
  tools: ["read", "bash", "search"],
});

// Keep defaults but remove HITL prompts
const { session } = await createAgentSession({
  excludedTools: ["ask_user_question"],
});

// Allowlist first, then subtract exclusions
const { session } = await createAgentSession({
  tools: ["read", "bash", "ask_user_question"],
  excludedTools: ["ask_user_question"], // final tools: read, bash
});

import { createAgentSession, SessionManager } from "@bastani/atomic";

const cwd = "/path/to/project";

// Use default tools for custom cwd
const { session } = await createAgentSession({
  cwd,
  sessionManager: SessionManager.inMemory(cwd),
});

// Or pick specific tools for custom cwd
const { session } = await createAgentSession({
  cwd,
  tools: ["read", "bash", "search"],
  sessionManager: SessionManager.inMemory(cwd),
});

import { Type } from "typebox";
import { createAgentSession, defineTool } from "@bastani/atomic";

// Inline custom tool
const myTool = defineTool({
  name: "my_tool",
  label: "My Tool",
  description: "Does something useful",
  parameters: Type.Object({
    input: Type.String({ description: "Input value" }),
  }),
  execute: async (_toolCallId, params) => ({
    content: [{ type: "text", text: `Result: ${params.input}` }],
    details: {},
  }),
});

// Pass custom tools directly
const { session } = await createAgentSession({
  customTools: [myTool],
});

import { Type, type Static } from "typebox";
import {
  createAgentSession,
  createStructuredOutputTool,
  type StructuredOutputCapture,
} from "@bastani/atomic";

const DecisionSchema = Type.Object({
  approved: Type.Boolean(),
  findings: Type.Array(Type.String()),
}, { additionalProperties: false });

type Decision = Static<typeof DecisionSchema>;
const capture: StructuredOutputCapture<Decision> = {
  called: false,
  value: undefined,
};

const structuredOutput = createStructuredOutputTool({
  schema: DecisionSchema,
  capture,
});

const { session } = await createAgentSession({
  customTools: [structuredOutput],
});

const finalDecision = createStructuredOutputTool({
  name: "final_decision",
  schema: DecisionSchema,
  capture,
});
// The model is prompted to call final_decision exactly once, not structured_output.

await createAgentSession({
  customTools: [finalDecision],
  tools: ["final_decision"], // only this tool is enabled
});

await createAgentSession({
  customTools: [createStructuredOutputTool({ schema: DecisionSchema, capture })],
  // Registers the standard structured_output tool for this session only.
});

import { createAgentSession, DefaultResourceLoader } from "@bastani/atomic";

const loader = new DefaultResourceLoader({
  additionalExtensionPaths: ["/path/to/my-extension.ts"],
  extensionFactories: [
    (pi) => {
      pi.on("agent_start", () => {
        console.log("[Inline Extension] Agent starting");
      });
    },
  ],
});
await loader.reload();

const { session } = await createAgentSession({ resourceLoader: loader });

import { createEventBus, DefaultResourceLoader } from "@bastani/atomic";

const eventBus = createEventBus();
const loader = new DefaultResourceLoader({
  eventBus,
});
await loader.reload();

eventBus.on("my-extension:status", (data) => console.log(data));

import {
  createAgentSession,
  DefaultResourceLoader,
  type Skill,
} from "@bastani/atomic";

const customSkill: Skill = {
  name: "my-skill",
  description: "Custom instructions",
  filePath: "/path/to/SKILL.md",
  baseDir: "/path/to",
  source: "custom",
};

const loader = new DefaultResourceLoader({
  skillsOverride: (current) => ({
    skills: [...current.skills, customSkill],
    diagnostics: current.diagnostics,
  }),
});
await loader.reload();

const { session } = await createAgentSession({ resourceLoader: loader });

import { createAgentSession, DefaultResourceLoader } from "@bastani/atomic";

const loader = new DefaultResourceLoader({
  agentsFilesOverride: (current) => ({
    agentsFiles: [
      ...current.agentsFiles,
      { path: "/virtual/AGENTS.md", content: "# Guidelines\n\n- Be concise" },
    ],
  }),
});
await loader.reload();

const { session } = await createAgentSession({ resourceLoader: loader });

import {
  createAgentSession,
  DefaultResourceLoader,
  type PromptTemplate,
} from "@bastani/atomic";

const customCommand: PromptTemplate = {
  name: "deploy",
  description: "Deploy the application",
  source: "(custom)",
  content: "# Deploy\n\n1. Build\n2. Test\n3. Deploy",
};

const loader = new DefaultResourceLoader({
  promptsOverride: (current) => ({
    prompts: [...current.prompts, customCommand],
    diagnostics: current.diagnostics,
  }),
});
await loader.reload();

const { session } = await createAgentSession({ resourceLoader: loader });

import {
  type CreateAgentSessionRuntimeFactory,
  createAgentSession,
  createAgentSessionFromServices,
  createAgentSessionRuntime,
  createAgentSessionServices,
  getAgentDir,
  SessionManager,
} from "@bastani/atomic";

// In-memory (no persistence)
const { session } = await createAgentSession({
  sessionManager: SessionManager.inMemory(),
});

// New persistent session
const { session: persisted } = await createAgentSession({
  sessionManager: SessionManager.create(process.cwd()),
});

// Continue most recent
const { session: continued, modelFallbackMessage } = await createAgentSession({
  sessionManager: SessionManager.continueRecent(process.cwd()),
});
if (modelFallbackMessage) {
  console.log("Note:", modelFallbackMessage);
}

// Open specific file
const { session: opened } = await createAgentSession({
  sessionManager: SessionManager.open("/path/to/session.jsonl"),
});

// List sessions
const currentProjectSessions = await SessionManager.list(process.cwd());
const allSessions = await SessionManager.listAll(process.cwd());

// Session replacement API for /new, /resume, /fork, /clone, and import flows.
const createRuntime: CreateAgentSessionRuntimeFactory = async ({ cwd, sessionManager, sessionStartEvent }) => {
  const services = await createAgentSessionServices({ cwd });
  return {
    ...(await createAgentSessionFromServices({
      services,
      sessionManager,
      sessionStartEvent,
    })),
    services,
    diagnostics: services.diagnostics,
  };
};

const runtime = await createAgentSessionRuntime(createRuntime, {
  cwd: process.cwd(),
  agentDir: getAgentDir(),
  sessionManager: SessionManager.create(process.cwd()),
});

// Replace the active session with a fresh one
await runtime.newSession();

// Replace the active session with another saved session
await runtime.switchSession("/path/to/session.jsonl");

// Replace the active session with a fork from a specific user entry
await runtime.fork("entry-id");

// Clone the active path through a specific entry
await runtime.fork("entry-id", { position: "at" });

const sm = SessionManager.open("/path/to/session.jsonl");

// Session listing
const currentProjectSessions = await SessionManager.list(process.cwd());
const allSessions = await SessionManager.listAll(process.cwd());

// Tree traversal
const entries = sm.getEntries();        // All entries (excludes header)
const tree = sm.getTree();              // Full tree structure
const path = sm.getPath();              // Path from root to current leaf
const leaf = sm.getLeafEntry();         // Current leaf entry
const entry = sm.getEntry(id);          // Get entry by ID
const children = sm.getChildren(id);    // Direct children of entry

// Labels
const label = sm.getLabel(id);          // Get label for entry
sm.appendLabelChange(id, "checkpoint"); // Set label

// Branching
sm.branch(entryId);                     // Move leaf to earlier entry
sm.branchWithSummary(id, "Summary...");  // Branch with context summary
sm.createBranchedSession(leafId);       // Extract path to new file

import { createAgentSession, SettingsManager, SessionManager } from "@bastani/atomic";

// Default: loads from files (global + project merged)
const { session } = await createAgentSession({
  settingsManager: SettingsManager.create(),
});

// With overrides
const settingsManager = SettingsManager.create();
settingsManager.applyOverrides({
  compaction: { enabled: false },
  retry: { enabled: true, maxRetries: 5 },
});
const { session } = await createAgentSession({ settingsManager });

// In-memory (no file I/O, for testing)
const { session } = await createAgentSession({
  settingsManager: SettingsManager.inMemory({ compaction: { enabled: false } }),
  sessionManager: SessionManager.inMemory(),
});

// Custom directories
const { session } = await createAgentSession({
  settingsManager: SettingsManager.create("/custom/cwd", "/custom/agent"),
});

import {
  DefaultResourceLoader,
  getAgentDir,
} from "@bastani/atomic";

const loader = new DefaultResourceLoader({
  cwd,
  agentDir: getAgentDir(),
});
await loader.reload();

const extensions = loader.getExtensions();
const skills = loader.getSkills();
const prompts = loader.getPrompts();
const themes = loader.getThemes();
const contextFiles = loader.getAgentsFiles().agentsFiles;

interface CreateAgentSessionResult {
  // The session
  session: AgentSession;
  
  // Extensions result (for runner setup)
  extensionsResult: LoadExtensionsResult;
  
  // Warning if session model couldn't be restored
  modelFallbackMessage?: string;

  // Warning if a saved/default context window could not be applied to the selected model
  contextWindowWarning?: string;

  // Error if an explicit strict context-window selection is unsupported
  contextWindowError?: string;
}

interface LoadExtensionsResult {
  extensions: Extension[];
  errors: Array<{ path: string; error: string }>;
  runtime: ExtensionRuntime;
}

import { getModel } from "@earendil-works/pi-ai/compat";
import { Type } from "typebox";
import {
  AuthStorage,
  createAgentSession,
  DefaultResourceLoader,
  defineTool,
  ModelRegistry,
  SessionManager,
  SettingsManager,
} from "@bastani/atomic";

// Set up auth storage (custom location)
const authStorage = AuthStorage.create("/custom/agent/auth.json");

// Runtime API key override (not persisted)
if (process.env.MY_KEY) {
  authStorage.setRuntimeApiKey("anthropic", process.env.MY_KEY);
}

// Model registry (no custom models.json)
const modelRegistry = ModelRegistry.create(authStorage);

// Inline tool
const statusTool = defineTool({
  name: "status",
  label: "Status",
  description: "Get system status",
  parameters: Type.Object({}),
  execute: async () => ({
    content: [{ type: "text", text: `Uptime: ${process.uptime()}s` }],
    details: {},
  }),
});

const model = getModel("anthropic", "claude-opus-4-5");
if (!model) throw new Error("Model not found");

// In-memory settings with overrides
const settingsManager = SettingsManager.inMemory({
  compaction: { enabled: false },
  retry: { enabled: true, maxRetries: 2 },
});

const loader = new DefaultResourceLoader({
  cwd: process.cwd(),
  agentDir: "/custom/agent",
  settingsManager,
  systemPromptOverride: () => "You are a minimal assistant. Be concise.",
});
await loader.reload();

const { session } = await createAgentSession({
  cwd: process.cwd(),
  agentDir: "/custom/agent",

  model,
  thinkingLevel: "off",
  authStorage,
  modelRegistry,

  tools: ["read", "bash", "status"],
  customTools: [statusTool],
  resourceLoader: loader,

  sessionManager: SessionManager.inMemory(),
  settingsManager,
});

session.subscribe((event) => {
  if (event.type === "message_update" && event.assistantMessageEvent.type === "text_delta") {
    process.stdout.write(event.assistantMessageEvent.delta);
  }
});

await session.prompt("Get status and list files.");

import {
  type CreateAgentSessionRuntimeFactory,
  createAgentSessionFromServices,
  createAgentSessionRuntime,
  createAgentSessionServices,
  getAgentDir,
  InteractiveMode,
  SessionManager,
} from "@bastani/atomic";

const createRuntime: CreateAgentSessionRuntimeFactory = async ({ cwd, sessionManager, sessionStartEvent }) => {
  const services = await createAgentSessionServices({ cwd });
  return {
    ...(await createAgentSessionFromServices({ services, sessionManager, sessionStartEvent })),
    services,
    diagnostics: services.diagnostics,
  };
};
const runtime = await createAgentSessionRuntime(createRuntime, {
  cwd: process.cwd(),
  agentDir: getAgentDir(),
  sessionManager: SessionManager.create(process.cwd()),
});

const mode = new InteractiveMode(runtime, {
  migratedProviders: [],
  modelFallbackMessage: undefined,
  initialMessage: "Hello",
  initialImages: [],
  initialMessages: [],
});

await mode.run();

import {
  type CreateAgentSessionRuntimeFactory,
  createAgentSessionFromServices,
  createAgentSessionRuntime,
  createAgentSessionServices,
  getAgentDir,
  runPrintMode,
  SessionManager,
} from "@bastani/atomic";

const createRuntime: CreateAgentSessionRuntimeFactory = async ({ cwd, sessionManager, sessionStartEvent }) => {
  const services = await createAgentSessionServices({ cwd });
  return {
    ...(await createAgentSessionFromServices({ services, sessionManager, sessionStartEvent })),
    services,
    diagnostics: services.diagnostics,
  };
};
const runtime = await createAgentSessionRuntime(createRuntime, {
  cwd: process.cwd(),
  agentDir: getAgentDir(),
  sessionManager: SessionManager.create(process.cwd()),
});

await runPrintMode(runtime, {
  mode: "text",
  initialMessage: "Hello",
  initialImages: [],
  messages: ["Follow up"],
});

import {
  type CreateAgentSessionRuntimeFactory,
  createAgentSessionFromServices,
  createAgentSessionRuntime,
  createAgentSessionServices,
  getAgentDir,
  runRpcMode,
  SessionManager,
} from "@bastani/atomic";

const createRuntime: CreateAgentSessionRuntimeFactory = async ({ cwd, sessionManager, sessionStartEvent }) => {
  const services = await createAgentSessionServices({ cwd });
  return {
    ...(await createAgentSessionFromServices({ services, sessionManager, sessionStartEvent })),
    services,
    diagnostics: services.diagnostics,
  };
};
const runtime = await createAgentSessionRuntime(createRuntime, {
  cwd: process.cwd(),
  agentDir: getAgentDir(),
  sessionManager: SessionManager.create(process.cwd()),
});

await runRpcMode(runtime);

atomic --mode rpc --no-session

// Factory
createAgentSession
createAgentSessionRuntime
AgentSessionRuntime

// Auth and Models
AuthStorage
ModelRegistry

// Resource loading
DefaultResourceLoader
type ResourceLoader
createEventBus

// Constants and helpers
CONFIG_DIR_NAME
defineTool
STRUCTURED_OUTPUT_TOOL_NAME
createStructuredOutputTool
createStructuredOutputCapture
getAgentDir
getPackageDir
getReadmePath
getDocsPath
getExamplesPath
generateDiffString
generateUnifiedPatch
type EditDiffResult

// Session management
SessionManager
SettingsManager

// Tool factories
createCodingTools
createReadOnlyTools
createReadTool, createBashTool, createEditTool, createWriteTool
createGrepTool, createFindTool, createLsTool

// Types
type CreateAgentSessionOptions
type CreateAgentSessionResult
type StructuredOutputCapture
type StructuredOutputToolOptions
type ExtensionFactory
type ExtensionAPI
type ToolDefinition
type Skill
type PromptTemplate
type Tool