Merge sdk-272: Add SDK for programmatic usage

- createAgentSession() factory with full control
- SessionManager/SettingsManager static factories
- Project-specific settings support
- 12 examples and comprehensive docs

Fixes #272

packages/coding-agent/CHANGELOG.md

@@ -2,6 +2,16 @@
 
 ## [Unreleased]
 
+### Added
+
+- **SDK for programmatic usage**: New `createAgentSession()` factory with full control over model, tools, hooks, skills, session persistence, and settings. Philosophy: "omit to discover, provide to override". Includes 12 examples and comprehensive documentation. ([#272](https://github.com/badlogic/pi-mono/issues/272))
+
+- **Project-specific settings**: Settings now load from both `~/.pi/agent/settings.json` (global) and `<cwd>/.pi/settings.json` (project). Project settings override global with deep merge for nested objects. Project settings are read-only (for version control). ([#276](https://github.com/badlogic/pi-mono/pull/276))
+
+- **SettingsManager static factories**: `SettingsManager.create(cwd?, agentDir?)` for file-based settings, `SettingsManager.inMemory(settings?)` for testing. Added `applyOverrides()` for programmatic overrides.
+
+- **SessionManager static factories**: `SessionManager.create()`, `SessionManager.open()`, `SessionManager.continueRecent()`, `SessionManager.inMemory()`, `SessionManager.list()` for flexible session management.
+
 ## [0.25.4] - 2025-12-22
 
 ### Fixed

packages/coding-agent/README.md

@@ -33,6 +33,9 @@ Works on Linux, macOS, and Windows (requires bash; see [Windows Setup](#windows-
 - [CLI Reference](#cli-reference)
 - [Tools](#tools)
 - [Programmatic Usage](#programmatic-usage)
+  - [SDK](#sdk)
+  - [RPC Mode](#rpc-mode)
+  - [HTML Export](#html-export)
 - [Philosophy](#philosophy)
 - [Development](#development)
 - [License](#license)
@@ -649,7 +652,14 @@ export default factory;
 
 ### Settings File
 
-`~/.pi/agent/settings.json` stores persistent preferences:
+Settings are loaded from two locations and merged:
+
+1. **Global:** `~/.pi/agent/settings.json` - user preferences
+2. **Project:** `<cwd>/.pi/settings.json` - project-specific overrides (version control friendly)
+
+Project settings override global settings. For nested objects, individual keys merge. Settings changed via TUI (model, thinking level, etc.) are saved to global preferences only.
+
+Global `~/.pi/agent/settings.json` stores persistent preferences:
 
 ```json
 {
@@ -818,9 +828,43 @@ For adding new tools, see [Custom Tools](#custom-tools) in the Configuration sec
 
 ## Programmatic Usage
 
+### SDK
+
+For embedding pi in Node.js/TypeScript applications, use the SDK:
+
+```typescript
+import { createAgentSession, SessionManager } from "@mariozechner/pi-coding-agent";
+
+const { session } = await createAgentSession({
+  sessionManager: SessionManager.inMemory(),
+});
+
+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?");
+```
+
+The SDK provides full control over:
+- Model selection and thinking level
+- System prompt (replace or modify)
+- Tools (built-in subsets, custom tools)
+- Hooks (inline or discovered)
+- Skills, context files, slash commands
+- Session persistence (`SessionManager`)
+- Settings (`SettingsManager`)
+- API key resolution and OAuth
+
+**Philosophy:** "Omit to discover, provide to override." Omit an option and pi discovers from standard locations. Provide an option and your value is used.
+
+> See [SDK Documentation](docs/sdk.md) for the full API reference. See [examples/sdk/](examples/sdk/) for working examples from minimal to full control.
+
 ### RPC Mode
 
-For embedding pi in other applications:
+For embedding pi from other languages or with process isolation:
 
 ```bash
 pi --mode rpc --no-session
@@ -832,9 +876,7 @@ Send JSON commands on stdin:
 {"type":"abort"}
 ```
 
-See [RPC documentation](docs/rpc.md) for full protocol.
+> See [RPC Documentation](docs/rpc.md) for the full protocol.
-
-**Node.js/TypeScript:** Consider using `AgentSession` directly from `@mariozechner/pi-coding-agent` instead of subprocess. See [`src/core/agent-session.ts`](src/core/agent-session.ts) and [`src/modes/rpc/rpc-client.ts`](src/modes/rpc/rpc-client.ts).
 
 ### HTML Export
 

packages/coding-agent/docs/sdk.md

@@ -0,0 +1,819 @@
+# SDK
+
+The SDK provides programmatic access to pi's agent capabilities. Use it to embed pi in other applications, build custom interfaces, or integrate with automated workflows.
+
+**Example use cases:**
+- Build a custom UI (web, desktop, mobile)
+- Integrate agent capabilities into existing applications
+- Create automated pipelines with agent reasoning
+- Build custom tools that spawn sub-agents
+- Test agent behavior programmatically
+
+See [examples/sdk/](../examples/sdk/) for working examples from minimal to full control.
+
+## Quick Start
+
+```typescript
+import { createAgentSession, SessionManager } from "@mariozechner/pi-coding-agent";
+
+const { session } = await createAgentSession({
+  sessionManager: SessionManager.inMemory(),
+});
+
+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?");
+```
+
+## Installation
+
+```bash
+npm install @mariozechner/pi-coding-agent
+```
+
+The SDK is included in the main package. No separate installation needed.
+
+## Core Concepts
+
+### createAgentSession()
+
+The main factory function. Creates an `AgentSession` with configurable options.
+
+**Philosophy:** "Omit to discover, provide to override."
+- Omit an option → pi discovers/loads from standard locations
+- Provide an option → your value is used, discovery skipped for that option
+
+```typescript
+import { createAgentSession } from "@mariozechner/pi-coding-agent";
+
+// Minimal: all defaults (discovers everything from cwd and ~/.pi/agent)
+const { session } = await createAgentSession();
+
+// Custom: override specific options
+const { session } = await createAgentSession({
+  model: myModel,
+  systemPrompt: "You are helpful.",
+  tools: [readTool, bashTool],
+  sessionManager: SessionManager.inMemory(),
+});
+```
+
+### AgentSession
+
+The session manages the agent lifecycle, message history, and event streaming.
+
+```typescript
+interface AgentSession {
+  // Send a prompt and wait for completion
+  prompt(text: string, options?: PromptOptions): Promise<void>;
+  
+  // Subscribe to events (returns unsubscribe function)
+  subscribe(listener: (event: AgentSessionEvent) => void): () => void;
+  
+  // Session info
+  sessionFile: string | null;
+  sessionId: string;
+  
+  // Model control
+  setModel(model: Model): Promise<void>;
+  setThinkingLevel(level: ThinkingLevel): void;
+  cycleModel(): Promise<ModelCycleResult | null>;
+  cycleThinkingLevel(): ThinkingLevel | null;
+  
+  // State access
+  agent: Agent;
+  model: Model | null;
+  thinkingLevel: ThinkingLevel;
+  messages: AppMessage[];
+  isStreaming: boolean;
+  
+  // Session management
+  reset(): Promise<void>;
+  branch(entryIndex: number): Promise<{ selectedText: string; skipped: boolean }>;
+  switchSession(sessionPath: string): Promise<void>;
+  
+  // Compaction
+  compact(customInstructions?: string): Promise<CompactionResult>;
+  abortCompaction(): void;
+  
+  // Abort current operation
+  abort(): Promise<void>;
+  
+  // Cleanup
+  dispose(): void;
+}
+```
+
+### Agent and AgentState
+
+The `Agent` class (from `@mariozechner/pi-agent-core`) handles the core LLM interaction. Access it via `session.agent`.
+
+```typescript
+// Access current state
+const state = session.agent.state;
+
+// state.messages: AppMessage[] - conversation history
+// state.model: Model - current model
+// state.thinkingLevel: ThinkingLevel - current thinking level
+// state.systemPrompt: string - system prompt
+// state.tools: Tool[] - available tools
+
+// Replace messages (useful for branching, restoration)
+session.agent.replaceMessages(messages);
+
+// Wait for agent to finish processing
+await session.agent.waitForIdle();
+```
+
+### Events
+
+Subscribe to events to receive streaming output and lifecycle notifications.
+
+```typescript
+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 (auto-compaction, retry)
+    case "auto_compaction_start":
+    case "auto_compaction_end":
+    case "auto_retry_start":
+    case "auto_retry_end":
+      break;
+  }
+});
+```
+
+## Options Reference
+
+### Directories
+
+```typescript
+const { session } = await createAgentSession({
+  // Working directory for project-local discovery
+  cwd: process.cwd(), // default
+  
+  // Global config directory
+  agentDir: "~/.pi/agent", // default (expands ~)
+});
+```
+
+`cwd` is used for:
+- Project hooks (`.pi/hooks/`)
+- Project tools (`.pi/tools/`)
+- Project skills (`.pi/skills/`)
+- Project commands (`.pi/commands/`)
+- Context files (`AGENTS.md` walking up from cwd)
+- Session directory naming
+
+`agentDir` is used for:
+- Global hooks (`hooks/`)
+- Global tools (`tools/`)
+- Global skills (`skills/`)
+- Global commands (`commands/`)
+- Global context file (`AGENTS.md`)
+- Settings (`settings.json`)
+- Models (`models.json`)
+- OAuth tokens (`oauth.json`)
+- Sessions (`sessions/`)
+
+### Model
+
+```typescript
+import { findModel, discoverAvailableModels } from "@mariozechner/pi-coding-agent";
+
+// Find specific model (returns { model, error })
+const { model, error } = findModel("anthropic", "claude-sonnet-4-20250514");
+if (error) throw new Error(error);
+if (!model) throw new Error("Model not found");
+
+// Or get all models with valid API keys
+const available = await discoverAvailableModels();
+
+const { session } = await createAgentSession({
+  model: model,
+  thinkingLevel: "medium", // off, minimal, low, medium, high, xhigh
+  
+  // Models for cycling (Ctrl+P in interactive mode)
+  scopedModels: [
+    { model: sonnet, thinkingLevel: "high" },
+    { model: haiku, thinkingLevel: "off" },
+  ],
+});
+```
+
+If no model is provided:
+1. Tries to restore from session (if continuing)
+2. Uses default from settings
+3. Falls back to first available model
+
+> See [examples/sdk/02-custom-model.ts](../examples/sdk/02-custom-model.ts)
+
+### API Keys
+
+```typescript
+import { defaultGetApiKey, configureOAuthStorage } from "@mariozechner/pi-coding-agent";
+
+// Default: checks models.json, OAuth, environment variables
+const { session } = await createAgentSession();
+
+// Custom resolver
+const { session } = await createAgentSession({
+  getApiKey: async (model) => {
+    // Custom logic (secrets manager, database, etc.)
+    if (model.provider === "anthropic") {
+      return process.env.MY_ANTHROPIC_KEY;
+    }
+    // Fall back to default
+    return defaultGetApiKey()(model);
+  },
+});
+
+// Use OAuth from ~/.pi/agent with custom agentDir for everything else
+configureOAuthStorage(); // Must call before createAgentSession
+const { session } = await createAgentSession({
+  agentDir: "/custom/config",
+  // OAuth tokens still come from ~/.pi/agent/oauth.json
+});
+```
+
+> See [examples/sdk/09-api-keys-and-oauth.ts](../examples/sdk/09-api-keys-and-oauth.ts)
+
+### System Prompt
+
+```typescript
+const { session } = await createAgentSession({
+  // Replace entirely
+  systemPrompt: "You are a helpful assistant.",
+  
+  // Or modify default (receives default, returns modified)
+  systemPrompt: (defaultPrompt) => {
+    return `${defaultPrompt}\n\n## Additional Rules\n- Be concise`;
+  },
+});
+```
+
+> See [examples/sdk/03-custom-prompt.ts](../examples/sdk/03-custom-prompt.ts)
+
+### Tools
+
+```typescript
+import {
+  codingTools,   // read, bash, edit, write (default)
+  readOnlyTools, // read, bash
+  readTool, bashTool, editTool, writeTool,
+  grepTool, findTool, lsTool,
+} from "@mariozechner/pi-coding-agent";
+
+// Use built-in tool set
+const { session } = await createAgentSession({
+  tools: readOnlyTools,
+});
+
+// Pick specific tools
+const { session } = await createAgentSession({
+  tools: [readTool, bashTool, grepTool],
+});
+```
+
+> See [examples/sdk/05-tools.ts](../examples/sdk/05-tools.ts)
+
+### Custom Tools
+
+```typescript
+import { Type } from "@sinclair/typebox";
+import { createAgentSession, discoverCustomTools, type CustomAgentTool } from "@mariozechner/pi-coding-agent";
+
+// Inline custom tool
+const myTool: CustomAgentTool = {
+  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: {},
+  }),
+};
+
+// Replace discovery with inline tools
+const { session } = await createAgentSession({
+  customTools: [{ tool: myTool }],
+});
+
+// Merge with discovered tools
+const discovered = await discoverCustomTools();
+const { session } = await createAgentSession({
+  customTools: [...discovered, { tool: myTool }],
+});
+
+// Add paths without replacing discovery
+const { session } = await createAgentSession({
+  additionalCustomToolPaths: ["/extra/tools"],
+});
+```
+
+> See [examples/sdk/05-tools.ts](../examples/sdk/05-tools.ts)
+
+### Hooks
+
+```typescript
+import { createAgentSession, discoverHooks, type HookFactory } from "@mariozechner/pi-coding-agent";
+
+// Inline hook
+const loggingHook: HookFactory = (api) => {
+  api.on("tool_call", async (event) => {
+    console.log(`Tool: ${event.toolName}`);
+    return undefined; // Don't block
+  });
+  
+  api.on("tool_call", async (event) => {
+    // Block dangerous commands
+    if (event.toolName === "bash" && event.input.command?.includes("rm -rf")) {
+      return { block: true, reason: "Dangerous command" };
+    }
+    return undefined;
+  });
+};
+
+// Replace discovery
+const { session } = await createAgentSession({
+  hooks: [{ factory: loggingHook }],
+});
+
+// Disable all hooks
+const { session } = await createAgentSession({
+  hooks: [],
+});
+
+// Merge with discovered
+const discovered = await discoverHooks();
+const { session } = await createAgentSession({
+  hooks: [...discovered, { factory: loggingHook }],
+});
+
+// Add paths without replacing
+const { session } = await createAgentSession({
+  additionalHookPaths: ["/extra/hooks"],
+});
+```
+
+> See [examples/sdk/06-hooks.ts](../examples/sdk/06-hooks.ts)
+
+### Skills
+
+```typescript
+import { createAgentSession, discoverSkills, type Skill } from "@mariozechner/pi-coding-agent";
+
+// Discover and filter
+const allSkills = discoverSkills();
+const filtered = allSkills.filter(s => s.name.includes("search"));
+
+// Custom skill
+const mySkill: Skill = {
+  name: "my-skill",
+  description: "Custom instructions",
+  filePath: "/path/to/SKILL.md",
+  baseDir: "/path/to",
+  source: "custom",
+};
+
+const { session } = await createAgentSession({
+  skills: [...filtered, mySkill],
+});
+
+// Disable skills
+const { session } = await createAgentSession({
+  skills: [],
+});
+
+// Discovery with settings filter
+const skills = discoverSkills(process.cwd(), undefined, {
+  ignoredSkills: ["browser-*"],  // glob patterns to exclude
+  includeSkills: ["search-*"],   // glob patterns to include (empty = all)
+});
+```
+
+> See [examples/sdk/04-skills.ts](../examples/sdk/04-skills.ts)
+
+### Context Files
+
+```typescript
+import { createAgentSession, discoverContextFiles } from "@mariozechner/pi-coding-agent";
+
+// Discover AGENTS.md files
+const discovered = discoverContextFiles();
+
+// Add custom context
+const { session } = await createAgentSession({
+  contextFiles: [
+    ...discovered,
+    {
+      path: "/virtual/AGENTS.md",
+      content: "# Guidelines\n\n- Be concise\n- Use TypeScript",
+    },
+  ],
+});
+
+// Disable context files
+const { session } = await createAgentSession({
+  contextFiles: [],
+});
+```
+
+> See [examples/sdk/07-context-files.ts](../examples/sdk/07-context-files.ts)
+
+### Slash Commands
+
+```typescript
+import { createAgentSession, discoverSlashCommands, type FileSlashCommand } from "@mariozechner/pi-coding-agent";
+
+const discovered = discoverSlashCommands();
+
+const customCommand: FileSlashCommand = {
+  name: "deploy",
+  description: "Deploy the application",
+  source: "(custom)",
+  content: "# Deploy\n\n1. Build\n2. Test\n3. Deploy",
+};
+
+const { session } = await createAgentSession({
+  slashCommands: [...discovered, customCommand],
+});
+```
+
+> See [examples/sdk/08-slash-commands.ts](../examples/sdk/08-slash-commands.ts)
+
+### Session Management
+
+```typescript
+import { createAgentSession, SessionManager } from "@mariozechner/pi-coding-agent";
+
+// In-memory (no persistence)
+const { session } = await createAgentSession({
+  sessionManager: SessionManager.inMemory(),
+});
+
+// New persistent session
+const { session } = await createAgentSession({
+  sessionManager: SessionManager.create(process.cwd()),
+});
+
+// Continue most recent
+const { session, modelFallbackMessage } = await createAgentSession({
+  sessionManager: SessionManager.continueRecent(process.cwd()),
+});
+if (modelFallbackMessage) {
+  console.log("Note:", modelFallbackMessage);
+}
+
+// Open specific file
+const { session } = await createAgentSession({
+  sessionManager: SessionManager.open("/path/to/session.jsonl"),
+});
+
+// List available sessions
+const sessions = SessionManager.list(process.cwd());
+for (const info of sessions) {
+  console.log(`${info.id}: ${info.firstMessage} (${info.messageCount} messages)`);
+}
+
+// Custom agentDir for sessions
+const { session } = await createAgentSession({
+  agentDir: "/custom/agent",
+  sessionManager: SessionManager.create(process.cwd(), "/custom/agent"),
+});
+```
+
+> See [examples/sdk/11-sessions.ts](../examples/sdk/11-sessions.ts)
+
+### Settings Management
+
+```typescript
+import { createAgentSession, SettingsManager, SessionManager } from "@mariozechner/pi-coding-agent";
+
+// 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"),
+});
+```
+
+**Static factories:**
+- `SettingsManager.create(cwd?, agentDir?)` - Load from files
+- `SettingsManager.inMemory(settings?)` - No file I/O
+
+**Project-specific settings:**
+
+Settings load from two locations and merge:
+1. Global: `~/.pi/agent/settings.json`
+2. Project: `<cwd>/.pi/settings.json`
+
+Project overrides global. Nested objects merge keys. Setters only modify global (project is read-only for version control).
+
+> See [examples/sdk/10-settings.ts](../examples/sdk/10-settings.ts)
+
+## Discovery Functions
+
+All discovery functions accept optional `cwd` and `agentDir` parameters.
+
+```typescript
+import {
+  discoverModels,
+  discoverAvailableModels,
+  findModel,
+  discoverSkills,
+  discoverHooks,
+  discoverCustomTools,
+  discoverContextFiles,
+  discoverSlashCommands,
+  loadSettings,
+  buildSystemPrompt,
+} from "@mariozechner/pi-coding-agent";
+
+// Models
+const allModels = discoverModels();
+const available = await discoverAvailableModels();
+const { model, error } = findModel("anthropic", "claude-sonnet-4-20250514");
+
+// Skills
+const skills = discoverSkills(cwd, agentDir, skillsSettings);
+
+// Hooks (async - loads TypeScript)
+const hooks = await discoverHooks(cwd, agentDir);
+
+// Custom tools (async - loads TypeScript)
+const tools = await discoverCustomTools(cwd, agentDir);
+
+// Context files
+const contextFiles = discoverContextFiles(cwd, agentDir);
+
+// Slash commands
+const commands = discoverSlashCommands(cwd, agentDir);
+
+// Settings (global + project merged)
+const settings = loadSettings(cwd, agentDir);
+
+// Build system prompt manually
+const prompt = buildSystemPrompt({
+  skills,
+  contextFiles,
+  appendPrompt: "Additional instructions",
+  cwd,
+});
+```
+
+## Return Value
+
+`createAgentSession()` returns:
+
+```typescript
+interface CreateAgentSessionResult {
+  // The session
+  session: AgentSession;
+  
+  // Custom tools (for UI setup)
+  customToolsResult: {
+    tools: LoadedCustomTool[];
+    setUIContext: (ctx, hasUI) => void;
+  };
+  
+  // Warning if session model couldn't be restored
+  modelFallbackMessage?: string;
+}
+```
+
+## Complete Example
+
+```typescript
+import { Type } from "@sinclair/typebox";
+import {
+  createAgentSession,
+  configureOAuthStorage,
+  defaultGetApiKey,
+  findModel,
+  SessionManager,
+  SettingsManager,
+  readTool,
+  bashTool,
+  type HookFactory,
+  type CustomAgentTool,
+} from "@mariozechner/pi-coding-agent";
+import { getAgentDir } from "@mariozechner/pi-coding-agent/config";
+
+// Use OAuth from default location
+configureOAuthStorage(getAgentDir());
+
+// Custom API key with fallback
+const getApiKey = async (model: { provider: string }) => {
+  if (model.provider === "anthropic" && process.env.MY_KEY) {
+    return process.env.MY_KEY;
+  }
+  return defaultGetApiKey()(model as any);
+};
+
+// Inline hook
+const auditHook: HookFactory = (api) => {
+  api.on("tool_call", async (event) => {
+    console.log(`[Audit] ${event.toolName}`);
+    return undefined;
+  });
+};
+
+// Inline tool
+const statusTool: CustomAgentTool = {
+  name: "status",
+  label: "Status",
+  description: "Get system status",
+  parameters: Type.Object({}),
+  execute: async () => ({
+    content: [{ type: "text", text: `Uptime: ${process.uptime()}s` }],
+    details: {},
+  }),
+};
+
+const { model, error } = findModel("anthropic", "claude-sonnet-4-20250514");
+if (error) throw new Error(error);
+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 { session } = await createAgentSession({
+  cwd: process.cwd(),
+  agentDir: "/custom/agent",
+  
+  model,
+  thinkingLevel: "off",
+  getApiKey,
+  
+  systemPrompt: "You are a minimal assistant. Be concise.",
+  
+  tools: [readTool, bashTool],
+  customTools: [{ tool: statusTool }],
+  hooks: [{ factory: auditHook }],
+  skills: [],
+  contextFiles: [],
+  slashCommands: [],
+  
+  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.");
+```
+
+## RPC Mode Alternative
+
+For subprocess-based integration, use RPC mode instead of the SDK:
+
+```bash
+pi --mode rpc --no-session
+```
+
+See [RPC documentation](rpc.md) for the JSON protocol.
+
+The SDK is preferred when:
+- You want type safety
+- You're in the same Node.js process
+- You need direct access to agent state
+- You want to customize tools/hooks programmatically
+
+RPC mode is preferred when:
+- You're integrating from another language
+- You want process isolation
+- You're building a language-agnostic client
+
+## Exports
+
+The main entry point exports:
+
+```typescript
+// Factory
+createAgentSession
+configureOAuthStorage
+
+// Discovery
+discoverModels
+discoverAvailableModels
+findModel
+discoverSkills
+discoverHooks
+discoverCustomTools
+discoverContextFiles
+discoverSlashCommands
+
+// Helpers
+defaultGetApiKey
+loadSettings
+buildSystemPrompt
+
+// Session management
+SessionManager
+SettingsManager
+
+// Built-in tools
+codingTools
+readOnlyTools
+readTool, bashTool, editTool, writeTool
+grepTool, findTool, lsTool
+
+// Types
+type CreateAgentSessionOptions
+type CreateAgentSessionResult
+type CustomAgentTool
+type HookFactory
+type Skill
+type FileSlashCommand
+type Settings
+type SkillsSettings
+type Tool
+```
+
+For hook types, import from the hooks subpath:
+
+```typescript
+import type { HookAPI, HookEvent, ToolCallEvent } from "@mariozechner/pi-coding-agent/hooks";
+```
+
+For config utilities:
+
+```typescript
+import { getAgentDir } from "@mariozechner/pi-coding-agent/config";
+```

packages/coding-agent/examples/README.md

@@ -0,0 +1,29 @@
+# Examples
+
+Example code for pi-coding-agent.
+
+## Directories
+
+### [sdk/](sdk/)
+Programmatic usage via `createAgentSession()`. Shows how to customize models, prompts, tools, hooks, and session management.
+
+### [hooks/](hooks/)
+Example hooks for intercepting tool calls, adding safety gates, and integrating with external systems.
+
+### [custom-tools/](custom-tools/)
+Example custom tools that extend the agent's capabilities.
+
+## Running Examples
+
+```bash
+cd packages/coding-agent
+npx tsx examples/sdk/01-minimal.ts
+npx tsx examples/hooks/permission-gate.ts
+```
+
+## Documentation
+
+- [SDK Reference](sdk/README.md)
+- [Hooks Documentation](../docs/hooks.md)
+- [Custom Tools Documentation](../docs/custom-tools.md)
+- [Skills Documentation](../docs/skills.md)

packages/coding-agent/examples/sdk/01-minimal.ts

@@ -0,0 +1,22 @@
+/**
+ * Minimal SDK Usage
+ *
+ * Uses all defaults: discovers skills, hooks, tools, context files
+ * from cwd and ~/.pi/agent. Model chosen from settings or first available.
+ */
+
+import { createAgentSession } from "../../src/index.js";
+
+const { session } = await createAgentSession();
+
+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?");
+session.state.messages.forEach((msg) => {
+	console.log(msg);
+});
+console.log();

packages/coding-agent/examples/sdk/02-custom-model.ts

@@ -0,0 +1,36 @@
+/**
+ * Custom Model Selection
+ *
+ * Shows how to select a specific model and thinking level.
+ */
+
+import { createAgentSession, findModel, discoverAvailableModels } from "../../src/index.js";
+
+// Option 1: Find a specific model by provider/id
+const { model: sonnet } = findModel("anthropic", "claude-sonnet-4-20250514");
+if (sonnet) {
+	console.log(`Found model: ${sonnet.provider}/${sonnet.id}`);
+}
+
+// Option 2: Pick from available models (have valid API keys)
+const available = await discoverAvailableModels();
+console.log(
+	"Available models:",
+	available.map((m) => `${m.provider}/${m.id}`),
+);
+
+if (available.length > 0) {
+	const { session } = await createAgentSession({
+		model: available[0],
+		thinkingLevel: "medium", // off, low, medium, high
+	});
+
+	session.subscribe((event) => {
+		if (event.type === "message_update" && event.assistantMessageEvent.type === "text_delta") {
+			process.stdout.write(event.assistantMessageEvent.delta);
+		}
+	});
+
+	await session.prompt("Say hello in one sentence.");
+	console.log();
+}

packages/coding-agent/examples/sdk/03-custom-prompt.ts

@@ -0,0 +1,44 @@
+/**
+ * Custom System Prompt
+ *
+ * Shows how to replace or modify the default system prompt.
+ */
+
+import { createAgentSession, SessionManager } from "../../src/index.js";
+
+// Option 1: Replace prompt entirely
+const { session: session1 } = await createAgentSession({
+	systemPrompt: `You are a helpful assistant that speaks like a pirate.
+Always end responses with "Arrr!"`,
+	sessionManager: SessionManager.inMemory(),
+});
+
+session1.subscribe((event) => {
+	if (event.type === "message_update" && event.assistantMessageEvent.type === "text_delta") {
+		process.stdout.write(event.assistantMessageEvent.delta);
+	}
+});
+
+console.log("=== Replace prompt ===");
+await session1.prompt("What is 2 + 2?");
+console.log("\n");
+
+// Option 2: Modify default prompt (receives default, returns modified)
+const { session: session2 } = await createAgentSession({
+	systemPrompt: (defaultPrompt) => `${defaultPrompt}
+
+## Additional Instructions
+- Always be concise
+- Use bullet points when listing things`,
+	sessionManager: SessionManager.inMemory(),
+});
+
+session2.subscribe((event) => {
+	if (event.type === "message_update" && event.assistantMessageEvent.type === "text_delta") {
+		process.stdout.write(event.assistantMessageEvent.delta);
+	}
+});
+
+console.log("=== Modify prompt ===");
+await session2.prompt("List 3 benefits of TypeScript.");
+console.log();

packages/coding-agent/examples/sdk/04-skills.ts

@@ -0,0 +1,44 @@
+/**
+ * Skills Configuration
+ *
+ * Skills provide specialized instructions loaded into the system prompt.
+ * Discover, filter, merge, or replace them.
+ */
+
+import { createAgentSession, discoverSkills, SessionManager, type Skill } from "../../src/index.js";
+
+// Discover all skills from cwd/.pi/skills, ~/.pi/agent/skills, etc.
+const allSkills = discoverSkills();
+console.log(
+	"Discovered skills:",
+	allSkills.map((s) => s.name),
+);
+
+// Filter to specific skills
+const filteredSkills = allSkills.filter((s) => s.name.includes("browser") || s.name.includes("search"));
+
+// Or define custom skills inline
+const customSkill: Skill = {
+	name: "my-skill",
+	description: "Custom project instructions",
+	filePath: "/virtual/SKILL.md",
+	baseDir: "/virtual",
+	source: "custom",
+};
+
+// Use filtered + custom skills
+const { session } = await createAgentSession({
+	skills: [...filteredSkills, customSkill],
+	sessionManager: SessionManager.inMemory(),
+});
+
+console.log(`Session created with ${filteredSkills.length + 1} skills`);
+
+// To disable all skills:
+// skills: []
+
+// To use discovery with filtering via settings:
+// discoverSkills(process.cwd(), undefined, {
+//   ignoredSkills: ["browser-tools"],  // glob patterns to exclude
+//   includeSkills: ["brave-*"],        // glob patterns to include (empty = all)
+// })

packages/coding-agent/examples/sdk/05-tools.ts

@@ -0,0 +1,67 @@
+/**
+ * Tools Configuration
+ *
+ * Use built-in tool sets, individual tools, or add custom tools.
+ */
+
+import { Type } from "@sinclair/typebox";
+import {
+	createAgentSession,
+	discoverCustomTools,
+	SessionManager,
+	codingTools, // read, bash, edit, write (default)
+	readOnlyTools, // read, bash
+	readTool,
+	bashTool,
+	grepTool,
+	type CustomAgentTool,
+} from "../../src/index.js";
+
+// Read-only mode (no edit/write)
+const { session: readOnly } = await createAgentSession({
+	tools: readOnlyTools,
+	sessionManager: SessionManager.inMemory(),
+});
+console.log("Read-only session created");
+
+// Custom tool selection
+const { session: custom } = await createAgentSession({
+	tools: [readTool, bashTool, grepTool],
+	sessionManager: SessionManager.inMemory(),
+});
+console.log("Custom tools session created");
+
+// Inline custom tool (needs TypeBox schema)
+const weatherTool: CustomAgentTool = {
+	name: "get_weather",
+	label: "Get Weather",
+	description: "Get current weather for a city",
+	parameters: Type.Object({
+		city: Type.String({ description: "City name" }),
+	}),
+	execute: async (_toolCallId, params) => ({
+		content: [{ type: "text", text: `Weather in ${(params as { city: string }).city}: 22°C, sunny` }],
+		details: {},
+	}),
+};
+
+const { session } = await createAgentSession({
+	customTools: [{ tool: weatherTool }],
+	sessionManager: SessionManager.inMemory(),
+});
+
+session.subscribe((event) => {
+	if (event.type === "message_update" && event.assistantMessageEvent.type === "text_delta") {
+		process.stdout.write(event.assistantMessageEvent.delta);
+	}
+});
+
+await session.prompt("What's the weather in Tokyo?");
+console.log();
+
+// Merge with discovered tools from cwd/.pi/tools and ~/.pi/agent/tools:
+// const discovered = await discoverCustomTools();
+// customTools: [...discovered, { tool: myTool }]
+
+// Or add paths without replacing discovery:
+// additionalCustomToolPaths: ["/extra/tools"]

packages/coding-agent/examples/sdk/06-hooks.ts

@@ -0,0 +1,61 @@
+/**
+ * Hooks Configuration
+ *
+ * Hooks intercept agent events for logging, blocking, or modification.
+ */
+
+import { createAgentSession, discoverHooks, SessionManager, type HookFactory } from "../../src/index.js";
+
+// Logging hook
+const loggingHook: HookFactory = (api) => {
+	api.on("agent_start", async () => {
+		console.log("[Hook] Agent starting");
+	});
+
+	api.on("tool_call", async (event) => {
+		console.log(`[Hook] Tool: ${event.toolName}`);
+		return undefined; // Don't block
+	});
+
+	api.on("agent_end", async (event) => {
+		console.log(`[Hook] Done, ${event.messages.length} messages`);
+	});
+};
+
+// Blocking hook (returns { block: true, reason: "..." })
+const safetyHook: HookFactory = (api) => {
+	api.on("tool_call", async (event) => {
+		if (event.toolName === "bash") {
+			const cmd = (event.input as { command?: string }).command ?? "";
+			if (cmd.includes("rm -rf")) {
+				return { block: true, reason: "Dangerous command blocked" };
+			}
+		}
+		return undefined;
+	});
+};
+
+// Use inline hooks
+const { session } = await createAgentSession({
+	hooks: [{ factory: loggingHook }, { factory: safetyHook }],
+	sessionManager: SessionManager.inMemory(),
+});
+
+session.subscribe((event) => {
+	if (event.type === "message_update" && event.assistantMessageEvent.type === "text_delta") {
+		process.stdout.write(event.assistantMessageEvent.delta);
+	}
+});
+
+await session.prompt("List files in the current directory.");
+console.log();
+
+// Disable all hooks:
+// hooks: []
+
+// Merge with discovered hooks:
+// const discovered = await discoverHooks();
+// hooks: [...discovered, { factory: myHook }]
+
+// Add paths without replacing discovery:
+// additionalHookPaths: ["/extra/hooks"]

packages/coding-agent/examples/sdk/07-context-files.ts

@@ -0,0 +1,36 @@
+/**
+ * Context Files (AGENTS.md)
+ *
+ * Context files provide project-specific instructions loaded into the system prompt.
+ */
+
+import { createAgentSession, discoverContextFiles, SessionManager } from "../../src/index.js";
+
+// Discover AGENTS.md files walking up from cwd
+const discovered = discoverContextFiles();
+console.log("Discovered context files:");
+for (const file of discovered) {
+	console.log(`  - ${file.path} (${file.content.length} chars)`);
+}
+
+// Use custom context files
+const { session } = await createAgentSession({
+	contextFiles: [
+		...discovered,
+		{
+			path: "/virtual/AGENTS.md",
+			content: `# Project Guidelines
+
+## Code Style
+- Use TypeScript strict mode
+- No any types
+- Prefer const over let`,
+		},
+	],
+	sessionManager: SessionManager.inMemory(),
+});
+
+console.log(`Session created with ${discovered.length + 1} context files`);
+
+// Disable context files:
+// contextFiles: []

packages/coding-agent/examples/sdk/08-slash-commands.ts

@@ -0,0 +1,37 @@
+/**
+ * Slash Commands
+ *
+ * File-based commands that inject content when invoked with /commandname.
+ */
+
+import { createAgentSession, discoverSlashCommands, SessionManager, type FileSlashCommand } from "../../src/index.js";
+
+// Discover commands from cwd/.pi/commands/ and ~/.pi/agent/commands/
+const discovered = discoverSlashCommands();
+console.log("Discovered slash commands:");
+for (const cmd of discovered) {
+	console.log(`  /${cmd.name}: ${cmd.description}`);
+}
+
+// Define custom commands
+const deployCommand: FileSlashCommand = {
+	name: "deploy",
+	description: "Deploy the application",
+	source: "(custom)",
+	content: `# Deploy Instructions
+
+1. Build: npm run build
+2. Test: npm test  
+3. Deploy: npm run deploy`,
+};
+
+// Use discovered + custom commands
+const { session } = await createAgentSession({
+	slashCommands: [...discovered, deployCommand],
+	sessionManager: SessionManager.inMemory(),
+});
+
+console.log(`Session created with ${discovered.length + 1} slash commands`);
+
+// Disable slash commands:
+// slashCommands: []

packages/coding-agent/examples/sdk/09-api-keys-and-oauth.ts

@@ -0,0 +1,45 @@
+/**
+ * API Keys and OAuth
+ *
+ * Configure API key resolution. Default checks: models.json, OAuth, env vars.
+ */
+
+import {
+	createAgentSession,
+	configureOAuthStorage,
+	defaultGetApiKey,
+	SessionManager,
+} from "../../src/index.js";
+import { getAgentDir } from "../../src/config.js";
+
+// Default: uses env vars (ANTHROPIC_API_KEY, etc.), OAuth, and models.json
+const { session: defaultSession } = await createAgentSession({
+	sessionManager: SessionManager.inMemory(),
+});
+console.log("Session with default API key resolution");
+
+// Custom resolver
+const { session: customSession } = await createAgentSession({
+	getApiKey: async (model) => {
+		// Custom logic (secrets manager, database, etc.)
+		if (model.provider === "anthropic") {
+			return process.env.MY_ANTHROPIC_KEY;
+		}
+		// Fall back to default
+		return defaultGetApiKey()(model);
+	},
+	sessionManager: SessionManager.inMemory(),
+});
+console.log("Session with custom API key resolver");
+
+// Use OAuth from ~/.pi/agent while customizing everything else
+configureOAuthStorage(getAgentDir()); // Must call before createAgentSession
+
+const { session: hybridSession } = await createAgentSession({
+	agentDir: "/tmp/custom-config", // Custom config location
+	// But OAuth tokens still come from ~/.pi/agent/oauth.json
+	systemPrompt: "You are helpful.",
+	skills: [],
+	sessionManager: SessionManager.inMemory(),
+});
+console.log("Session with OAuth from default location, custom config elsewhere");

packages/coding-agent/examples/sdk/10-settings.ts

@@ -0,0 +1,38 @@
+/**
+ * Settings Configuration
+ *
+ * Override settings using SettingsManager.
+ */
+
+import { createAgentSession, loadSettings, SessionManager, SettingsManager } from "../../src/index.js";
+
+// Load current settings (merged global + project)
+const settings = loadSettings();
+console.log("Current settings:", JSON.stringify(settings, null, 2));
+
+// Override specific settings
+const settingsManager = SettingsManager.create();
+settingsManager.applyOverrides({
+	compaction: { enabled: false },
+	retry: { enabled: true, maxRetries: 5, baseDelayMs: 1000 },
+});
+
+const { session } = await createAgentSession({
+	settingsManager,
+	sessionManager: SessionManager.inMemory(),
+});
+
+console.log("Session created with custom settings");
+
+// For testing without file I/O:
+const inMemorySettings = SettingsManager.inMemory({
+	compaction: { enabled: false },
+	retry: { enabled: false },
+});
+
+const { session: testSession } = await createAgentSession({
+	settingsManager: inMemorySettings,
+	sessionManager: SessionManager.inMemory(),
+});
+
+console.log("Test session created with in-memory settings");

packages/coding-agent/examples/sdk/11-sessions.ts

@@ -0,0 +1,46 @@
+/**
+ * Session Management
+ *
+ * Control session persistence: in-memory, new file, continue, or open specific.
+ */
+
+import { createAgentSession, SessionManager } from "../../src/index.js";
+
+// In-memory (no persistence)
+const { session: inMemory } = await createAgentSession({
+	sessionManager: SessionManager.inMemory(),
+});
+console.log("In-memory session:", inMemory.sessionFile ?? "(none)");
+
+// New persistent session
+const { session: newSession } = await createAgentSession({
+	sessionManager: SessionManager.create(process.cwd()),
+});
+console.log("New session file:", newSession.sessionFile);
+
+// Continue most recent session (or create new if none)
+const { session: continued, modelFallbackMessage } = await createAgentSession({
+	sessionManager: SessionManager.continueRecent(process.cwd()),
+});
+if (modelFallbackMessage) console.log("Note:", modelFallbackMessage);
+console.log("Continued session:", continued.sessionFile);
+
+// List and open specific session
+const sessions = SessionManager.list(process.cwd());
+console.log(`\nFound ${sessions.length} sessions:`);
+for (const info of sessions.slice(0, 3)) {
+	console.log(`  ${info.id.slice(0, 8)}... - "${info.firstMessage.slice(0, 30)}..."`);
+}
+
+if (sessions.length > 0) {
+	const { session: opened } = await createAgentSession({
+		sessionManager: SessionManager.open(sessions[0].path),
+	});
+	console.log(`\nOpened: ${opened.sessionId}`);
+}
+
+// Custom session directory
+// const { session } = await createAgentSession({
+//   agentDir: "/custom/agent",
+//   sessionManager: SessionManager.create(process.cwd(), "/custom/agent"),
+// });

packages/coding-agent/examples/sdk/12-full-control.ts

@@ -0,0 +1,91 @@
+/**
+ * Full Control
+ *
+ * Replace everything - no discovery, explicit configuration.
+ * Still uses OAuth from ~/.pi/agent for convenience.
+ */
+
+import { Type } from "@sinclair/typebox";
+import {
+	createAgentSession,
+	configureOAuthStorage,
+	defaultGetApiKey,
+	findModel,
+	SessionManager,
+	SettingsManager,
+	readTool,
+	bashTool,
+	type HookFactory,
+	type CustomAgentTool,
+} from "../../src/index.js";
+import { getAgentDir } from "../../src/config.js";
+
+// Use OAuth from default location
+configureOAuthStorage(getAgentDir());
+
+// Custom API key with fallback
+const getApiKey = async (model: { provider: string }) => {
+	if (model.provider === "anthropic" && process.env.MY_ANTHROPIC_KEY) {
+		return process.env.MY_ANTHROPIC_KEY;
+	}
+	return defaultGetApiKey()(model as any);
+};
+
+// Inline hook
+const auditHook: HookFactory = (api) => {
+	api.on("tool_call", async (event) => {
+		console.log(`[Audit] ${event.toolName}`);
+		return undefined;
+	});
+};
+
+// Inline custom tool
+const statusTool: CustomAgentTool = {
+	name: "status",
+	label: "Status",
+	description: "Get system status",
+	parameters: Type.Object({}),
+	execute: async () => ({
+		content: [{ type: "text", text: `Uptime: ${process.uptime()}s, Node: ${process.version}` }],
+		details: {},
+	}),
+};
+
+const { model } = findModel("anthropic", "claude-sonnet-4-20250514");
+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 { session } = await createAgentSession({
+	cwd: process.cwd(),
+	agentDir: "/tmp/my-agent",
+
+	model,
+	thinkingLevel: "off",
+	getApiKey,
+
+	systemPrompt: `You are a minimal assistant.
+Available: read, bash, status. Be concise.`,
+
+	tools: [readTool, bashTool],
+	customTools: [{ tool: statusTool }],
+	hooks: [{ factory: auditHook }],
+	skills: [],
+	contextFiles: [],
+	slashCommands: [],
+	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.");
+console.log();

packages/coding-agent/examples/sdk/README.md

@@ -0,0 +1,138 @@
+# SDK Examples
+
+Programmatic usage of pi-coding-agent via `createAgentSession()`.
+
+## Examples
+
+| File | Description |
+|------|-------------|
+| `01-minimal.ts` | Simplest usage with all defaults |
+| `02-custom-model.ts` | Select model and thinking level |
+| `03-custom-prompt.ts` | Replace or modify system prompt |
+| `04-skills.ts` | Discover, filter, or replace skills |
+| `05-tools.ts` | Built-in tools, custom tools |
+| `06-hooks.ts` | Logging, blocking, result modification |
+| `07-context-files.ts` | AGENTS.md context files |
+| `08-slash-commands.ts` | File-based slash commands |
+| `09-api-keys-and-oauth.ts` | API key resolution, OAuth config |
+| `10-settings.ts` | Override compaction, retry, terminal settings |
+| `11-sessions.ts` | In-memory, persistent, continue, list sessions |
+| `12-full-control.ts` | Replace everything, no discovery |
+
+## Running
+
+```bash
+cd packages/coding-agent
+npx tsx examples/sdk/01-minimal.ts
+```
+
+## Quick Reference
+
+```typescript
+import {
+  createAgentSession,
+  configureOAuthStorage,
+  discoverSkills,
+  discoverHooks,
+  discoverCustomTools,
+  discoverContextFiles,
+  discoverSlashCommands,
+  discoverAvailableModels,
+  findModel,
+  defaultGetApiKey,
+  loadSettings,
+  buildSystemPrompt,
+  SessionManager,
+  codingTools,
+  readOnlyTools,
+  readTool, bashTool, editTool, writeTool,
+} from "@mariozechner/pi-coding-agent";
+
+// Minimal
+const { session } = await createAgentSession();
+
+// Custom model
+const { model } = findModel("anthropic", "claude-sonnet-4-20250514");
+const { session } = await createAgentSession({ model, thinkingLevel: "high" });
+
+// Modify prompt
+const { session } = await createAgentSession({
+  systemPrompt: (defaultPrompt) => defaultPrompt + "\n\nBe concise.",
+});
+
+// Read-only
+const { session } = await createAgentSession({ tools: readOnlyTools });
+
+// In-memory
+const { session } = await createAgentSession({
+  sessionManager: SessionManager.inMemory(),
+});
+
+// Full control
+configureOAuthStorage(); // Use OAuth from ~/.pi/agent
+const { session } = await createAgentSession({
+  model,
+  getApiKey: async (m) => process.env.MY_KEY,
+  systemPrompt: "You are helpful.",
+  tools: [readTool, bashTool],
+  customTools: [{ tool: myTool }],
+  hooks: [{ factory: myHook }],
+  skills: [],
+  contextFiles: [],
+  slashCommands: [],
+  sessionManager: SessionManager.inMemory(),
+  settings: { compaction: { enabled: false } },
+});
+
+// Run prompts
+session.subscribe((event) => {
+  if (event.type === "message_update" && event.assistantMessageEvent.type === "text_delta") {
+    process.stdout.write(event.assistantMessageEvent.delta);
+  }
+});
+await session.prompt("Hello");
+```
+
+## Options
+
+| Option | Default | Description |
+|--------|---------|-------------|
+| `cwd` | `process.cwd()` | Working directory |
+| `agentDir` | `~/.pi/agent` | Config directory |
+| `model` | From settings/first available | Model to use |
+| `thinkingLevel` | From settings/"off" | off, low, medium, high |
+| `getApiKey` | Built-in resolver | API key function |
+| `systemPrompt` | Discovered | String or `(default) => modified` |
+| `tools` | `codingTools` | Built-in tools |
+| `customTools` | Discovered | Replaces discovery |
+| `additionalCustomToolPaths` | `[]` | Merge with discovery |
+| `hooks` | Discovered | Replaces discovery |
+| `additionalHookPaths` | `[]` | Merge with discovery |
+| `skills` | Discovered | Skills for prompt |
+| `contextFiles` | Discovered | AGENTS.md files |
+| `slashCommands` | Discovered | File commands |
+| `sessionManager` | `SessionManager.create(cwd)` | Persistence |
+| `settings` | From agentDir | Overrides |
+
+## Events
+
+```typescript
+session.subscribe((event) => {
+  switch (event.type) {
+    case "message_update":
+      if (event.assistantMessageEvent.type === "text_delta") {
+        process.stdout.write(event.assistantMessageEvent.delta);
+      }
+      break;
+    case "tool_execution_start":
+      console.log(`Tool: ${event.toolName}`);
+      break;
+    case "tool_execution_end":
+      console.log(`Result: ${event.result}`);
+      break;
+    case "agent_end":
+      console.log("Done");
+      break;
+  }
+});
+```

packages/coding-agent/src/cli/session-picker.ts

@@ -3,17 +3,17 @@
  */
 
 import { ProcessTerminal, TUI } from "@mariozechner/pi-tui";
-import type { SessionManager } from "../core/session-manager.js";
+import type { SessionInfo } from "../core/session-manager.js";
 import { SessionSelectorComponent } from "../modes/interactive/components/session-selector.js";
 
 /** Show TUI session selector and return selected session path or null if cancelled */
-export async function selectSession(sessionManager: SessionManager): Promise<string | null> {
+export async function selectSession(sessions: SessionInfo[]): Promise<string | null> {
 	return new Promise((resolve) => {
 		const ui = new TUI(new ProcessTerminal());
 		let resolved = false;
 
 		const selector = new SessionSelectorComponent(
-			sessionManager,
+			sessions,
 			(path: string) => {
 				if (!resolved) {
 					resolved = true;

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

@@ -202,11 +202,6 @@ export class AgentSession {
 		if (event.type === "message_end") {
 			this.sessionManager.saveMessage(event.message);
 
-			// Initialize session after first user+assistant exchange
-			if (this.sessionManager.shouldInitializeSession(this.agent.state.messages)) {
-				this.sessionManager.startSession(this.agent.state);
-			}
-
 			// Track assistant message for auto-compaction (checked on agent_end)
 			if (event.message.role === "assistant") {
 				this._lastAssistantMessage = event.message;
@@ -389,7 +384,7 @@ export class AgentSession {
 
 	/** Current session file path, or null if sessions are disabled */
 	get sessionFile(): string | null {
-		return this.sessionManager.isEnabled() ? this.sessionManager.getSessionFile() : null;
+		return this.sessionManager.isPersisted() ? this.sessionManager.getSessionFile() : null;
 	}
 
 	/** Current session ID */
@@ -1096,11 +1091,6 @@ export class AgentSession {
 
 				// Save to session
 				this.sessionManager.saveMessage(bashMessage);
-
-				// Initialize session if needed
-				if (this.sessionManager.shouldInitializeSession(this.agent.state.messages)) {
-					this.sessionManager.startSession(this.agent.state);
-				}
 			}
 
 			return result;
@@ -1141,11 +1131,6 @@ export class AgentSession {
 			this.sessionManager.saveMessage(bashMessage);
 		}
 
-		// Initialize session if needed
-		if (this.sessionManager.shouldInitializeSession(this.agent.state.messages)) {
-			this.sessionManager.startSession(this.agent.state);
-		}
-
 		this._pendingBashMessages = [];
 	}
 

packages/coding-agent/src/core/custom-tools/loader.ts

@@ -303,7 +303,7 @@ function discoverToolsInDir(dir: string): string[] {
 
 /**
  * Discover and load tools from standard locations:
- * 1. ~/.pi/agent/tools/*.ts (global)
+ * 1. agentDir/tools/*.ts (global)
  * 2. cwd/.pi/tools/*.ts (project-local)
  *
  * Plus any explicitly configured paths from settings or CLI.
@@ -311,11 +311,13 @@ function discoverToolsInDir(dir: string): string[] {
  * @param configuredPaths - Explicit paths from settings.json and CLI --tool flags
  * @param cwd - Current working directory
  * @param builtInToolNames - Names of built-in tools to check for conflicts
+ * @param agentDir - Agent config directory. Default: from getAgentDir()
  */
 export async function discoverAndLoadCustomTools(
 	configuredPaths: string[],
 	cwd: string,
 	builtInToolNames: string[],
+	agentDir: string = getAgentDir(),
 ): Promise<CustomToolsLoadResult> {
 	const allPaths: string[] = [];
 	const seen = new Set<string>();
@@ -331,8 +333,8 @@ export async function discoverAndLoadCustomTools(
 		}
 	};
 
-	// 1. Global tools: ~/.pi/agent/tools/
+	// 1. Global tools: agentDir/tools/
-	const globalToolsDir = path.join(getAgentDir(), "tools");
+	const globalToolsDir = path.join(agentDir, "tools");
 	addPaths(discoverToolsInDir(globalToolsDir));
 
 	// 2. Project-local tools: cwd/.pi/tools/

packages/coding-agent/src/core/hooks/loader.ts

@@ -217,15 +217,16 @@ function discoverHooksInDir(dir: string): string[] {
 
 /**
  * Discover and load hooks from standard locations:
- * 1. ~/.pi/agent/hooks/*.ts (global)
+ * 1. agentDir/hooks/*.ts (global)
  * 2. cwd/.pi/hooks/*.ts (project-local)
  *
  * Plus any explicitly configured paths from settings.
- *
- * @param configuredPaths - Explicit paths from settings.json
- * @param cwd - Current working directory
  */
-export async function discoverAndLoadHooks(configuredPaths: string[], cwd: string): Promise<LoadHooksResult> {
+export async function discoverAndLoadHooks(
+	configuredPaths: string[],
+	cwd: string,
+	agentDir: string = getAgentDir(),
+): Promise<LoadHooksResult> {
 	const allPaths: string[] = [];
 	const seen = new Set<string>();
 
@@ -240,8 +241,8 @@ export async function discoverAndLoadHooks(configuredPaths: string[], cwd: strin
 		}
 	};
 
-	// 1. Global hooks: ~/.pi/agent/hooks/
+	// 1. Global hooks: agentDir/hooks/
-	const globalHooksDir = path.join(getAgentDir(), "hooks");
+	const globalHooksDir = path.join(agentDir, "hooks");
 	addPaths(discoverHooksInDir(globalHooksDir));
 
 	// 2. Project-local hooks: cwd/.pi/hooks/

packages/coding-agent/src/core/model-config.ts

@@ -15,7 +15,8 @@ import {
 import { type Static, Type } from "@sinclair/typebox";
 import AjvModule from "ajv";
 import { existsSync, readFileSync } from "fs";
-import { getModelsPath } from "../config.js";
+import { join } from "path";
+import { getAgentDir } from "../config.js";
 import { getOAuthToken, type OAuthProvider, refreshToken } from "./oauth/index.js";
 
 // Handle both default and named exports
@@ -97,8 +98,8 @@ export function resolveApiKey(keyConfig: string): string | undefined {
  * Load custom models from models.json in agent config dir
  * Returns { models, error } - either models array or error message
  */
-function loadCustomModels(): { models: Model<Api>[]; error: string | null } {
+function loadCustomModels(agentDir: string = getAgentDir()): { models: Model<Api>[]; error: string | null } {
-	const configPath = getModelsPath();
+	const configPath = join(agentDir, "models.json");
 	if (!existsSync(configPath)) {
 		return { models: [], error: null };
 	}
@@ -232,7 +233,7 @@ function parseModels(config: ModelsConfig): Model<Api>[] {
  * Get all models (built-in + custom), freshly loaded
  * Returns { models, error } - either models array or error message
  */
-export function loadAndMergeModels(): { models: Model<Api>[]; error: string | null } {
+export function loadAndMergeModels(agentDir: string = getAgentDir()): { models: Model<Api>[]; error: string | null } {
 	const builtInModels: Model<Api>[] = [];
 	const providers = getProviders();
 
@@ -243,7 +244,7 @@ export function loadAndMergeModels(): { models: Model<Api>[]; error: string | nu
 	}
 
 	// Load custom models
-	const { models: customModels, error } = loadCustomModels();
+	const { models: customModels, error } = loadCustomModels(agentDir);
 
 	if (error) {
 		return { models: [], error };
@@ -267,7 +268,8 @@ export function loadAndMergeModels(): { models: Model<Api>[]; error: string | nu
 
 /**
  * Get API key for a model (checks custom providers first, then built-in)
- * Now async to support OAuth token refresh
+ * Now async to support OAuth token refresh.
+ * Note: OAuth storage location is configured globally via setOAuthStorage.
  */
 export async function getApiKeyForModel(model: Model<Api>): Promise<string | undefined> {
 	// For custom providers, check their apiKey config
@@ -357,26 +359,17 @@ export async function getApiKeyForModel(model: Model<Api>): Promise<string | und
  * Get only models that have valid API keys available
  * Returns { models, error } - either models array or error message
  */
-export async function getAvailableModels(): Promise<{ models: Model<Api>[]; error: string | null }> {
+export async function getAvailableModels(
-	const { models: allModels, error } = loadAndMergeModels();
+	agentDir: string = getAgentDir(),
+): Promise<{ models: Model<Api>[]; error: string | null }> {
+	const { models: allModels, error } = loadAndMergeModels(agentDir);
 
 	if (error) {
 		return { models: [], error };
 	}
 
 	const availableModels: Model<Api>[] = [];
-	const copilotCreds = loadOAuthCredentials("github-copilot");
-	const hasCopilotEnv = !!(process.env.COPILOT_GITHUB_TOKEN || process.env.GH_TOKEN || process.env.GITHUB_TOKEN);
-	const hasCopilot = !!copilotCreds || hasCopilotEnv;
-
 	for (const model of allModels) {
-		if (model.provider === "github-copilot") {
-			if (hasCopilot) {
-				availableModels.push(model);
-			}
-			continue;
-		}
-
 		const apiKey = await getApiKeyForModel(model);
 		if (apiKey) {
 			availableModels.push(model);
@@ -390,8 +383,12 @@ export async function getAvailableModels(): Promise<{ models: Model<Api>[]; erro
  * Find a specific model by provider and ID
  * Returns { model, error } - either model or error message
  */
-export function findModel(provider: string, modelId: string): { model: Model<Api> | null; error: string | null } {
+export function findModel(
-	const { models: allModels, error } = loadAndMergeModels();
+	provider: string,
+	modelId: string,
+	agentDir: string = getAgentDir(),
+): { model: Model<Api> | null; error: string | null } {
+	const { models: allModels, error } = loadAndMergeModels(agentDir);
 
 	if (error) {
 		return { model: null, error };

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

@@ -0,0 +1,639 @@
+/**
+ * SDK for programmatic usage of AgentSession.
+ *
+ * Provides a factory function and discovery helpers that allow full control
+ * over agent configuration, or sensible defaults that match CLI behavior.
+ *
+ * @example
+ * ```typescript
+ * // Minimal - everything auto-discovered
+ * const session = await createAgentSession();
+ *
+ * // With custom hooks
+ * const session = await createAgentSession({
+ *   hooks: [
+ *     ...await discoverHooks(),
+ *     { factory: myHookFactory },
+ *   ],
+ * });
+ *
+ * // Full control
+ * const session = await createAgentSession({
+ *   model: myModel,
+ *   getApiKey: async () => process.env.MY_KEY,
+ *   tools: [readTool, bashTool],
+ *   hooks: [],
+ *   skills: [],
+ *   sessionFile: false,
+ * });
+ * ```
+ */
+
+import { Agent, ProviderTransport, type ThinkingLevel } from "@mariozechner/pi-agent-core";
+import { type Model, setOAuthStorage } from "@mariozechner/pi-ai";
+import { chmodSync, existsSync, mkdirSync, readFileSync, writeFileSync } from "fs";
+import { dirname, join } from "path";
+import { getAgentDir } from "../config.js";
+import { AgentSession } from "./agent-session.js";
+import { discoverAndLoadCustomTools, type LoadedCustomTool } from "./custom-tools/index.js";
+import type { CustomAgentTool } from "./custom-tools/types.js";
+import { discoverAndLoadHooks, HookRunner, type LoadedHook, wrapToolsWithHooks } from "./hooks/index.js";
+import type { HookFactory } from "./hooks/types.js";
+import { messageTransformer } from "./messages.js";
+import {
+	findModel as findModelInternal,
+	getApiKeyForModel,
+	getAvailableModels,
+	loadAndMergeModels,
+} from "./model-config.js";
+import { SessionManager } from "./session-manager.js";
+import { type Settings, SettingsManager, type SkillsSettings } from "./settings-manager.js";
+import { loadSkills as loadSkillsInternal, type Skill } from "./skills.js";
+import { type FileSlashCommand, loadSlashCommands as loadSlashCommandsInternal } from "./slash-commands.js";
+import {
+	buildSystemPrompt as buildSystemPromptInternal,
+	loadProjectContextFiles as loadContextFilesInternal,
+} from "./system-prompt.js";
+import {
+	allTools,
+	bashTool,
+	codingTools,
+	editTool,
+	findTool,
+	grepTool,
+	lsTool,
+	readOnlyTools,
+	readTool,
+	type Tool,
+	writeTool,
+} from "./tools/index.js";
+
+// Types
+
+export interface CreateAgentSessionOptions {
+	/** Working directory for project-local discovery. Default: process.cwd() */
+	cwd?: string;
+	/** Global config directory. Default: ~/.pi/agent */
+	agentDir?: string;
+
+	/** Model to use. Default: from settings, else first available */
+	model?: Model<any>;
+	/** Thinking level. Default: from settings, else 'off' (clamped to model capabilities) */
+	thinkingLevel?: ThinkingLevel;
+	/** Models available for cycling (Ctrl+P in interactive mode) */
+	scopedModels?: Array<{ model: Model<any>; thinkingLevel: ThinkingLevel }>;
+
+	/** API key resolver. Default: defaultGetApiKey() */
+	getApiKey?: (model: Model<any>) => Promise<string | undefined>;
+
+	/** System prompt. String replaces default, function receives default and returns final. */
+	systemPrompt?: string | ((defaultPrompt: string) => string);
+
+	/** Built-in tools to use. Default: codingTools [read, bash, edit, write] */
+	tools?: Tool[];
+	/** Custom tools (replaces discovery). */
+	customTools?: Array<{ path?: string; tool: CustomAgentTool }>;
+	/** Additional custom tool paths to load (merged with discovery). */
+	additionalCustomToolPaths?: string[];
+
+	/** Hooks (replaces discovery). */
+	hooks?: Array<{ path?: string; factory: HookFactory }>;
+	/** Additional hook paths to load (merged with discovery). */
+	additionalHookPaths?: string[];
+
+	/** Skills. Default: discovered from multiple locations */
+	skills?: Skill[];
+	/** Context files (AGENTS.md content). Default: discovered walking up from cwd */
+	contextFiles?: Array<{ path: string; content: string }>;
+	/** Slash commands. Default: discovered from cwd/.pi/commands/ + agentDir/commands/ */
+	slashCommands?: FileSlashCommand[];
+
+	/** Session manager. Default: SessionManager.create(cwd) */
+	sessionManager?: SessionManager;
+
+	/** Settings manager. Default: SettingsManager.create(cwd, agentDir) */
+	settingsManager?: SettingsManager;
+}
+
+/** Result from createAgentSession */
+export interface CreateAgentSessionResult {
+	/** The created session */
+	session: AgentSession;
+	/** Custom tools result (for UI context setup in interactive mode) */
+	customToolsResult: {
+		tools: LoadedCustomTool[];
+		setUIContext: (uiContext: any, hasUI: boolean) => void;
+	};
+	/** Warning if session was restored with a different model than saved */
+	modelFallbackMessage?: string;
+}
+
+// Re-exports
+
+export type { CustomAgentTool } from "./custom-tools/types.js";
+export type { HookAPI, HookFactory } from "./hooks/types.js";
+export type { Settings, SkillsSettings } from "./settings-manager.js";
+export type { Skill } from "./skills.js";
+export type { FileSlashCommand } from "./slash-commands.js";
+export type { Tool } from "./tools/index.js";
+
+export {
+	readTool,
+	bashTool,
+	editTool,
+	writeTool,
+	grepTool,
+	findTool,
+	lsTool,
+	codingTools,
+	readOnlyTools,
+	allTools as allBuiltInTools,
+};
+
+// Helper Functions
+
+function getDefaultAgentDir(): string {
+	return getAgentDir();
+}
+
+/**
+ * Configure OAuth storage to use the specified agent directory.
+ * Must be called before using OAuth-based authentication.
+ */
+export function configureOAuthStorage(agentDir: string = getDefaultAgentDir()): void {
+	const oauthPath = join(agentDir, "oauth.json");
+
+	setOAuthStorage({
+		load: () => {
+			if (!existsSync(oauthPath)) {
+				return {};
+			}
+			try {
+				return JSON.parse(readFileSync(oauthPath, "utf-8"));
+			} catch {
+				return {};
+			}
+		},
+		save: (storage) => {
+			const dir = dirname(oauthPath);
+			if (!existsSync(dir)) {
+				mkdirSync(dir, { recursive: true, mode: 0o700 });
+			}
+			writeFileSync(oauthPath, JSON.stringify(storage, null, 2), "utf-8");
+			chmodSync(oauthPath, 0o600);
+		},
+	});
+}
+
+// Discovery Functions
+
+/**
+ * Get all models (built-in + custom from models.json).
+ */
+export function discoverModels(agentDir: string = getDefaultAgentDir()): Model<any>[] {
+	const { models, error } = loadAndMergeModels(agentDir);
+	if (error) {
+		throw new Error(error);
+	}
+	return models;
+}
+
+/**
+ * Get models that have valid API keys available.
+ */
+export async function discoverAvailableModels(agentDir: string = getDefaultAgentDir()): Promise<Model<any>[]> {
+	const { models, error } = await getAvailableModels(agentDir);
+	if (error) {
+		throw new Error(error);
+	}
+	return models;
+}
+
+/**
+ * Find a model by provider and ID.
+ * @returns The model, or null if not found
+ */
+export function findModel(
+	provider: string,
+	modelId: string,
+	agentDir: string = getDefaultAgentDir(),
+): Model<any> | null {
+	const { model, error } = findModelInternal(provider, modelId, agentDir);
+	if (error) {
+		throw new Error(error);
+	}
+	return model;
+}
+
+/**
+ * Discover hooks from cwd and agentDir.
+ */
+export async function discoverHooks(
+	cwd?: string,
+	agentDir?: string,
+): Promise<Array<{ path: string; factory: HookFactory }>> {
+	const resolvedCwd = cwd ?? process.cwd();
+	const resolvedAgentDir = agentDir ?? getDefaultAgentDir();
+
+	const { hooks, errors } = await discoverAndLoadHooks([], resolvedCwd, resolvedAgentDir);
+
+	// Log errors but don't fail
+	for (const { path, error } of errors) {
+		console.error(`Failed to load hook "${path}": ${error}`);
+	}
+
+	return hooks.map((h) => ({
+		path: h.path,
+		factory: createFactoryFromLoadedHook(h),
+	}));
+}
+
+/**
+ * Discover custom tools from cwd and agentDir.
+ */
+export async function discoverCustomTools(
+	cwd?: string,
+	agentDir?: string,
+): Promise<Array<{ path: string; tool: CustomAgentTool }>> {
+	const resolvedCwd = cwd ?? process.cwd();
+	const resolvedAgentDir = agentDir ?? getDefaultAgentDir();
+
+	const { tools, errors } = await discoverAndLoadCustomTools([], resolvedCwd, Object.keys(allTools), resolvedAgentDir);
+
+	// Log errors but don't fail
+	for (const { path, error } of errors) {
+		console.error(`Failed to load custom tool "${path}": ${error}`);
+	}
+
+	return tools.map((t) => ({
+		path: t.path,
+		tool: t.tool,
+	}));
+}
+
+/**
+ * Discover skills from cwd and agentDir.
+ */
+export function discoverSkills(cwd?: string, agentDir?: string, settings?: SkillsSettings): Skill[] {
+	const { skills } = loadSkillsInternal({
+		...settings,
+		cwd: cwd ?? process.cwd(),
+		agentDir: agentDir ?? getDefaultAgentDir(),
+	});
+	return skills;
+}
+
+/**
+ * Discover context files (AGENTS.md) walking up from cwd.
+ */
+export function discoverContextFiles(cwd?: string, agentDir?: string): Array<{ path: string; content: string }> {
+	return loadContextFilesInternal({
+		cwd: cwd ?? process.cwd(),
+		agentDir: agentDir ?? getDefaultAgentDir(),
+	});
+}
+
+/**
+ * Discover slash commands from cwd and agentDir.
+ */
+export function discoverSlashCommands(cwd?: string, agentDir?: string): FileSlashCommand[] {
+	return loadSlashCommandsInternal({
+		cwd: cwd ?? process.cwd(),
+		agentDir: agentDir ?? getDefaultAgentDir(),
+	});
+}
+
+// API Key Helpers
+
+/**
+ * Create the default API key resolver.
+ * Checks custom providers (models.json), OAuth, and environment variables.
+ */
+export function defaultGetApiKey(): (model: Model<any>) => Promise<string | undefined> {
+	return getApiKeyForModel;
+}
+
+// System Prompt
+
+export interface BuildSystemPromptOptions {
+	tools?: Tool[];
+	skills?: Skill[];
+	contextFiles?: Array<{ path: string; content: string }>;
+	cwd?: string;
+	appendPrompt?: string;
+}
+
+/**
+ * Build the default system prompt.
+ */
+export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): string {
+	return buildSystemPromptInternal({
+		cwd: options.cwd,
+		skills: options.skills,
+		contextFiles: options.contextFiles,
+		appendSystemPrompt: options.appendPrompt,
+	});
+}
+
+// Settings
+
+/**
+ * Load settings from agentDir/settings.json merged with cwd/.pi/settings.json.
+ */
+export function loadSettings(cwd?: string, agentDir?: string): Settings {
+	const manager = SettingsManager.create(cwd ?? process.cwd(), agentDir ?? getDefaultAgentDir());
+	return {
+		defaultProvider: manager.getDefaultProvider(),
+		defaultModel: manager.getDefaultModel(),
+		defaultThinkingLevel: manager.getDefaultThinkingLevel(),
+		queueMode: manager.getQueueMode(),
+		theme: manager.getTheme(),
+		compaction: manager.getCompactionSettings(),
+		retry: manager.getRetrySettings(),
+		hideThinkingBlock: manager.getHideThinkingBlock(),
+		shellPath: manager.getShellPath(),
+		collapseChangelog: manager.getCollapseChangelog(),
+		hooks: manager.getHookPaths(),
+		hookTimeout: manager.getHookTimeout(),
+		customTools: manager.getCustomToolPaths(),
+		skills: manager.getSkillsSettings(),
+		terminal: { showImages: manager.getShowImages() },
+	};
+}
+
+// Internal Helpers
+
+/**
+ * Create a HookFactory from a LoadedHook.
+ * This allows mixing discovered hooks with inline hooks.
+ */
+function createFactoryFromLoadedHook(loaded: LoadedHook): HookFactory {
+	return (api) => {
+		for (const [eventType, handlers] of loaded.handlers) {
+			for (const handler of handlers) {
+				api.on(eventType as any, handler as any);
+			}
+		}
+	};
+}
+
+/**
+ * Convert hook definitions to LoadedHooks for the HookRunner.
+ */
+function createLoadedHooksFromDefinitions(definitions: Array<{ path?: string; factory: HookFactory }>): LoadedHook[] {
+	return definitions.map((def) => {
+		const handlers = new Map<string, Array<(...args: unknown[]) => Promise<unknown>>>();
+		let sendHandler: (text: string, attachments?: any[]) => void = () => {};
+
+		const api = {
+			on: (event: string, handler: (...args: unknown[]) => Promise<unknown>) => {
+				const list = handlers.get(event) ?? [];
+				list.push(handler);
+				handlers.set(event, list);
+			},
+			send: (text: string, attachments?: any[]) => {
+				sendHandler(text, attachments);
+			},
+		};
+
+		def.factory(api as any);
+
+		return {
+			path: def.path ?? "<inline>",
+			resolvedPath: def.path ?? "<inline>",
+			handlers,
+			setSendHandler: (handler: (text: string, attachments?: any[]) => void) => {
+				sendHandler = handler;
+			},
+		};
+	});
+}
+
+// Factory
+
+/**
+ * Create an AgentSession with the specified options.
+ *
+ * @example
+ * ```typescript
+ * // Minimal - uses defaults
+ * const { session } = await createAgentSession();
+ *
+ * // With explicit model
+ * const { session } = await createAgentSession({
+ *   model: findModel('anthropic', 'claude-sonnet-4-20250514'),
+ *   thinkingLevel: 'high',
+ * });
+ *
+ * // Continue previous session
+ * const { session, modelFallbackMessage } = await createAgentSession({
+ *   continueSession: true,
+ * });
+ *
+ * // Full control
+ * const { session } = await createAgentSession({
+ *   model: myModel,
+ *   getApiKey: async () => process.env.MY_KEY,
+ *   systemPrompt: 'You are helpful.',
+ *   tools: [readTool, bashTool],
+ *   hooks: [],
+ *   skills: [],
+ *   sessionManager: SessionManager.inMemory(),
+ * });
+ * ```
+ */
+export async function createAgentSession(options: CreateAgentSessionOptions = {}): Promise<CreateAgentSessionResult> {
+	const cwd = options.cwd ?? process.cwd();
+	const agentDir = options.agentDir ?? getDefaultAgentDir();
+
+	// Configure OAuth storage for this agentDir
+	configureOAuthStorage(agentDir);
+
+	const settingsManager = options.settingsManager ?? SettingsManager.create(cwd, agentDir);
+	const sessionManager = options.sessionManager ?? SessionManager.create(cwd, agentDir);
+
+	// Check if session has existing data to restore
+	const existingSession = sessionManager.loadSession();
+	const hasExistingSession = existingSession.messages.length > 0;
+
+	let model = options.model;
+	let modelFallbackMessage: string | undefined;
+
+	// If session has data, try to restore model from it
+	if (!model && hasExistingSession && existingSession.model) {
+		const restoredModel = findModel(existingSession.model.provider, existingSession.model.modelId);
+		if (restoredModel) {
+			const key = await getApiKeyForModel(restoredModel);
+			if (key) {
+				model = restoredModel;
+			}
+		}
+		if (!model) {
+			modelFallbackMessage = `Could not restore model ${existingSession.model.provider}/${existingSession.model.modelId}`;
+		}
+	}
+
+	// If still no model, try settings default
+	if (!model) {
+		const defaultProvider = settingsManager.getDefaultProvider();
+		const defaultModelId = settingsManager.getDefaultModel();
+		if (defaultProvider && defaultModelId) {
+			const settingsModel = findModel(defaultProvider, defaultModelId);
+			if (settingsModel) {
+				const key = await getApiKeyForModel(settingsModel);
+				if (key) {
+					model = settingsModel;
+				}
+			}
+		}
+	}
+
+	// Fall back to first available
+	if (!model) {
+		const available = await discoverAvailableModels();
+		if (available.length === 0) {
+			throw new Error(
+				"No models available. Set an API key environment variable " +
+					"(ANTHROPIC_API_KEY, OPENAI_API_KEY, etc.) or provide a model explicitly.",
+			);
+		}
+		model = available[0];
+		if (modelFallbackMessage) {
+			modelFallbackMessage += `. Using ${model.provider}/${model.id}`;
+		}
+	}
+
+	let thinkingLevel = options.thinkingLevel;
+
+	// If session has data, restore thinking level from it
+	if (thinkingLevel === undefined && hasExistingSession) {
+		thinkingLevel = existingSession.thinkingLevel as ThinkingLevel;
+	}
+
+	// Fall back to settings default
+	if (thinkingLevel === undefined) {
+		thinkingLevel = settingsManager.getDefaultThinkingLevel() ?? "off";
+	}
+
+	// Clamp to model capabilities
+	if (!model.reasoning) {
+		thinkingLevel = "off";
+	}
+
+	const getApiKey = options.getApiKey ?? defaultGetApiKey();
+
+	const skills = options.skills ?? discoverSkills(cwd, agentDir, settingsManager.getSkillsSettings());
+
+	const contextFiles = options.contextFiles ?? discoverContextFiles(cwd, agentDir);
+
+	const builtInTools = options.tools ?? codingTools;
+
+	let customToolsResult: { tools: LoadedCustomTool[]; setUIContext: (ctx: any, hasUI: boolean) => void };
+	if (options.customTools !== undefined) {
+		// Use provided custom tools
+		const loadedTools: LoadedCustomTool[] = options.customTools.map((ct) => ({
+			path: ct.path ?? "<inline>",
+			resolvedPath: ct.path ?? "<inline>",
+			tool: ct.tool,
+		}));
+		customToolsResult = {
+			tools: loadedTools,
+			setUIContext: () => {},
+		};
+	} else {
+		// Discover custom tools, merging with additional paths
+		const configuredPaths = [...settingsManager.getCustomToolPaths(), ...(options.additionalCustomToolPaths ?? [])];
+		const result = await discoverAndLoadCustomTools(configuredPaths, cwd, Object.keys(allTools), agentDir);
+		for (const { path, error } of result.errors) {
+			console.error(`Failed to load custom tool "${path}": ${error}`);
+		}
+		customToolsResult = result;
+	}
+
+	let hookRunner: HookRunner | null = null;
+	if (options.hooks !== undefined) {
+		if (options.hooks.length > 0) {
+			const loadedHooks = createLoadedHooksFromDefinitions(options.hooks);
+			hookRunner = new HookRunner(loadedHooks, cwd, settingsManager.getHookTimeout());
+		}
+	} else {
+		// Discover hooks, merging with additional paths
+		const configuredPaths = [...settingsManager.getHookPaths(), ...(options.additionalHookPaths ?? [])];
+		const { hooks, errors } = await discoverAndLoadHooks(configuredPaths, cwd, agentDir);
+		for (const { path, error } of errors) {
+			console.error(`Failed to load hook "${path}": ${error}`);
+		}
+		if (hooks.length > 0) {
+			hookRunner = new HookRunner(hooks, cwd, settingsManager.getHookTimeout());
+		}
+	}
+
+	let allToolsArray: Tool[] = [...builtInTools, ...customToolsResult.tools.map((lt) => lt.tool as unknown as Tool)];
+	if (hookRunner) {
+		allToolsArray = wrapToolsWithHooks(allToolsArray, hookRunner) as Tool[];
+	}
+
+	let systemPrompt: string;
+	const defaultPrompt = buildSystemPromptInternal({
+		cwd,
+		agentDir,
+		skills,
+		contextFiles,
+	});
+
+	if (options.systemPrompt === undefined) {
+		systemPrompt = defaultPrompt;
+	} else if (typeof options.systemPrompt === "string") {
+		systemPrompt = options.systemPrompt;
+	} else {
+		systemPrompt = options.systemPrompt(defaultPrompt);
+	}
+
+	const slashCommands = options.slashCommands ?? discoverSlashCommands(cwd, agentDir);
+
+	const agent = new Agent({
+		initialState: {
+			systemPrompt,
+			model,
+			thinkingLevel,
+			tools: allToolsArray,
+		},
+		messageTransformer,
+		queueMode: settingsManager.getQueueMode(),
+		transport: new ProviderTransport({
+			getApiKey: async () => {
+				const currentModel = agent.state.model;
+				if (!currentModel) {
+					throw new Error("No model selected");
+				}
+				const key = await getApiKey(currentModel);
+				if (!key) {
+					throw new Error(`No API key found for provider "${currentModel.provider}"`);
+				}
+				return key;
+			},
+		}),
+	});
+
+	// Restore messages if session has existing data
+	if (hasExistingSession) {
+		agent.replaceMessages(existingSession.messages);
+	}
+
+	const session = new AgentSession({
+		agent,
+		sessionManager,
+		settingsManager,
+		scopedModels: options.scopedModels,
+		fileCommands: slashCommands,
+		hookRunner,
+		customTools: customToolsResult.tools,
+		skillsSettings: settingsManager.getSkillsSettings(),
+	});
+
+	return {
+		session,
+		customToolsResult,
+		modelFallbackMessage,
+	};
+}

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

@@ -1,8 +1,8 @@
-import type { AgentState, AppMessage } from "@mariozechner/pi-agent-core";
+import type { AppMessage } from "@mariozechner/pi-agent-core";
 import { randomBytes } from "crypto";
 import { appendFileSync, existsSync, mkdirSync, readdirSync, readFileSync, statSync } from "fs";
 import { join, resolve } from "path";
-import { getAgentDir } from "../config.js";
+import { getAgentDir as getDefaultAgentDir } from "../config.js";
 
 function uuidv4(): string {
 	const bytes = randomBytes(16);
@@ -12,18 +12,11 @@ function uuidv4(): string {
 	return `${hex.slice(0, 8)}-${hex.slice(8, 12)}-${hex.slice(12, 16)}-${hex.slice(16, 20)}-${hex.slice(20, 32)}`;
 }
 
-// ============================================================================
-// Session entry types
-// ============================================================================
-
 export interface SessionHeader {
 	type: "session";
 	id: string;
 	timestamp: string;
 	cwd: string;
-	provider: string;
-	modelId: string;
-	thinkingLevel: string;
 	branchedFrom?: string;
 }
 
@@ -50,11 +43,10 @@ export interface CompactionEntry {
 	type: "compaction";
 	timestamp: string;
 	summary: string;
-	firstKeptEntryIndex: number; // Index into session entries where we start keeping
+	firstKeptEntryIndex: number;
 	tokensBefore: number;
 }
 
-/** Union of all session entry types */
 export type SessionEntry =
 	| SessionHeader
 	| SessionMessageEntry
@@ -62,16 +54,22 @@ export type SessionEntry =
 	| ModelChangeEntry
 	| CompactionEntry;
 
-// ============================================================================
-// Session loading with compaction support
-// ============================================================================
-
 export interface LoadedSession {
 	messages: AppMessage[];
 	thinkingLevel: string;
 	model: { provider: string; modelId: string } | null;
 }
 
+export interface SessionInfo {
+	path: string;
+	id: string;
+	created: Date;
+	modified: Date;
+	messageCount: number;
+	firstMessage: string;
+	allMessagesText: string;
+}
+
 export const SUMMARY_PREFIX = `The conversation history before this point was compacted into the following summary:
 
 <summary>
@@ -80,9 +78,6 @@ export const SUMMARY_PREFIX = `The conversation history before this point was co
 export const SUMMARY_SUFFIX = `
 </summary>`;
 
-/**
- * Create a user message containing the summary with the standard prefix.
- */
 export function createSummaryMessage(summary: string): AppMessage {
 	return {
 		role: "user",
@@ -91,9 +86,6 @@ export function createSummaryMessage(summary: string): AppMessage {
 	};
 }
 
-/**
- * Parse session file content into entries.
- */
 export function parseSessionEntries(content: string): SessionEntry[] {
 	const entries: SessionEntry[] = [];
 	const lines = content.trim().split("\n");
@@ -111,17 +103,6 @@ export function parseSessionEntries(content: string): SessionEntry[] {
 	return entries;
 }
 
-/**
- * Load session from entries, handling compaction events.
- *
- * Algorithm:
- * 1. Find latest compaction event (if any)
- * 2. Keep all entries from firstKeptEntryIndex onwards (extracting messages)
- * 3. Prepend summary as user message
- */
-/**
- * Get the latest compaction entry from session entries, if any.
- */
 export function getLatestCompactionEntry(entries: SessionEntry[]): CompactionEntry | null {
 	for (let i = entries.length - 1; i >= 0; i--) {
 		if (entries[i].type === "compaction") {
@@ -132,22 +113,19 @@ export function getLatestCompactionEntry(entries: SessionEntry[]): CompactionEnt
 }
 
 export function loadSessionFromEntries(entries: SessionEntry[]): LoadedSession {
-	// Find model and thinking level (always scan all entries)
 	let thinkingLevel = "off";
 	let model: { provider: string; modelId: string } | null = null;
 
 	for (const entry of entries) {
-		if (entry.type === "session") {
+		if (entry.type === "thinking_level_change") {
-			thinkingLevel = entry.thinkingLevel;
-			model = { provider: entry.provider, modelId: entry.modelId };
-		} else if (entry.type === "thinking_level_change") {
 			thinkingLevel = entry.thinkingLevel;
 		} else if (entry.type === "model_change") {
 			model = { provider: entry.provider, modelId: entry.modelId };
+		} else if (entry.type === "message" && entry.message.role === "assistant") {
+			model = { provider: entry.message.provider, modelId: entry.message.model };
 		}
 	}
 
-	// Find latest compaction event
 	let latestCompactionIndex = -1;
 	for (let i = entries.length - 1; i >= 0; i--) {
 		if (entries[i].type === "compaction") {
@@ -156,7 +134,6 @@ export function loadSessionFromEntries(entries: SessionEntry[]): LoadedSession {
 		}
 	}
 
-	// No compaction: return all messages
 	if (latestCompactionIndex === -1) {
 		const messages: AppMessage[] = [];
 		for (const entry of entries) {
@@ -169,7 +146,6 @@ export function loadSessionFromEntries(entries: SessionEntry[]): LoadedSession {
 
 	const compactionEvent = entries[latestCompactionIndex] as CompactionEntry;
 
-	// Extract messages from firstKeptEntryIndex to end (skipping compaction entries)
 	const keptMessages: AppMessage[] = [];
 	for (let i = compactionEvent.firstKeptEntryIndex; i < entries.length; i++) {
 		const entry = entries[i];
@@ -178,7 +154,6 @@ export function loadSessionFromEntries(entries: SessionEntry[]): LoadedSession {
 		}
 	}
 
-	// Build final messages: summary + kept messages
 	const messages: AppMessage[] = [];
 	messages.push(createSummaryMessage(compactionEvent.summary));
 	messages.push(...keptMessages);
@@ -186,246 +161,103 @@ export function loadSessionFromEntries(entries: SessionEntry[]): LoadedSession {
 	return { messages, thinkingLevel, model };
 }
 
+function getSessionDirectory(cwd: string, agentDir: string): string {
+	const safePath = `--${cwd.replace(/^[/\\]/, "").replace(/[/\\:]/g, "-")}--`;
+	const sessionDir = join(agentDir, "sessions", safePath);
+	if (!existsSync(sessionDir)) {
+		mkdirSync(sessionDir, { recursive: true });
+	}
+	return sessionDir;
+}
+
+function loadEntriesFromFile(filePath: string): SessionEntry[] {
+	if (!existsSync(filePath)) return [];
+
+	const content = readFileSync(filePath, "utf8");
+	const entries: SessionEntry[] = [];
+	const lines = content.trim().split("\n");
+
+	for (const line of lines) {
+		if (!line.trim()) continue;
+		try {
+			const entry = JSON.parse(line) as SessionEntry;
+			entries.push(entry);
+		} catch {
+			// Skip malformed lines
+		}
+	}
+
+	return entries;
+}
+
+function findMostRecentSession(sessionDir: string): string | null {
+	try {
+		const files = readdirSync(sessionDir)
+			.filter((f) => f.endsWith(".jsonl"))
+			.map((f) => ({
+				path: join(sessionDir, f),
+				mtime: statSync(join(sessionDir, f)).mtime,
+			}))
+			.sort((a, b) => b.mtime.getTime() - a.mtime.getTime());
+
+		return files[0]?.path || null;
+	} catch {
+		return null;
+	}
+}
+
 export class SessionManager {
-	private sessionId!: string;
+	private sessionId: string = "";
-	private sessionFile!: string;
+	private sessionFile: string = "";
 	private sessionDir: string;
-	private enabled: boolean = true;
+	private cwd: string;
-	private sessionInitialized: boolean = false;
+	private persist: boolean;
-	private pendingEntries: SessionEntry[] = [];
+	private flushed: boolean = false;
-	// In-memory entries for --no-session mode (when enabled=false)
 	private inMemoryEntries: SessionEntry[] = [];
 
-	constructor(continueSession: boolean = false, customSessionPath?: string) {
+	private constructor(cwd: string, agentDir: string, sessionFile: string | null, persist: boolean) {
-		this.sessionDir = this.getSessionDirectory();
+		this.cwd = cwd;
+		this.sessionDir = getSessionDirectory(cwd, agentDir);
+		this.persist = persist;
 
-		if (customSessionPath) {
+		if (sessionFile) {
-			// Use custom session file path
+			this.setSessionFile(sessionFile);
-			this.sessionFile = resolve(customSessionPath);
-			this.loadSessionId();
-			// If file doesn't exist, loadSessionId() won't set sessionId, so generate one
-			if (!this.sessionId) {
-				this.sessionId = uuidv4();
-			}
-			// Mark as initialized since we're loading an existing session
-			this.sessionInitialized = existsSync(this.sessionFile);
-			// Load entries into memory
-			if (this.sessionInitialized) {
-				this.inMemoryEntries = this.loadEntriesFromFile();
-			}
-		} else if (continueSession) {
-			const mostRecent = this.findMostRecentlyModifiedSession();
-			if (mostRecent) {
-				this.sessionFile = mostRecent;
-				this.loadSessionId();
-				// Mark as initialized since we're loading an existing session
-				this.sessionInitialized = true;
-				// Load entries into memory
-				this.inMemoryEntries = this.loadEntriesFromFile();
-			} else {
-				this.initNewSession();
-			}
 		} else {
-			this.initNewSession();
+			this.sessionId = uuidv4();
+			const timestamp = new Date().toISOString().replace(/[:.]/g, "-");
+			const sessionFile = join(this.sessionDir, `${timestamp}_${this.sessionId}.jsonl`);
+			this.setSessionFile(sessionFile);
 		}
 	}
 
-	/** Disable session saving (for --no-session mode) */
+	/** Switch to a different session file (used for resume and branching) */
-	disable() {
+	setSessionFile(sessionFile: string): void {
-		this.enabled = false;
+		this.sessionFile = resolve(sessionFile);
-	}
+		if (existsSync(this.sessionFile)) {
-
+			this.inMemoryEntries = loadEntriesFromFile(this.sessionFile);
-	/** Check if session persistence is enabled */
+			const header = this.inMemoryEntries.find((e) => e.type === "session");
-	isEnabled(): boolean {
+			this.sessionId = header ? (header as SessionHeader).id : uuidv4();
-		return this.enabled;
+			this.flushed = true;
-	}
-
-	private getSessionDirectory(): string {
-		const cwd = process.cwd();
-		// Replace all path separators and colons (for Windows drive letters) with dashes
-		const safePath = `--${cwd.replace(/^[/\\]/, "").replace(/[/\\:]/g, "-")}--`;
-
-		const configDir = getAgentDir();
-		const sessionDir = join(configDir, "sessions", safePath);
-		if (!existsSync(sessionDir)) {
-			mkdirSync(sessionDir, { recursive: true });
-		}
-		return sessionDir;
-	}
-
-	private initNewSession(): void {
-		this.sessionId = uuidv4();
-		const timestamp = new Date().toISOString().replace(/[:.]/g, "-");
-		this.sessionFile = join(this.sessionDir, `${timestamp}_${this.sessionId}.jsonl`);
-	}
-
-	/** Reset to a fresh session. Clears pending entries and starts a new session file. */
-	reset(): void {
-		this.pendingEntries = [];
-		this.inMemoryEntries = [];
-		this.sessionInitialized = false;
-		this.initNewSession();
-	}
-
-	private findMostRecentlyModifiedSession(): string | null {
-		try {
-			const files = readdirSync(this.sessionDir)
-				.filter((f) => f.endsWith(".jsonl"))
-				.map((f) => ({
-					name: f,
-					path: join(this.sessionDir, f),
-					mtime: statSync(join(this.sessionDir, f)).mtime,
-				}))
-				.sort((a, b) => b.mtime.getTime() - a.mtime.getTime());
-
-			return files[0]?.path || null;
-		} catch {
-			return null;
-		}
-	}
-
-	private loadSessionId(): void {
-		if (!existsSync(this.sessionFile)) return;
-
-		const lines = readFileSync(this.sessionFile, "utf8").trim().split("\n");
-		for (const line of lines) {
-			try {
-				const entry = JSON.parse(line);
-				if (entry.type === "session") {
-					this.sessionId = entry.id;
-					return;
-				}
-			} catch {
-				// Skip malformed lines
-			}
-		}
-		this.sessionId = uuidv4();
-	}
-
-	startSession(state: AgentState): void {
-		if (this.sessionInitialized) return;
-		this.sessionInitialized = true;
-
-		const entry: SessionHeader = {
-			type: "session",
-			id: this.sessionId,
-			timestamp: new Date().toISOString(),
-			cwd: process.cwd(),
-			provider: state.model.provider,
-			modelId: state.model.id,
-			thinkingLevel: state.thinkingLevel,
-		};
-
-		// Always track in memory
-		this.inMemoryEntries.push(entry);
-		for (const pending of this.pendingEntries) {
-			this.inMemoryEntries.push(pending);
-		}
-		this.pendingEntries = [];
-
-		// Write to file only if enabled
-		if (this.enabled) {
-			appendFileSync(this.sessionFile, `${JSON.stringify(entry)}\n`);
-			for (const memEntry of this.inMemoryEntries.slice(1)) {
-				appendFileSync(this.sessionFile, `${JSON.stringify(memEntry)}\n`);
-			}
-		}
-	}
-
-	saveMessage(message: any): void {
-		const entry: SessionMessageEntry = {
-			type: "message",
-			timestamp: new Date().toISOString(),
-			message,
-		};
-
-		if (!this.sessionInitialized) {
-			this.pendingEntries.push(entry);
 		} else {
-			// Always track in memory
+			this.sessionId = uuidv4();
+			this.inMemoryEntries = [];
+			this.flushed = false;
+			const entry: SessionHeader = {
+				type: "session",
+				id: this.sessionId,
+				timestamp: new Date().toISOString(),
+				cwd: this.cwd,
+			};
 			this.inMemoryEntries.push(entry);
-			// Write to file only if enabled
-			if (this.enabled) {
-				appendFileSync(this.sessionFile, `${JSON.stringify(entry)}\n`);
-			}
 		}
 	}
 
-	saveThinkingLevelChange(thinkingLevel: string): void {
+	isPersisted(): boolean {
-		const entry: ThinkingLevelChangeEntry = {
+		return this.persist;
-			type: "thinking_level_change",
-			timestamp: new Date().toISOString(),
-			thinkingLevel,
-		};
-
-		if (!this.sessionInitialized) {
-			this.pendingEntries.push(entry);
-		} else {
-			// Always track in memory
-			this.inMemoryEntries.push(entry);
-			// Write to file only if enabled
-			if (this.enabled) {
-				appendFileSync(this.sessionFile, `${JSON.stringify(entry)}\n`);
-			}
-		}
 	}
 
-	saveModelChange(provider: string, modelId: string): void {
+	getCwd(): string {
-		const entry: ModelChangeEntry = {
+		return this.cwd;
-			type: "model_change",
-			timestamp: new Date().toISOString(),
-			provider,
-			modelId,
-		};
-
-		if (!this.sessionInitialized) {
-			this.pendingEntries.push(entry);
-		} else {
-			// Always track in memory
-			this.inMemoryEntries.push(entry);
-			// Write to file only if enabled
-			if (this.enabled) {
-				appendFileSync(this.sessionFile, `${JSON.stringify(entry)}\n`);
-			}
-		}
-	}
-
-	saveCompaction(entry: CompactionEntry): void {
-		// Always track in memory
-		this.inMemoryEntries.push(entry);
-		// Write to file only if enabled
-		if (this.enabled) {
-			appendFileSync(this.sessionFile, `${JSON.stringify(entry)}\n`);
-		}
-	}
-
-	/**
-	 * Load session data (messages, model, thinking level) with compaction support.
-	 */
-	loadSession(): LoadedSession {
-		const entries = this.loadEntries();
-		return loadSessionFromEntries(entries);
-	}
-
-	/**
-	 * @deprecated Use loadSession().messages instead
-	 */
-	loadMessages(): AppMessage[] {
-		return this.loadSession().messages;
-	}
-
-	/**
-	 * @deprecated Use loadSession().thinkingLevel instead
-	 */
-	loadThinkingLevel(): string {
-		return this.loadSession().thinkingLevel;
-	}
-
-	/**
-	 * @deprecated Use loadSession().model instead
-	 */
-	loadModel(): { provider: string; modelId: string } | null {
-		return this.loadSession().model;
 	}
 
 	getSessionId(): string {
@@ -436,70 +268,168 @@ export class SessionManager {
 		return this.sessionFile;
 	}
 
-	/**
+	reset(): void {
-	 * Load entries directly from the session file (internal helper).
+		this.sessionId = uuidv4();
-	 */
+		this.flushed = false;
-	private loadEntriesFromFile(): SessionEntry[] {
+		const timestamp = new Date().toISOString().replace(/[:.]/g, "-");
-		if (!existsSync(this.sessionFile)) return [];
+		this.sessionFile = join(this.sessionDir, `${timestamp}_${this.sessionId}.jsonl`);
+		this.inMemoryEntries = [
+			{
+				type: "session",
+				id: this.sessionId,
+				timestamp: new Date().toISOString(),
+				cwd: this.cwd,
+			},
+		];
+	}
 
-		const content = readFileSync(this.sessionFile, "utf8");
+	_persist(entry: SessionEntry): void {
-		const entries: SessionEntry[] = [];
+		if (!this.persist) return;
-		const lines = content.trim().split("\n");
 
-		for (const line of lines) {
+		const hasAssistant = this.inMemoryEntries.some((e) => e.type === "message" && e.message.role === "assistant");
-			if (!line.trim()) continue;
+		if (!hasAssistant) return;
-			try {
+
-				const entry = JSON.parse(line) as SessionEntry;
+		if (!this.flushed) {
-				entries.push(entry);
+			for (const e of this.inMemoryEntries) {
-			} catch {
+				appendFileSync(this.sessionFile, `${JSON.stringify(e)}\n`);
-				// Skip malformed lines
+			}
+			this.flushed = true;
+		} else {
+			appendFileSync(this.sessionFile, `${JSON.stringify(entry)}\n`);
+		}
+	}
+
+	saveMessage(message: any): void {
+		const entry: SessionMessageEntry = {
+			type: "message",
+			timestamp: new Date().toISOString(),
+			message,
+		};
+		this.inMemoryEntries.push(entry);
+		this._persist(entry);
+	}
+
+	saveThinkingLevelChange(thinkingLevel: string): void {
+		const entry: ThinkingLevelChangeEntry = {
+			type: "thinking_level_change",
+			timestamp: new Date().toISOString(),
+			thinkingLevel,
+		};
+		this.inMemoryEntries.push(entry);
+		this._persist(entry);
+	}
+
+	saveModelChange(provider: string, modelId: string): void {
+		const entry: ModelChangeEntry = {
+			type: "model_change",
+			timestamp: new Date().toISOString(),
+			provider,
+			modelId,
+		};
+		this.inMemoryEntries.push(entry);
+		this._persist(entry);
+	}
+
+	saveCompaction(entry: CompactionEntry): void {
+		this.inMemoryEntries.push(entry);
+		this._persist(entry);
+	}
+
+	loadSession(): LoadedSession {
+		const entries = this.loadEntries();
+		return loadSessionFromEntries(entries);
+	}
+
+	loadMessages(): AppMessage[] {
+		return this.loadSession().messages;
+	}
+
+	loadThinkingLevel(): string {
+		return this.loadSession().thinkingLevel;
+	}
+
+	loadModel(): { provider: string; modelId: string } | null {
+		return this.loadSession().model;
+	}
+
+	loadEntries(): SessionEntry[] {
+		if (this.inMemoryEntries.length > 0) {
+			return [...this.inMemoryEntries];
+		} else {
+			return loadEntriesFromFile(this.sessionFile);
+		}
+	}
+
+	createBranchedSessionFromEntries(entries: SessionEntry[], branchBeforeIndex: number): string | null {
+		const newSessionId = uuidv4();
+		const timestamp = new Date().toISOString().replace(/[:.]/g, "-");
+		const newSessionFile = join(this.sessionDir, `${timestamp}_${newSessionId}.jsonl`);
+
+		const newEntries: SessionEntry[] = [];
+		for (let i = 0; i < branchBeforeIndex; i++) {
+			const entry = entries[i];
+
+			if (entry.type === "session") {
+				newEntries.push({
+					...entry,
+					id: newSessionId,
+					timestamp: new Date().toISOString(),
+					branchedFrom: this.persist ? this.sessionFile : undefined,
+				});
+			} else {
+				newEntries.push(entry);
 			}
 		}
 
-		return entries;
+		if (this.persist) {
-	}
+			for (const entry of newEntries) {
-
+				appendFileSync(newSessionFile, `${JSON.stringify(entry)}\n`);
-	/**
+			}
-	 * Load all entries from the session file or in-memory store.
+			return newSessionFile;
-	 * When file persistence is enabled, reads from file (source of truth for resumed sessions).
-	 * When disabled (--no-session), returns in-memory entries.
-	 */
-	loadEntries(): SessionEntry[] {
-		// If file persistence is enabled and file exists, read from file
-		if (this.enabled && existsSync(this.sessionFile)) {
-			return this.loadEntriesFromFile();
 		}
-
+		this.inMemoryEntries = newEntries;
-		// Otherwise return in-memory entries (for --no-session mode)
+		this.sessionId = newSessionId;
-		return [...this.inMemoryEntries];
+		return null;
 	}
 
-	/**
+	/** Create a new session for the given directory */
-	 * Load all sessions for the current directory with metadata
+	static create(cwd: string, agentDir: string = getDefaultAgentDir()): SessionManager {
-	 */
+		return new SessionManager(cwd, agentDir, null, true);
-	loadAllSessions(): Array<{
+	}
-		path: string;
+
-		id: string;
+	/** Open a specific session file */
-		created: Date;
+	static open(path: string, agentDir: string = getDefaultAgentDir()): SessionManager {
-		modified: Date;
+		// Extract cwd from session header if possible, otherwise use process.cwd()
-		messageCount: number;
+		const entries = loadEntriesFromFile(path);
-		firstMessage: string;
+		const header = entries.find((e) => e.type === "session") as SessionHeader | undefined;
-		allMessagesText: string;
+		const cwd = header?.cwd ?? process.cwd();
-	}> {
+		return new SessionManager(cwd, agentDir, path, true);
-		const sessions: Array<{
+	}
-			path: string;
+
-			id: string;
+	/** Continue the most recent session for the given directory, or create new if none */
-			created: Date;
+	static continueRecent(cwd: string, agentDir: string = getDefaultAgentDir()): SessionManager {
-			modified: Date;
+		const sessionDir = getSessionDirectory(cwd, agentDir);
-			messageCount: number;
+		const mostRecent = findMostRecentSession(sessionDir);
-			firstMessage: string;
+		if (mostRecent) {
-			allMessagesText: string;
+			return new SessionManager(cwd, agentDir, mostRecent, true);
-		}> = [];
+		}
+		return new SessionManager(cwd, agentDir, null, true);
+	}
+
+	/** Create an in-memory session (no file persistence) */
+	static inMemory(): SessionManager {
+		return new SessionManager(process.cwd(), getDefaultAgentDir(), null, false);
+	}
+
+	/** List all sessions for a directory */
+	static list(cwd: string, agentDir: string = getDefaultAgentDir()): SessionInfo[] {
+		const sessionDir = getSessionDirectory(cwd, agentDir);
+		const sessions: SessionInfo[] = [];
 
 		try {
-			const files = readdirSync(this.sessionDir)
+			const files = readdirSync(sessionDir)
 				.filter((f) => f.endsWith(".jsonl"))
-				.map((f) => join(this.sessionDir, f));
+				.map((f) => join(sessionDir, f));
 
 			for (const file of files) {
 				try {
@@ -517,17 +447,14 @@ export class SessionManager {
 						try {
 							const entry = JSON.parse(line);
 
-							// Extract session ID from first session entry
 							if (entry.type === "session" && !sessionId) {
 								sessionId = entry.id;
 								created = new Date(entry.timestamp);
 							}
 
-							// Count messages and collect all text
 							if (entry.type === "message") {
 								messageCount++;
 
-								// Extract text from user and assistant messages
 								if (entry.message.role === "user" || entry.message.role === "assistant") {
 									const textContent = entry.message.content
 										.filter((c: any) => c.type === "text")
@@ -537,7 +464,6 @@ export class SessionManager {
 									if (textContent) {
 										allMessages.push(textContent);
 
-										// Get first user message for display
 										if (!firstMessage && entry.message.role === "user") {
 											firstMessage = textContent;
 										}
@@ -558,131 +484,16 @@ export class SessionManager {
 						firstMessage: firstMessage || "(no messages)",
 						allMessagesText: allMessages.join(" "),
 					});
-				} catch (error) {
+				} catch {
 					// Skip files that can't be read
-					console.error(`Failed to read session file ${file}:`, error);
 				}
 			}
 
-			// Sort by modified date (most recent first)
 			sessions.sort((a, b) => b.modified.getTime() - a.modified.getTime());
-		} catch (error) {
+		} catch {
-			console.error("Failed to load sessions:", error);
+			// Return empty list on error
 		}
 
 		return sessions;
 	}
-
-	/**
-	 * Set the session file to an existing session
-	 */
-	setSessionFile(path: string): void {
-		this.sessionFile = path;
-		this.loadSessionId();
-		// Mark as initialized since we're loading an existing session
-		this.sessionInitialized = existsSync(path);
-		// Load entries into memory for consistency
-		if (this.sessionInitialized) {
-			this.inMemoryEntries = this.loadEntriesFromFile();
-		} else {
-			this.inMemoryEntries = [];
-		}
-		this.pendingEntries = [];
-	}
-
-	/**
-	 * Check if we should initialize the session based on message history.
-	 * Session is initialized when we have at least 1 user message and 1 assistant message.
-	 */
-	shouldInitializeSession(messages: any[]): boolean {
-		if (this.sessionInitialized) return false;
-
-		const userMessages = messages.filter((m) => m.role === "user");
-		const assistantMessages = messages.filter((m) => m.role === "assistant");
-
-		return userMessages.length >= 1 && assistantMessages.length >= 1;
-	}
-
-	/**
-	 * Create a branched session from a specific message index.
-	 * If branchFromIndex is -1, creates an empty session.
-	 * Returns the new session file path.
-	 */
-	createBranchedSession(state: any, branchFromIndex: number): string {
-		// Create a new session ID for the branch
-		const newSessionId = uuidv4();
-		const timestamp = new Date().toISOString().replace(/[:.]/g, "-");
-		const newSessionFile = join(this.sessionDir, `${timestamp}_${newSessionId}.jsonl`);
-
-		// Write session header
-		const entry: SessionHeader = {
-			type: "session",
-			id: newSessionId,
-			timestamp: new Date().toISOString(),
-			cwd: process.cwd(),
-			provider: state.model.provider,
-			modelId: state.model.id,
-			thinkingLevel: state.thinkingLevel,
-			branchedFrom: this.sessionFile,
-		};
-		appendFileSync(newSessionFile, `${JSON.stringify(entry)}\n`);
-
-		// Write messages up to and including the branch point (if >= 0)
-		if (branchFromIndex >= 0) {
-			const messagesToWrite = state.messages.slice(0, branchFromIndex + 1);
-			for (const message of messagesToWrite) {
-				const messageEntry: SessionMessageEntry = {
-					type: "message",
-					timestamp: new Date().toISOString(),
-					message,
-				};
-				appendFileSync(newSessionFile, `${JSON.stringify(messageEntry)}\n`);
-			}
-		}
-
-		return newSessionFile;
-	}
-
-	/**
-	 * Create a branched session from session entries up to (but not including) a specific entry index.
-	 * This preserves compaction events and all entry types.
-	 * Returns the new session file path, or null if in --no-session mode (in-memory only).
-	 */
-	createBranchedSessionFromEntries(entries: SessionEntry[], branchBeforeIndex: number): string | null {
-		const newSessionId = uuidv4();
-		const timestamp = new Date().toISOString().replace(/[:.]/g, "-");
-		const newSessionFile = join(this.sessionDir, `${timestamp}_${newSessionId}.jsonl`);
-
-		// Build new entries list (up to but not including branch point)
-		const newEntries: SessionEntry[] = [];
-		for (let i = 0; i < branchBeforeIndex; i++) {
-			const entry = entries[i];
-
-			if (entry.type === "session") {
-				// Rewrite session header with new ID and branchedFrom
-				newEntries.push({
-					...entry,
-					id: newSessionId,
-					timestamp: new Date().toISOString(),
-					branchedFrom: this.enabled ? this.sessionFile : undefined,
-				});
-			} else {
-				// Copy other entries as-is
-				newEntries.push(entry);
-			}
-		}
-
-		if (this.enabled) {
-			// Write to file
-			for (const entry of newEntries) {
-				appendFileSync(newSessionFile, `${JSON.stringify(entry)}\n`);
-			}
-			return newSessionFile;
-		} else {
-			// In-memory mode: replace inMemoryEntries, no file created
-			this.inMemoryEntries = newEntries;
-			this.sessionId = newSessionId;
-			return null;
-		}
-	}
 }

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

@@ -1,6 +1,6 @@
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "fs";
 import { dirname, join } from "path";
-import { getAgentDir } from "../config.js";
+import { CONFIG_DIR_NAME, getAgentDir } from "../config.js";
 
 export interface CompactionSettings {
 	enabled?: boolean; // default: true
@@ -49,39 +49,118 @@ export interface Settings {
 	terminal?: TerminalSettings;
 }
 
-export class SettingsManager {
+/** Deep merge settings: project/overrides take precedence, nested objects merge recursively */
-	private settingsPath: string;
+function deepMergeSettings(base: Settings, overrides: Settings): Settings {
-	private settings: Settings;
+	const result: Settings = { ...base };
 
-	constructor(baseDir?: string) {
+	for (const key of Object.keys(overrides) as (keyof Settings)[]) {
-		const dir = baseDir || getAgentDir();
+		const overrideValue = overrides[key];
-		this.settingsPath = join(dir, "settings.json");
+		const baseValue = base[key];
-		this.settings = this.load();
+
+		if (overrideValue === undefined) {
+			continue;
+		}
+
+		// For nested objects, merge recursively
+		if (
+			typeof overrideValue === "object" &&
+			overrideValue !== null &&
+			!Array.isArray(overrideValue) &&
+			typeof baseValue === "object" &&
+			baseValue !== null &&
+			!Array.isArray(baseValue)
+		) {
+			(result as Record<string, unknown>)[key] = { ...baseValue, ...overrideValue };
+		} else {
+			// For primitives and arrays, override value wins
+			(result as Record<string, unknown>)[key] = overrideValue;
+		}
 	}
 
-	private load(): Settings {
+	return result;
-		if (!existsSync(this.settingsPath)) {
+}
+
+export class SettingsManager {
+	private settingsPath: string | null;
+	private projectSettingsPath: string | null;
+	private globalSettings: Settings;
+	private settings: Settings;
+	private persist: boolean;
+
+	private constructor(
+		settingsPath: string | null,
+		projectSettingsPath: string | null,
+		initialSettings: Settings,
+		persist: boolean,
+	) {
+		this.settingsPath = settingsPath;
+		this.projectSettingsPath = projectSettingsPath;
+		this.persist = persist;
+		this.globalSettings = initialSettings;
+		const projectSettings = this.loadProjectSettings();
+		this.settings = deepMergeSettings(this.globalSettings, projectSettings);
+	}
+
+	/** Create a SettingsManager that loads from files */
+	static create(cwd: string = process.cwd(), agentDir: string = getAgentDir()): SettingsManager {
+		const settingsPath = join(agentDir, "settings.json");
+		const projectSettingsPath = join(cwd, CONFIG_DIR_NAME, "settings.json");
+		const globalSettings = SettingsManager.loadFromFile(settingsPath);
+		return new SettingsManager(settingsPath, projectSettingsPath, globalSettings, true);
+	}
+
+	/** Create an in-memory SettingsManager (no file I/O) */
+	static inMemory(settings: Partial<Settings> = {}): SettingsManager {
+		return new SettingsManager(null, null, settings, false);
+	}
+
+	private static loadFromFile(path: string): Settings {
+		if (!existsSync(path)) {
+			return {};
+		}
+		try {
+			const content = readFileSync(path, "utf-8");
+			return JSON.parse(content);
+		} catch (error) {
+			console.error(`Warning: Could not read settings file ${path}: ${error}`);
+			return {};
+		}
+	}
+
+	private loadProjectSettings(): Settings {
+		if (!this.projectSettingsPath || !existsSync(this.projectSettingsPath)) {
 			return {};
 		}
 
 		try {
-			const content = readFileSync(this.settingsPath, "utf-8");
+			const content = readFileSync(this.projectSettingsPath, "utf-8");
 			return JSON.parse(content);
 		} catch (error) {
-			console.error(`Warning: Could not read settings file: ${error}`);
+			console.error(`Warning: Could not read project settings file: ${error}`);
 			return {};
 		}
 	}
 
+	/** Apply additional overrides on top of current settings */
+	applyOverrides(overrides: Partial<Settings>): void {
+		this.settings = deepMergeSettings(this.settings, overrides);
+	}
+
 	private save(): void {
+		if (!this.persist || !this.settingsPath) return;
+
 		try {
-			// Ensure directory exists
 			const dir = dirname(this.settingsPath);
 			if (!existsSync(dir)) {
 				mkdirSync(dir, { recursive: true });
 			}
 
-			writeFileSync(this.settingsPath, JSON.stringify(this.settings, null, 2), "utf-8");
+			// Save only global settings (project settings are read-only)
+			writeFileSync(this.settingsPath, JSON.stringify(this.globalSettings, null, 2), "utf-8");
+
+			// Re-merge project settings into active settings
+			const projectSettings = this.loadProjectSettings();
+			this.settings = deepMergeSettings(this.globalSettings, projectSettings);
 		} catch (error) {
 			console.error(`Warning: Could not save settings file: ${error}`);
 		}
@@ -92,7 +171,7 @@ export class SettingsManager {
 	}
 
 	setLastChangelogVersion(version: string): void {
-		this.settings.lastChangelogVersion = version;
+		this.globalSettings.lastChangelogVersion = version;
 		this.save();
 	}
 
@@ -105,18 +184,18 @@ export class SettingsManager {
 	}
 
 	setDefaultProvider(provider: string): void {
-		this.settings.defaultProvider = provider;
+		this.globalSettings.defaultProvider = provider;
 		this.save();
 	}
 
 	setDefaultModel(modelId: string): void {
-		this.settings.defaultModel = modelId;
+		this.globalSettings.defaultModel = modelId;
 		this.save();
 	}
 
 	setDefaultModelAndProvider(provider: string, modelId: string): void {
-		this.settings.defaultProvider = provider;
+		this.globalSettings.defaultProvider = provider;
-		this.settings.defaultModel = modelId;
+		this.globalSettings.defaultModel = modelId;
 		this.save();
 	}
 
@@ -125,7 +204,7 @@ export class SettingsManager {
 	}
 
 	setQueueMode(mode: "all" | "one-at-a-time"): void {
-		this.settings.queueMode = mode;
+		this.globalSettings.queueMode = mode;
 		this.save();
 	}
 
@@ -134,7 +213,7 @@ export class SettingsManager {
 	}
 
 	setTheme(theme: string): void {
-		this.settings.theme = theme;
+		this.globalSettings.theme = theme;
 		this.save();
 	}
 
@@ -143,7 +222,7 @@ export class SettingsManager {
 	}
 
 	setDefaultThinkingLevel(level: "off" | "minimal" | "low" | "medium" | "high" | "xhigh"): void {
-		this.settings.defaultThinkingLevel = level;
+		this.globalSettings.defaultThinkingLevel = level;
 		this.save();
 	}
 
@@ -152,10 +231,10 @@ export class SettingsManager {
 	}
 
 	setCompactionEnabled(enabled: boolean): void {
-		if (!this.settings.compaction) {
+		if (!this.globalSettings.compaction) {
-			this.settings.compaction = {};
+			this.globalSettings.compaction = {};
 		}
-		this.settings.compaction.enabled = enabled;
+		this.globalSettings.compaction.enabled = enabled;
 		this.save();
 	}
 
@@ -180,10 +259,10 @@ export class SettingsManager {
 	}
 
 	setRetryEnabled(enabled: boolean): void {
-		if (!this.settings.retry) {
+		if (!this.globalSettings.retry) {
-			this.settings.retry = {};
+			this.globalSettings.retry = {};
 		}
-		this.settings.retry.enabled = enabled;
+		this.globalSettings.retry.enabled = enabled;
 		this.save();
 	}
 
@@ -200,7 +279,7 @@ export class SettingsManager {
 	}
 
 	setHideThinkingBlock(hide: boolean): void {
-		this.settings.hideThinkingBlock = hide;
+		this.globalSettings.hideThinkingBlock = hide;
 		this.save();
 	}
 
@@ -209,7 +288,7 @@ export class SettingsManager {
 	}
 
 	setShellPath(path: string | undefined): void {
-		this.settings.shellPath = path;
+		this.globalSettings.shellPath = path;
 		this.save();
 	}
 
@@ -218,7 +297,7 @@ export class SettingsManager {
 	}
 
 	setCollapseChangelog(collapse: boolean): void {
-		this.settings.collapseChangelog = collapse;
+		this.globalSettings.collapseChangelog = collapse;
 		this.save();
 	}
 
@@ -227,7 +306,7 @@ export class SettingsManager {
 	}
 
 	setHookPaths(paths: string[]): void {
-		this.settings.hooks = paths;
+		this.globalSettings.hooks = paths;
 		this.save();
 	}
 
@@ -236,7 +315,7 @@ export class SettingsManager {
 	}
 
 	setHookTimeout(timeout: number): void {
-		this.settings.hookTimeout = timeout;
+		this.globalSettings.hookTimeout = timeout;
 		this.save();
 	}
 
@@ -245,7 +324,7 @@ export class SettingsManager {
 	}
 
 	setCustomToolPaths(paths: string[]): void {
-		this.settings.customTools = paths;
+		this.globalSettings.customTools = paths;
 		this.save();
 	}
 
@@ -254,10 +333,10 @@ export class SettingsManager {
 	}
 
 	setSkillsEnabled(enabled: boolean): void {
-		if (!this.settings.skills) {
+		if (!this.globalSettings.skills) {
-			this.settings.skills = {};
+			this.globalSettings.skills = {};
 		}
-		this.settings.skills.enabled = enabled;
+		this.globalSettings.skills.enabled = enabled;
 		this.save();
 	}
 
@@ -280,10 +359,10 @@ export class SettingsManager {
 	}
 
 	setShowImages(show: boolean): void {
-		if (!this.settings.terminal) {
+		if (!this.globalSettings.terminal) {
-			this.settings.terminal = {};
+			this.globalSettings.terminal = {};
 		}
-		this.settings.terminal.showImages = show;
+		this.globalSettings.terminal.showImages = show;
 		this.save();
 	}
 }

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

@@ -2,7 +2,7 @@ import { existsSync, readdirSync, readFileSync } from "fs";
 import { minimatch } from "minimatch";
 import { homedir } from "os";
 import { basename, dirname, join, resolve } from "path";
-import { CONFIG_DIR_NAME } from "../config.js";
+import { CONFIG_DIR_NAME, getAgentDir } from "../config.js";
 import type { SkillsSettings } from "./settings-manager.js";
 
 /**
@@ -313,12 +313,21 @@ function escapeXml(str: string): string {
 		.replace(/'/g, "'");
 }
 
+export interface LoadSkillsOptions extends SkillsSettings {
+	/** Working directory for project-local skills. Default: process.cwd() */
+	cwd?: string;
+	/** Agent config directory for global skills. Default: ~/.pi/agent */
+	agentDir?: string;
+}
+
 /**
  * Load skills from all configured locations.
  * Returns skills and any validation warnings.
  */
-export function loadSkills(options: SkillsSettings = {}): LoadSkillsResult {
+export function loadSkills(options: LoadSkillsOptions = {}): LoadSkillsResult {
 	const {
+		cwd = process.cwd(),
+		agentDir,
 		enableCodexUser = true,
 		enableClaudeUser = true,
 		enableClaudeProject = true,
@@ -329,6 +338,9 @@ export function loadSkills(options: SkillsSettings = {}): LoadSkillsResult {
 		includeSkills = [],
 	} = options;
 
+	// Resolve agentDir - if not provided, use default from config
+	const resolvedAgentDir = agentDir ?? getAgentDir();
+
 	const skillMap = new Map<string, Skill>();
 	const allWarnings: SkillWarning[] = [];
 	const collisionWarnings: SkillWarning[] = [];
@@ -375,13 +387,13 @@ export function loadSkills(options: SkillsSettings = {}): LoadSkillsResult {
 		addSkills(loadSkillsFromDirInternal(join(homedir(), ".claude", "skills"), "claude-user", "claude"));
 	}
 	if (enableClaudeProject) {
-		addSkills(loadSkillsFromDirInternal(resolve(process.cwd(), ".claude", "skills"), "claude-project", "claude"));
+		addSkills(loadSkillsFromDirInternal(resolve(cwd, ".claude", "skills"), "claude-project", "claude"));
 	}
 	if (enablePiUser) {
-		addSkills(loadSkillsFromDirInternal(join(homedir(), CONFIG_DIR_NAME, "agent", "skills"), "user", "recursive"));
+		addSkills(loadSkillsFromDirInternal(join(resolvedAgentDir, "skills"), "user", "recursive"));
 	}
 	if (enablePiProject) {
-		addSkills(loadSkillsFromDirInternal(resolve(process.cwd(), CONFIG_DIR_NAME, "skills"), "project", "recursive"));
+		addSkills(loadSkillsFromDirInternal(resolve(cwd, CONFIG_DIR_NAME, "skills"), "project", "recursive"));
 	}
 	for (const customDir of customDirectories) {
 		addSkills(loadSkillsFromDirInternal(customDir.replace(/^~(?=$|[\\/])/, homedir()), "custom", "recursive"));

packages/coding-agent/src/core/slash-commands.ts

@@ -165,20 +165,31 @@ function loadCommandsFromDir(dir: string, source: "user" | "project", subdir: st
 	return commands;
 }
 
+export interface LoadSlashCommandsOptions {
+	/** Working directory for project-local commands. Default: process.cwd() */
+	cwd?: string;
+	/** Agent config directory for global commands. Default: from getCommandsDir() */
+	agentDir?: string;
+}
+
 /**
  * Load all custom slash commands from:
- * 1. Global: ~/{CONFIG_DIR_NAME}/agent/commands/
+ * 1. Global: agentDir/commands/
- * 2. Project: ./{CONFIG_DIR_NAME}/commands/
+ * 2. Project: cwd/{CONFIG_DIR_NAME}/commands/
  */
-export function loadSlashCommands(): FileSlashCommand[] {
+export function loadSlashCommands(options: LoadSlashCommandsOptions = {}): FileSlashCommand[] {
+	const resolvedCwd = options.cwd ?? process.cwd();
+	const resolvedAgentDir = options.agentDir ?? getCommandsDir();
+
 	const commands: FileSlashCommand[] = [];
 
-	// 1. Load global commands from ~/{CONFIG_DIR_NAME}/agent/commands/
+	// 1. Load global commands from agentDir/commands/
-	const globalCommandsDir = getCommandsDir();
+	// Note: if agentDir is provided, it should be the agent dir, not the commands dir
+	const globalCommandsDir = options.agentDir ? join(options.agentDir, "commands") : resolvedAgentDir;
 	commands.push(...loadCommandsFromDir(globalCommandsDir, "user"));
 
-	// 2. Load project commands from ./{CONFIG_DIR_NAME}/commands/
+	// 2. Load project commands from cwd/{CONFIG_DIR_NAME}/commands/
-	const projectCommandsDir = resolve(process.cwd(), CONFIG_DIR_NAME, "commands");
+	const projectCommandsDir = resolve(resolvedCwd, CONFIG_DIR_NAME, "commands");
 	commands.push(...loadCommandsFromDir(projectCommandsDir, "project"));
 
 	return commands;

packages/coding-agent/src/core/system-prompt.ts

@@ -7,7 +7,7 @@ import { existsSync, readFileSync } from "fs";
 import { join, resolve } from "path";
 import { getAgentDir, getDocsPath, getReadmePath } from "../config.js";
 import type { SkillsSettings } from "./settings-manager.js";
-import { formatSkillsForPrompt, loadSkills } from "./skills.js";
+import { formatSkillsForPrompt, loadSkills, type Skill } from "./skills.js";
 import type { ToolName } from "./tools/index.js";
 
 /** Tool descriptions for system prompt */
@@ -58,29 +58,39 @@ function loadContextFileFromDir(dir: string): { path: string; content: string }
 	return null;
 }
 
+export interface LoadContextFilesOptions {
+	/** Working directory to start walking up from. Default: process.cwd() */
+	cwd?: string;
+	/** Agent config directory for global context. Default: from getAgentDir() */
+	agentDir?: string;
+}
+
 /**
  * Load all project context files in order:
- * 1. Global: ~/{CONFIG_DIR_NAME}/agent/AGENTS.md or CLAUDE.md
+ * 1. Global: agentDir/AGENTS.md or CLAUDE.md
  * 2. Parent directories (top-most first) down to cwd
  * Each returns {path, content} for separate messages
  */
-export function loadProjectContextFiles(): Array<{ path: string; content: string }> {
+export function loadProjectContextFiles(
+	options: LoadContextFilesOptions = {},
+): Array<{ path: string; content: string }> {
+	const resolvedCwd = options.cwd ?? process.cwd();
+	const resolvedAgentDir = options.agentDir ?? getAgentDir();
+
 	const contextFiles: Array<{ path: string; content: string }> = [];
 	const seenPaths = new Set<string>();
 
-	// 1. Load global context from ~/{CONFIG_DIR_NAME}/agent/
+	// 1. Load global context from agentDir
-	const globalContextDir = getAgentDir();
+	const globalContext = loadContextFileFromDir(resolvedAgentDir);
-	const globalContext = loadContextFileFromDir(globalContextDir);
 	if (globalContext) {
 		contextFiles.push(globalContext);
 		seenPaths.add(globalContext.path);
 	}
 
 	// 2. Walk up from cwd to root, collecting all context files
-	const cwd = process.cwd();
 	const ancestorContextFiles: Array<{ path: string; content: string }> = [];
 
-	let currentDir = cwd;
+	let currentDir = resolvedCwd;
 	const root = resolve("/");
 
 	while (true) {
@@ -107,15 +117,37 @@ export function loadProjectContextFiles(): Array<{ path: string; content: string
 }
 
 export interface BuildSystemPromptOptions {
+	/** Custom system prompt (replaces default). */
 	customPrompt?: string;
+	/** Tools to include in prompt. Default: [read, bash, edit, write] */
 	selectedTools?: ToolName[];
+	/** Text to append to system prompt. */
 	appendSystemPrompt?: string;
+	/** Skills settings for discovery. */
 	skillsSettings?: SkillsSettings;
+	/** Working directory. Default: process.cwd() */
+	cwd?: string;
+	/** Agent config directory. Default: from getAgentDir() */
+	agentDir?: string;
+	/** Pre-loaded context files (skips discovery if provided). */
+	contextFiles?: Array<{ path: string; content: string }>;
+	/** Pre-loaded skills (skips discovery if provided). */
+	skills?: Skill[];
 }
 
 /** Build the system prompt with tools, guidelines, and context */
 export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): string {
-	const { customPrompt, selectedTools, appendSystemPrompt, skillsSettings } = options;
+	const {
+		customPrompt,
+		selectedTools,
+		appendSystemPrompt,
+		skillsSettings,
+		cwd,
+		agentDir,
+		contextFiles: providedContextFiles,
+		skills: providedSkills,
+	} = options;
+	const resolvedCwd = cwd ?? process.cwd();
 	const resolvedCustomPrompt = resolvePromptInput(customPrompt, "system prompt");
 	const resolvedAppendPrompt = resolvePromptInput(appendSystemPrompt, "append system prompt");
 
@@ -133,6 +165,14 @@ export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): strin
 
 	const appendSection = resolvedAppendPrompt ? `\n\n${resolvedAppendPrompt}` : "";
 
+	// Resolve context files: use provided or discover
+	const contextFiles = providedContextFiles ?? loadProjectContextFiles({ cwd: resolvedCwd, agentDir });
+
+	// Resolve skills: use provided or discover
+	const skills =
+		providedSkills ??
+		(skillsSettings?.enabled !== false ? loadSkills({ ...skillsSettings, cwd: resolvedCwd, agentDir }).skills : []);
+
 	if (resolvedCustomPrompt) {
 		let prompt = resolvedCustomPrompt;
 
@@ -141,7 +181,6 @@ export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): strin
 		}
 
 		// Append project context files
-		const contextFiles = loadProjectContextFiles();
 		if (contextFiles.length > 0) {
 			prompt += "\n\n# Project Context\n\n";
 			prompt += "The following project context files have been loaded:\n\n";
@@ -152,14 +191,13 @@ export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): strin
 
 		// Append skills section (only if read tool is available)
 		const customPromptHasRead = !selectedTools || selectedTools.includes("read");
-		if (skillsSettings?.enabled !== false && customPromptHasRead) {
+		if (customPromptHasRead && skills.length > 0) {
-			const { skills } = loadSkills(skillsSettings ?? {});
 			prompt += formatSkillsForPrompt(skills);
 		}
 
 		// Add date/time and working directory last
 		prompt += `\nCurrent date and time: ${dateTime}`;
-		prompt += `\nCurrent working directory: ${process.cwd()}`;
+		prompt += `\nCurrent working directory: ${resolvedCwd}`;
 
 		return prompt;
 	}
@@ -248,7 +286,6 @@ Documentation:
 	}
 
 	// Append project context files
-	const contextFiles = loadProjectContextFiles();
 	if (contextFiles.length > 0) {
 		prompt += "\n\n# Project Context\n\n";
 		prompt += "The following project context files have been loaded:\n\n";
@@ -258,14 +295,13 @@ Documentation:
 	}
 
 	// Append skills section (only if read tool is available)
-	if (skillsSettings?.enabled !== false && hasRead) {
+	if (hasRead && skills.length > 0) {
-		const { skills } = loadSkills(skillsSettings ?? {});
 		prompt += formatSkillsForPrompt(skills);
 	}
 
 	// Add date/time and working directory last
 	prompt += `\nCurrent date and time: ${dateTime}`;
-	prompt += `\nCurrent working directory: ${process.cwd()}`;
+	prompt += `\nCurrent working directory: ${resolvedCwd}`;
 
 	return prompt;
 }

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

@@ -1,3 +1,5 @@
+import type { AgentTool } from "@mariozechner/pi-ai";
+
 export { type BashToolDetails, bashTool } from "./bash.js";
 export { editTool } from "./edit.js";
 export { type FindToolDetails, findTool } from "./find.js";
@@ -15,8 +17,14 @@ import { lsTool } from "./ls.js";
 import { readTool } from "./read.js";
 import { writeTool } from "./write.js";
 
+/** Tool type (AgentTool from pi-ai) */
+export type Tool = AgentTool<any>;
+
 // Default tools for full access mode
-export const codingTools = [readTool, bashTool, editTool, writeTool];
+export const codingTools: Tool[] = [readTool, bashTool, editTool, writeTool];
+
+// Read-only tools for exploration without modification
+export const readOnlyTools: Tool[] = [readTool, grepTool, findTool, lsTool];
 
 // All available tools (including read-only exploration tools)
 export const allTools = {

packages/coding-agent/src/index.ts

@@ -83,6 +83,32 @@ export {
 	type OAuthPrompt,
 	type OAuthProvider,
 } from "./core/oauth/index.js";
+// SDK for programmatic usage
+export {
+	type BuildSystemPromptOptions,
+	buildSystemPrompt,
+	type CreateAgentSessionOptions,
+	type CreateAgentSessionResult,
+	// Configuration
+	configureOAuthStorage,
+	// Factory
+	createAgentSession,
+	// Helpers
+	defaultGetApiKey,
+	discoverAvailableModels,
+	discoverContextFiles,
+	discoverCustomTools,
+	discoverHooks,
+	// Discovery
+	discoverModels,
+	discoverSkills,
+	discoverSlashCommands,
+	type FileSlashCommand,
+	findModel as findModelByProviderAndId,
+	loadSettings,
+	// Tools
+	readOnlyTools,
+} from "./core/sdk.js";
 export {
 	type CompactionEntry,
 	createSummaryMessage,
@@ -93,6 +119,7 @@ export {
 	parseSessionEntries,
 	type SessionEntry,
 	type SessionHeader,
+	type SessionInfo,
 	SessionManager,
 	type SessionMessageEntry,
 	SUMMARY_PREFIX,

packages/coding-agent/src/main.ts

@@ -1,61 +1,34 @@
 /**
- * Main entry point for the coding agent
+ * Main entry point for the coding agent CLI.
+ *
+ * This file handles CLI argument parsing and translates them into
+ * createAgentSession() options. The SDK does the heavy lifting.
  */
 
-import { Agent, type Attachment, ProviderTransport, type ThinkingLevel } from "@mariozechner/pi-agent-core";
+import type { Attachment } from "@mariozechner/pi-agent-core";
-import { setOAuthStorage, supportsXhigh } from "@mariozechner/pi-ai";
+import { supportsXhigh } from "@mariozechner/pi-ai";
 import chalk from "chalk";
-import { chmodSync, existsSync, mkdirSync, readFileSync, writeFileSync } from "fs";
+
-import { dirname } from "path";
 import { type Args, parseArgs, printHelp } from "./cli/args.js";
 import { processFileArguments } from "./cli/file-processor.js";
 import { listModels } from "./cli/list-models.js";
 import { selectSession } from "./cli/session-picker.js";
-import { getModelsPath, getOAuthPath, VERSION } from "./config.js";
+import { getModelsPath, VERSION } from "./config.js";
-import { AgentSession } from "./core/agent-session.js";
+import type { AgentSession } from "./core/agent-session.js";
-import { discoverAndLoadCustomTools, type LoadedCustomTool } from "./core/custom-tools/index.js";
+import type { LoadedCustomTool } from "./core/custom-tools/index.js";
 import { exportFromFile } from "./core/export-html.js";
-import { discoverAndLoadHooks, HookRunner, wrapToolsWithHooks } from "./core/hooks/index.js";
+import type { HookUIContext } from "./core/index.js";
-import { messageTransformer } from "./core/messages.js";
+import { findModel } from "./core/model-config.js";
-import { findModel, getApiKeyForModel, getAvailableModels } from "./core/model-config.js";
+import { resolveModelScope, type ScopedModel } from "./core/model-resolver.js";
-import { resolveModelScope, restoreModelFromSession, type ScopedModel } from "./core/model-resolver.js";
+import { type CreateAgentSessionOptions, configureOAuthStorage, createAgentSession } from "./core/sdk.js";
 import { SessionManager } from "./core/session-manager.js";
 import { SettingsManager } from "./core/settings-manager.js";
-import { loadSlashCommands } from "./core/slash-commands.js";
+import { allTools } from "./core/tools/index.js";
-import { buildSystemPrompt } from "./core/system-prompt.js";
-import { allTools, codingTools } from "./core/tools/index.js";
 import { InteractiveMode, runPrintMode, runRpcMode } from "./modes/index.js";
 import { initTheme, stopThemeWatcher } from "./modes/interactive/theme/theme.js";
 import { getChangelogPath, getNewEntries, parseChangelog } from "./utils/changelog.js";
 import { ensureTool } from "./utils/tools-manager.js";
 
-/** Configure OAuth storage to use the coding-agent's configurable path */
-function configureOAuthStorage(): void {
-	const oauthPath = getOAuthPath();
-
-	setOAuthStorage({
-		load: () => {
-			if (!existsSync(oauthPath)) {
-				return {};
-			}
-			try {
-				return JSON.parse(readFileSync(oauthPath, "utf-8"));
-			} catch {
-				return {};
-			}
-		},
-		save: (storage) => {
-			const dir = dirname(oauthPath);
-			if (!existsSync(dir)) {
-				mkdirSync(dir, { recursive: true, mode: 0o700 });
-			}
-			writeFileSync(oauthPath, JSON.stringify(storage, null, 2), "utf-8");
-			chmodSync(oauthPath, 0o600);
-		},
-	});
-}
-
-/** Check npm registry for new version (non-blocking) */
 async function checkForNewVersion(currentVersion: string): Promise<string | null> {
 	try {
 		const response = await fetch("https://registry.npmjs.org/@mariozechner/pi-coding-agent/latest");
@@ -70,46 +43,39 @@ async function checkForNewVersion(currentVersion: string): Promise<string | null
 
 		return null;
 	} catch {
-		// Silently fail - don't disrupt the user experience
 		return null;
 	}
 }
 
-/** Run interactive mode with TUI */
 async function runInteractiveMode(
 	session: AgentSession,
 	version: string,
 	changelogMarkdown: string | null,
-	modelFallbackMessage: string | null,
+	modelFallbackMessage: string | undefined,
 	versionCheckPromise: Promise<string | null>,
 	initialMessages: string[],
 	customTools: LoadedCustomTool[],
-	setToolUIContext: (uiContext: import("./core/hooks/types.js").HookUIContext, hasUI: boolean) => void,
+	setToolUIContext: (uiContext: HookUIContext, hasUI: boolean) => void,
 	initialMessage?: string,
 	initialAttachments?: Attachment[],
 	fdPath: string | null = null,
 ): Promise<void> {
 	const mode = new InteractiveMode(session, version, changelogMarkdown, customTools, setToolUIContext, fdPath);
 
-	// Initialize TUI (subscribes to agent events internally)
 	await mode.init();
 
-	// Handle version check result when it completes (don't block)
 	versionCheckPromise.then((newVersion) => {
 		if (newVersion) {
 			mode.showNewVersionNotification(newVersion);
 		}
 	});
 
-	// Render any existing messages (from --continue mode)
 	mode.renderInitialMessages(session.state);
 
-	// Show model fallback warning at the end of the chat if applicable
 	if (modelFallbackMessage) {
 		mode.showWarning(modelFallbackMessage);
 	}
 
-	// Process initial message with attachments if provided (from @file args)
 	if (initialMessage) {
 		try {
 			await session.prompt(initialMessage, { attachments: initialAttachments });
@@ -119,7 +85,6 @@ async function runInteractiveMode(
 		}
 	}
 
-	// Process remaining initial messages if provided (from CLI args)
 	for (const message of initialMessages) {
 		try {
 			await session.prompt(message);
@@ -129,11 +94,8 @@ async function runInteractiveMode(
 		}
 	}
 
-	// Interactive loop
 	while (true) {
 		const userInput = await mode.getUserInput();
-
-		// Process the message
 		try {
 			await session.prompt(userInput);
 		} catch (error: unknown) {
@@ -143,7 +105,6 @@ async function runInteractiveMode(
 	}
 }
 
-/** Prepare initial message from @file arguments */
 async function prepareInitialMessage(parsed: Args): Promise<{
 	initialMessage?: string;
 	initialAttachments?: Attachment[];
@@ -154,11 +115,10 @@ async function prepareInitialMessage(parsed: Args): Promise<{
 
 	const { textContent, imageAttachments } = await processFileArguments(parsed.fileArgs);
 
-	// Combine file content with first plain text message (if any)
 	let initialMessage: string;
 	if (parsed.messages.length > 0) {
 		initialMessage = textContent + parsed.messages[0];
-		parsed.messages.shift(); // Remove first message as it's been combined
+		parsed.messages.shift();
 	} else {
 		initialMessage = textContent;
 	}
@@ -169,9 +129,123 @@ async function prepareInitialMessage(parsed: Args): Promise<{
 	};
 }
 
+function getChangelogForDisplay(parsed: Args, settingsManager: SettingsManager): string | null {
+	if (parsed.continue || parsed.resume) {
+		return null;
+	}
+
+	const lastVersion = settingsManager.getLastChangelogVersion();
+	const changelogPath = getChangelogPath();
+	const entries = parseChangelog(changelogPath);
+
+	if (!lastVersion) {
+		if (entries.length > 0) {
+			settingsManager.setLastChangelogVersion(VERSION);
+			return entries.map((e) => e.content).join("\n\n");
+		}
+	} else {
+		const newEntries = getNewEntries(entries, lastVersion);
+		if (newEntries.length > 0) {
+			settingsManager.setLastChangelogVersion(VERSION);
+			return newEntries.map((e) => e.content).join("\n\n");
+		}
+	}
+
+	return null;
+}
+
+function createSessionManager(parsed: Args, cwd: string): SessionManager | null {
+	if (parsed.noSession) {
+		return SessionManager.inMemory();
+	}
+	if (parsed.session) {
+		return SessionManager.open(parsed.session);
+	}
+	if (parsed.continue) {
+		return SessionManager.continueRecent(cwd);
+	}
+	// --resume is handled separately (needs picker UI)
+	// Default case (new session) returns null, SDK will create one
+	return null;
+}
+
+function buildSessionOptions(
+	parsed: Args,
+	scopedModels: ScopedModel[],
+	sessionManager: SessionManager | null,
+): CreateAgentSessionOptions {
+	const options: CreateAgentSessionOptions = {};
+
+	if (sessionManager) {
+		options.sessionManager = sessionManager;
+	}
+
+	// Model from CLI
+	if (parsed.provider && parsed.model) {
+		const { model, error } = findModel(parsed.provider, parsed.model);
+		if (error) {
+			console.error(chalk.red(error));
+			process.exit(1);
+		}
+		if (!model) {
+			console.error(chalk.red(`Model ${parsed.provider}/${parsed.model} not found`));
+			process.exit(1);
+		}
+		options.model = model;
+	} else if (scopedModels.length > 0 && !parsed.continue && !parsed.resume) {
+		options.model = scopedModels[0].model;
+	}
+
+	// Thinking level
+	if (parsed.thinking) {
+		options.thinkingLevel = parsed.thinking;
+	} else if (scopedModels.length > 0 && !parsed.continue && !parsed.resume) {
+		options.thinkingLevel = scopedModels[0].thinkingLevel;
+	}
+
+	// Scoped models for Ctrl+P cycling
+	if (scopedModels.length > 0) {
+		options.scopedModels = scopedModels;
+	}
+
+	// API key from CLI
+	if (parsed.apiKey) {
+		options.getApiKey = async () => parsed.apiKey!;
+	}
+
+	// System prompt
+	if (parsed.systemPrompt && parsed.appendSystemPrompt) {
+		options.systemPrompt = `${parsed.systemPrompt}\n\n${parsed.appendSystemPrompt}`;
+	} else if (parsed.systemPrompt) {
+		options.systemPrompt = parsed.systemPrompt;
+	} else if (parsed.appendSystemPrompt) {
+		options.systemPrompt = (defaultPrompt) => `${defaultPrompt}\n\n${parsed.appendSystemPrompt}`;
+	}
+
+	// Tools
+	if (parsed.tools) {
+		options.tools = parsed.tools.map((name) => allTools[name]);
+	}
+
+	// Skills
+	if (parsed.noSkills) {
+		options.skills = [];
+	}
+
+	// Additional hook paths from CLI
+	if (parsed.hooks && parsed.hooks.length > 0) {
+		options.additionalHookPaths = parsed.hooks;
+	}
+
+	// Additional custom tool paths from CLI
+	if (parsed.customTools && parsed.customTools.length > 0) {
+		options.additionalCustomToolPaths = parsed.customTools;
+	}
+
+	return options;
+}
+
 export async function main(args: string[]) {
-	// Configure OAuth storage to use the coding-agent's configurable path
-	// This must happen before any OAuth operations
 	configureOAuthStorage();
 
 	const parsed = parseArgs(args);
@@ -186,14 +260,12 @@ export async function main(args: string[]) {
 		return;
 	}
 
-	// Handle --list-models flag: list available models and exit
 	if (parsed.listModels !== undefined) {
 		const searchPattern = typeof parsed.listModels === "string" ? parsed.listModels : undefined;
 		await listModels(searchPattern);
 		return;
 	}
 
-	// Handle --export flag: convert session file to HTML and exit
 	if (parsed.export) {
 		try {
 			const outputPath = parsed.messages.length > 0 ? parsed.messages[0] : undefined;
@@ -207,67 +279,46 @@ export async function main(args: string[]) {
 		}
 	}
 
-	// Validate: RPC mode doesn't support @file arguments
 	if (parsed.mode === "rpc" && parsed.fileArgs.length > 0) {
 		console.error(chalk.red("Error: @file arguments are not supported in RPC mode"));
 		process.exit(1);
 	}
 
-	// Process @file arguments
+	const cwd = process.cwd();
 	const { initialMessage, initialAttachments } = await prepareInitialMessage(parsed);
-
-	// Determine if we're in interactive mode (needed for theme watcher)
 	const isInteractive = !parsed.print && parsed.mode === undefined;
+	const mode = parsed.mode || "text";
 
-	// Initialize theme (before any TUI rendering)
+	const settingsManager = SettingsManager.create(cwd);
-	const settingsManager = new SettingsManager();
+	initTheme(settingsManager.getTheme(), isInteractive);
-	const themeName = settingsManager.getTheme();
-	initTheme(themeName, isInteractive);
 
-	// Setup session manager
-	const sessionManager = new SessionManager(parsed.continue && !parsed.resume, parsed.session);
-
-	if (parsed.noSession) {
-		sessionManager.disable();
-	}
-
-	// Handle --resume flag: show session selector
-	if (parsed.resume) {
-		const selectedSession = await selectSession(sessionManager);
-		if (!selectedSession) {
-			console.log(chalk.dim("No session selected"));
-			return;
-		}
-		sessionManager.setSessionFile(selectedSession);
-	}
-
-	// Resolve model scope early if provided
 	let scopedModels: ScopedModel[] = [];
 	if (parsed.models && parsed.models.length > 0) {
 		scopedModels = await resolveModelScope(parsed.models);
 	}
 
-	// Determine mode and output behavior
+	// Create session manager based on CLI flags
-	const mode = parsed.mode || "text";
+	let sessionManager = createSessionManager(parsed, cwd);
-	const shouldPrintMessages = isInteractive;
 
-	// Find initial model
+	// Handle --resume: show session picker
-	let initialModel = await findInitialModelForSession(parsed, scopedModels, settingsManager);
+	if (parsed.resume) {
-	let initialThinking: ThinkingLevel = "off";
+		const sessions = SessionManager.list(cwd);
-
+		if (sessions.length === 0) {
-	// Get thinking level from scoped models if applicable
+			console.log(chalk.dim("No sessions found"));
-	if (scopedModels.length > 0 && !parsed.continue && !parsed.resume) {
+			return;
-		initialThinking = scopedModels[0].thinkingLevel;
-	} else {
-		// Try saved thinking level
-		const savedThinking = settingsManager.getDefaultThinkingLevel();
-		if (savedThinking) {
-			initialThinking = savedThinking;
 		}
+		const selectedPath = await selectSession(sessions);
+		if (!selectedPath) {
+			console.log(chalk.dim("No session selected"));
+			return;
+		}
+		sessionManager = SessionManager.open(selectedPath);
 	}
 
-	// Non-interactive mode: fail early if no model available
+	const sessionOptions = buildSessionOptions(parsed, scopedModels, sessionManager);
-	if (!isInteractive && !initialModel) {
+	const { session, customToolsResult, modelFallbackMessage } = await createAgentSession(sessionOptions);
+
+	if (!isInteractive && !session.model) {
 		console.error(chalk.red("No models available."));
 		console.error(chalk.yellow("\nSet an API key environment variable:"));
 		console.error("  ANTHROPIC_API_KEY, OPENAI_API_KEY, GEMINI_API_KEY, etc.");
@@ -275,191 +326,25 @@ export async function main(args: string[]) {
 		process.exit(1);
 	}
 
-	// Non-interactive mode: validate API key exists
+	// Clamp thinking level to model capabilities (for CLI override case)
-	if (!isInteractive && initialModel) {
+	if (session.model && parsed.thinking) {
-		const apiKey = parsed.apiKey || (await getApiKeyForModel(initialModel));
+		let effectiveThinking = parsed.thinking;
-		if (!apiKey) {
+		if (!session.model.reasoning) {
-			console.error(chalk.red(`No API key found for ${initialModel.provider}`));
+			effectiveThinking = "off";
-			process.exit(1);
+		} else if (effectiveThinking === "xhigh" && !supportsXhigh(session.model)) {
+			effectiveThinking = "high";
+		}
+		if (effectiveThinking !== session.thinkingLevel) {
+			session.setThinkingLevel(effectiveThinking);
 		}
 	}
 
-	// Build system prompt
-	const skillsSettings = settingsManager.getSkillsSettings();
-	if (parsed.noSkills) {
-		skillsSettings.enabled = false;
-	}
-	if (parsed.skills && parsed.skills.length > 0) {
-		skillsSettings.includeSkills = parsed.skills;
-	}
-	const systemPrompt = buildSystemPrompt({
-		customPrompt: parsed.systemPrompt,
-		selectedTools: parsed.tools,
-		appendSystemPrompt: parsed.appendSystemPrompt,
-		skillsSettings,
-	});
-
-	// Handle session restoration
-	let modelFallbackMessage: string | null = null;
-
-	if (parsed.continue || parsed.resume || parsed.session) {
-		const savedModel = sessionManager.loadModel();
-		if (savedModel) {
-			const result = await restoreModelFromSession(
-				savedModel.provider,
-				savedModel.modelId,
-				initialModel,
-				shouldPrintMessages,
-			);
-
-			if (result.model) {
-				initialModel = result.model;
-			}
-			modelFallbackMessage = result.fallbackMessage;
-		}
-
-		// Load and restore thinking level
-		const thinkingLevel = sessionManager.loadThinkingLevel() as ThinkingLevel;
-		if (thinkingLevel) {
-			initialThinking = thinkingLevel;
-			if (shouldPrintMessages) {
-				console.log(chalk.dim(`Restored thinking level: ${thinkingLevel}`));
-			}
-		}
-	}
-
-	// CLI --thinking flag takes highest priority
-	if (parsed.thinking) {
-		initialThinking = parsed.thinking;
-	}
-
-	// Clamp thinking level to model capabilities
-	if (initialModel) {
-		if (!initialModel.reasoning) {
-			initialThinking = "off";
-		} else if (initialThinking === "xhigh" && !supportsXhigh(initialModel)) {
-			initialThinking = "high";
-		}
-	}
-
-	// Determine which tools to use
-	let selectedTools = parsed.tools ? parsed.tools.map((name) => allTools[name]) : codingTools;
-
-	// Discover and load hooks from:
-	// 1. ~/.pi/agent/hooks/*.ts (global)
-	// 2. cwd/.pi/hooks/*.ts (project-local)
-	// 3. Explicit paths in settings.json
-	// 4. CLI --hook flags
-	let hookRunner: HookRunner | null = null;
-	const cwd = process.cwd();
-	const configuredHookPaths = [...settingsManager.getHookPaths(), ...(parsed.hooks ?? [])];
-	const { hooks, errors } = await discoverAndLoadHooks(configuredHookPaths, cwd);
-
-	// Report hook loading errors
-	for (const { path, error } of errors) {
-		console.error(chalk.red(`Failed to load hook "${path}": ${error}`));
-	}
-
-	if (hooks.length > 0) {
-		const timeout = settingsManager.getHookTimeout();
-		hookRunner = new HookRunner(hooks, cwd, timeout);
-	}
-
-	// Discover and load custom tools from:
-	// 1. ~/.pi/agent/tools/*.ts (global)
-	// 2. cwd/.pi/tools/*.ts (project-local)
-	// 3. Explicit paths in settings.json
-	// 4. CLI --tool flags
-	const configuredToolPaths = [...settingsManager.getCustomToolPaths(), ...(parsed.customTools ?? [])];
-	const builtInToolNames = Object.keys(allTools);
-	const {
-		tools: loadedCustomTools,
-		errors: toolErrors,
-		setUIContext: setToolUIContext,
-	} = await discoverAndLoadCustomTools(configuredToolPaths, cwd, builtInToolNames);
-
-	// Report custom tool loading errors
-	for (const { path, error } of toolErrors) {
-		console.error(chalk.red(`Failed to load custom tool "${path}": ${error}`));
-	}
-
-	// Add custom tools to selected tools
-	if (loadedCustomTools.length > 0) {
-		const customToolInstances = loadedCustomTools.map((lt) => lt.tool);
-		selectedTools = [...selectedTools, ...customToolInstances] as typeof selectedTools;
-	}
-
-	// Wrap tools with hook callbacks (built-in and custom)
-	if (hookRunner) {
-		selectedTools = wrapToolsWithHooks(selectedTools, hookRunner);
-	}
-
-	// Create agent
-	const agent = new Agent({
-		initialState: {
-			systemPrompt,
-			model: initialModel as any, // Can be null in interactive mode
-			thinkingLevel: initialThinking,
-			tools: selectedTools,
-		},
-		messageTransformer,
-		queueMode: settingsManager.getQueueMode(),
-		transport: new ProviderTransport({
-			getApiKey: async () => {
-				const currentModel = agent.state.model;
-				if (!currentModel) {
-					throw new Error("No model selected");
-				}
-
-				if (parsed.apiKey) {
-					return parsed.apiKey;
-				}
-
-				const key = await getApiKeyForModel(currentModel);
-				if (!key) {
-					throw new Error(
-						`No API key found for provider "${currentModel.provider}". Please set the appropriate environment variable or update ${getModelsPath()}`,
-					);
-				}
-				return key;
-			},
-		}),
-	});
-
-	// Load previous messages if continuing, resuming, or using --session
-	if (parsed.continue || parsed.resume || parsed.session) {
-		const messages = sessionManager.loadMessages();
-		if (messages.length > 0) {
-			agent.replaceMessages(messages);
-		}
-	}
-
-	// Load file commands for slash command expansion
-	const fileCommands = loadSlashCommands();
-
-	// Create session
-	const session = new AgentSession({
-		agent,
-		sessionManager,
-		settingsManager,
-		scopedModels,
-		fileCommands,
-		hookRunner,
-		customTools: loadedCustomTools,
-		skillsSettings,
-	});
-
-	// Route to appropriate mode
 	if (mode === "rpc") {
 		await runRpcMode(session);
 	} else if (isInteractive) {
-		// Check for new version in the background
 		const versionCheckPromise = checkForNewVersion(VERSION).catch(() => null);
-
-		// Check if we should show changelog
 		const changelogMarkdown = getChangelogForDisplay(parsed, settingsManager);
 
-		// Show model scope if provided
 		if (scopedModels.length > 0) {
 			const modelList = scopedModels
 				.map((sm) => {
@@ -470,7 +355,6 @@ export async function main(args: string[]) {
 			console.log(chalk.dim(`Model scope: ${modelList} ${chalk.gray("(Ctrl+P to cycle)")}`));
 		}
 
-		// Ensure fd tool is available for file autocomplete
 		const fdPath = await ensureTool("fd");
 
 		await runInteractiveMode(
@@ -480,99 +364,18 @@ export async function main(args: string[]) {
 			modelFallbackMessage,
 			versionCheckPromise,
 			parsed.messages,
-			loadedCustomTools,
+			customToolsResult.tools,
-			setToolUIContext,
+			customToolsResult.setUIContext,
 			initialMessage,
 			initialAttachments,
 			fdPath,
 		);
 	} else {
-		// Non-interactive mode (--print flag or --mode flag)
 		await runPrintMode(session, mode, parsed.messages, initialMessage, initialAttachments);
-		// Clean up and exit (file watchers keep process alive)
 		stopThemeWatcher();
-		// Wait for stdout to fully flush before exiting
 		if (process.stdout.writableLength > 0) {
 			await new Promise<void>((resolve) => process.stdout.once("drain", resolve));
 		}
 		process.exit(0);
 	}
 }
-
-/** Find initial model based on CLI args, scoped models, settings, or available models */
-async function findInitialModelForSession(parsed: Args, scopedModels: ScopedModel[], settingsManager: SettingsManager) {
-	// 1. CLI args take priority
-	if (parsed.provider && parsed.model) {
-		const { model, error } = findModel(parsed.provider, parsed.model);
-		if (error) {
-			console.error(chalk.red(error));
-			process.exit(1);
-		}
-		if (!model) {
-			console.error(chalk.red(`Model ${parsed.provider}/${parsed.model} not found`));
-			process.exit(1);
-		}
-		return model;
-	}
-
-	// 2. Use first model from scoped models (skip if continuing/resuming)
-	if (scopedModels.length > 0 && !parsed.continue && !parsed.resume) {
-		return scopedModels[0].model;
-	}
-
-	// 3. Try saved default from settings
-	const defaultProvider = settingsManager.getDefaultProvider();
-	const defaultModelId = settingsManager.getDefaultModel();
-	if (defaultProvider && defaultModelId) {
-		const { model, error } = findModel(defaultProvider, defaultModelId);
-		if (error) {
-			console.error(chalk.red(error));
-			process.exit(1);
-		}
-		if (model) {
-			return model;
-		}
-	}
-
-	// 4. Try first available model with valid API key
-	const { models: availableModels, error } = await getAvailableModels();
-
-	if (error) {
-		console.error(chalk.red(error));
-		process.exit(1);
-	}
-
-	if (availableModels.length > 0) {
-		return availableModels[0];
-	}
-
-	return null;
-}
-
-/** Get changelog markdown to display (only for new sessions with updates) */
-function getChangelogForDisplay(parsed: Args, settingsManager: SettingsManager): string | null {
-	if (parsed.continue || parsed.resume) {
-		return null;
-	}
-
-	const lastVersion = settingsManager.getLastChangelogVersion();
-	const changelogPath = getChangelogPath();
-	const entries = parseChangelog(changelogPath);
-
-	if (!lastVersion) {
-		// First run - show all entries
-		if (entries.length > 0) {
-			settingsManager.setLastChangelogVersion(VERSION);
-			return entries.map((e) => e.content).join("\n\n");
-		}
-	} else {
-		// Check for new entries since last version
-		const newEntries = getNewEntries(entries, lastVersion);
-		if (newEntries.length > 0) {
-			settingsManager.setLastChangelogVersion(VERSION);
-			return newEntries.map((e) => e.content).join("\n\n");
-		}
-	}
-
-	return null;
-}

packages/coding-agent/src/modes/interactive/components/session-selector.ts

@@ -11,27 +11,17 @@ import {
 	Text,
 	truncateToWidth,
 } from "@mariozechner/pi-tui";
-import type { SessionManager } from "../../../core/session-manager.js";
+import type { SessionInfo } from "../../../core/session-manager.js";
 import { fuzzyFilter } from "../../../utils/fuzzy.js";
 import { theme } from "../theme/theme.js";
 import { DynamicBorder } from "./dynamic-border.js";
 
-interface SessionItem {
-	path: string;
-	id: string;
-	created: Date;
-	modified: Date;
-	messageCount: number;
-	firstMessage: string;
-	allMessagesText: string;
-}
-
 /**
  * Custom session list component with multi-line items and search
  */
 class SessionList implements Component {
-	private allSessions: SessionItem[] = [];
+	private allSessions: SessionInfo[] = [];
-	private filteredSessions: SessionItem[] = [];
+	private filteredSessions: SessionInfo[] = [];
 	private selectedIndex: number = 0;
 	private searchInput: Input;
 	public onSelect?: (sessionPath: string) => void;
@@ -39,7 +29,7 @@ class SessionList implements Component {
 	public onExit: () => void = () => {};
 	private maxVisible: number = 5; // Max sessions visible (each session is 3 lines: msg + metadata + blank)
 
-	constructor(sessions: SessionItem[]) {
+	constructor(sessions: SessionInfo[]) {
 		this.allSessions = sessions;
 		this.filteredSessions = sessions;
 		this.searchInput = new Input();
@@ -176,16 +166,13 @@ export class SessionSelectorComponent extends Container {
 	private sessionList: SessionList;
 
 	constructor(
-		sessionManager: SessionManager,
+		sessions: SessionInfo[],
 		onSelect: (sessionPath: string) => void,
 		onCancel: () => void,
 		onExit: () => void,
 	) {
 		super();
 
-		// Load all sessions
-		const sessions = sessionManager.loadAllSessions();
-
 		// Add header
 		this.addChild(new Spacer(1));
 		this.addChild(new Text(theme.bold("Resume Session"), 1, 0));

packages/coding-agent/src/modes/interactive/interactive-mode.ts

@@ -32,7 +32,12 @@ import type { HookUIContext } from "../../core/hooks/index.js";
 import { isBashExecutionMessage } from "../../core/messages.js";
 import { invalidateOAuthCache } from "../../core/model-config.js";
 import { listOAuthProviders, login, logout, type OAuthProvider } from "../../core/oauth/index.js";
-import { getLatestCompactionEntry, SUMMARY_PREFIX, SUMMARY_SUFFIX } from "../../core/session-manager.js";
+import {
+	getLatestCompactionEntry,
+	SessionManager,
+	SUMMARY_PREFIX,
+	SUMMARY_SUFFIX,
+} from "../../core/session-manager.js";
 import { loadSkills } from "../../core/skills.js";
 import { loadProjectContextFiles } from "../../core/system-prompt.js";
 import type { TruncationResult } from "../../core/tools/truncate.js";
@@ -1513,8 +1518,9 @@ export class InteractiveMode {
 
 	private showSessionSelector(): void {
 		this.showSelector((done) => {
+			const sessions = SessionManager.list(this.sessionManager.getCwd());
 			const selector = new SessionSelectorComponent(
-				this.sessionManager,
+				sessions,
 				async (sessionPath) => {
 					done();
 					await this.handleResumeSession(sessionPath);

packages/coding-agent/src/utils/shell.ts

@@ -34,7 +34,7 @@ export function getShellConfig(): { shell: string; args: string[] } {
 		return cachedShellConfig;
 	}
 
-	const settings = new SettingsManager();
+	const settings = SettingsManager.create();
 	const customShellPath = settings.getShellPath();
 
 	// 1. Check user-specified shell path

packages/coding-agent/test/agent-session-branching.test.ts

@@ -56,11 +56,8 @@ describe.skipIf(!API_KEY)("AgentSession branching", () => {
 			},
 		});
 
-		sessionManager = new SessionManager(false);
+		sessionManager = noSession ? SessionManager.inMemory() : SessionManager.create(tempDir);
-		if (noSession) {
+		const settingsManager = SettingsManager.create(tempDir, tempDir);
-			sessionManager.disable();
-		}
-		const settingsManager = new SettingsManager(tempDir);
 
 		session = new AgentSession({
 			agent,

packages/coding-agent/test/agent-session-compaction.test.ts

@@ -60,8 +60,8 @@ describe.skipIf(!API_KEY)("AgentSession compaction e2e", () => {
 			},
 		});
 
-		sessionManager = new SessionManager(false);
+		sessionManager = SessionManager.create(tempDir);
-		const settingsManager = new SettingsManager(tempDir);
+		const settingsManager = SettingsManager.create(tempDir, tempDir);
 
 		session = new AgentSession({
 			agent,
@@ -174,11 +174,10 @@ describe.skipIf(!API_KEY)("AgentSession compaction e2e", () => {
 			},
 		});
 
-		// Create session manager and disable file persistence
+		// Create in-memory session manager
-		const noSessionManager = new SessionManager(false);
+		const noSessionManager = SessionManager.inMemory();
-		noSessionManager.disable();
 
-		const settingsManager = new SettingsManager(tempDir);
+		const settingsManager = SettingsManager.create(tempDir, tempDir);
 
 		const noSessionSession = new AgentSession({
 			agent,

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

@@ -234,9 +234,6 @@ describe("loadSessionFromEntries", () => {
 				id: "1",
 				timestamp: "",
 				cwd: "",
-				provider: "anthropic",
-				modelId: "claude",
-				thinkingLevel: "off",
 			},
 			createMessageEntry(createUserMessage("1")),
 			createMessageEntry(createAssistantMessage("a")),
@@ -247,7 +244,7 @@ describe("loadSessionFromEntries", () => {
 		const loaded = loadSessionFromEntries(entries);
 		expect(loaded.messages.length).toBe(4);
 		expect(loaded.thinkingLevel).toBe("off");
-		expect(loaded.model).toEqual({ provider: "anthropic", modelId: "claude" });
+		expect(loaded.model).toEqual({ provider: "anthropic", modelId: "claude-sonnet-4-5" });
 	});
 
 	it("should handle single compaction", () => {
@@ -258,9 +255,6 @@ describe("loadSessionFromEntries", () => {
 				id: "1",
 				timestamp: "",
 				cwd: "",
-				provider: "anthropic",
-				modelId: "claude",
-				thinkingLevel: "off",
 			},
 			createMessageEntry(createUserMessage("1")),
 			createMessageEntry(createAssistantMessage("a")),
@@ -286,9 +280,6 @@ describe("loadSessionFromEntries", () => {
 				id: "1",
 				timestamp: "",
 				cwd: "",
-				provider: "anthropic",
-				modelId: "claude",
-				thinkingLevel: "off",
 			},
 			createMessageEntry(createUserMessage("1")),
 			createMessageEntry(createAssistantMessage("a")),
@@ -316,9 +307,6 @@ describe("loadSessionFromEntries", () => {
 				id: "1",
 				timestamp: "",
 				cwd: "",
-				provider: "anthropic",
-				modelId: "claude",
-				thinkingLevel: "off",
 			},
 			createMessageEntry(createUserMessage("1")),
 			createMessageEntry(createAssistantMessage("a")),
@@ -341,9 +329,6 @@ describe("loadSessionFromEntries", () => {
 				id: "1",
 				timestamp: "",
 				cwd: "",
-				provider: "anthropic",
-				modelId: "claude",
-				thinkingLevel: "off",
 			},
 			createMessageEntry(createUserMessage("1")),
 			{ type: "model_change", timestamp: "", provider: "openai", modelId: "gpt-4" },
@@ -352,7 +337,8 @@ describe("loadSessionFromEntries", () => {
 		];
 
 		const loaded = loadSessionFromEntries(entries);
-		expect(loaded.model).toEqual({ provider: "openai", modelId: "gpt-4" });
+		// model_change is later overwritten by assistant message's model info
+		expect(loaded.model).toEqual({ provider: "anthropic", modelId: "claude-sonnet-4-5" });
 		expect(loaded.thinkingLevel).toBe("high");
 	});
 });

packages/mom/src/agent.ts

@@ -411,12 +411,7 @@ function createRunner(sandboxConfig: SandboxConfig, channelId: string, channelDi
 	const systemPrompt = buildSystemPrompt(workspacePath, channelId, memory, sandboxConfig, [], [], skills);
 
 	// Create session manager and settings manager
-	// Pass model info so new sessions get a header written immediately
+	const sessionManager = new MomSessionManager(channelDir);
-	const sessionManager = new MomSessionManager(channelDir, {
-		provider: model.provider,
-		id: model.id,
-		thinkingLevel: "off",
-	});
 	const settingsManager = new MomSettingsManager(join(channelDir, ".."));
 
 	// Create agent

packages/mom/src/context.ts

@@ -10,14 +10,13 @@
  * - MomSettingsManager: Simple settings for mom (compaction, retry, model preferences)
  */
 
-import type { AgentState, AppMessage } from "@mariozechner/pi-agent-core";
+import type { AppMessage } from "@mariozechner/pi-agent-core";
 import {
 	type CompactionEntry,
 	type LoadedSession,
 	loadSessionFromEntries,
 	type ModelChangeEntry,
 	type SessionEntry,
-	type SessionHeader,
 	type SessionMessageEntry,
 	type ThinkingLevelChangeEntry,
 } from "@mariozechner/pi-coding-agent";
@@ -48,11 +47,10 @@ export class MomSessionManager {
 	private contextFile: string;
 	private logFile: string;
 	private channelDir: string;
-	private sessionInitialized: boolean = false;
+	private flushed: boolean = false;
 	private inMemoryEntries: SessionEntry[] = [];
-	private pendingEntries: SessionEntry[] = [];
 
-	constructor(channelDir: string, initialModel?: { provider: string; id: string; thinkingLevel?: string }) {
+	constructor(channelDir: string) {
 		this.channelDir = channelDir;
 		this.contextFile = join(channelDir, "context.jsonl");
 		this.logFile = join(channelDir, "log.jsonl");
@@ -66,33 +64,33 @@ export class MomSessionManager {
 		if (existsSync(this.contextFile)) {
 			this.inMemoryEntries = this.loadEntriesFromFile();
 			this.sessionId = this.extractSessionId() || uuidv4();
-			this.sessionInitialized = this.inMemoryEntries.length > 0;
+			this.flushed = true;
 		} else {
-			// New session - write header immediately
 			this.sessionId = uuidv4();
-			if (initialModel) {
+			this.inMemoryEntries = [
-				this.writeSessionHeader(initialModel);
+				{
-			}
+					type: "session",
+					id: this.sessionId,
+					timestamp: new Date().toISOString(),
+					cwd: this.channelDir,
+				},
+			];
 		}
 		// Note: syncFromLog() is called explicitly from agent.ts with excludeTimestamp
 	}
 
-	/** Write session header to file (called on new session creation) */
+	private _persist(entry: SessionEntry): void {
-	private writeSessionHeader(model: { provider: string; id: string; thinkingLevel?: string }): void {
+		const hasAssistant = this.inMemoryEntries.some((e) => e.type === "message" && e.message.role === "assistant");
-		this.sessionInitialized = true;
+		if (!hasAssistant) return;
 
-		const entry: SessionHeader = {
+		if (!this.flushed) {
-			type: "session",
+			for (const e of this.inMemoryEntries) {
-			id: this.sessionId,
+				appendFileSync(this.contextFile, `${JSON.stringify(e)}\n`);
-			timestamp: new Date().toISOString(),
+			}
-			cwd: this.channelDir,
+			this.flushed = true;
-			provider: model.provider,
+		} else {
-			modelId: model.id,
+			appendFileSync(this.contextFile, `${JSON.stringify(entry)}\n`);
-			thinkingLevel: model.thinkingLevel || "off",
+		}
-		};
-
-		this.inMemoryEntries.push(entry);
-		appendFileSync(this.contextFile, `${JSON.stringify(entry)}\n`);
 	}
 
 	/**
@@ -248,47 +246,14 @@ export class MomSessionManager {
 		return entries;
 	}
 
-	/** Initialize session with header if not already done */
-	startSession(state: AgentState): void {
-		if (this.sessionInitialized) return;
-		this.sessionInitialized = true;
-
-		const entry: SessionHeader = {
-			type: "session",
-			id: this.sessionId,
-			timestamp: new Date().toISOString(),
-			cwd: this.channelDir,
-			provider: state.model?.provider || "unknown",
-			modelId: state.model?.id || "unknown",
-			thinkingLevel: state.thinkingLevel,
-		};
-
-		this.inMemoryEntries.push(entry);
-		for (const pending of this.pendingEntries) {
-			this.inMemoryEntries.push(pending);
-		}
-		this.pendingEntries = [];
-
-		// Write to file
-		appendFileSync(this.contextFile, `${JSON.stringify(entry)}\n`);
-		for (const memEntry of this.inMemoryEntries.slice(1)) {
-			appendFileSync(this.contextFile, `${JSON.stringify(memEntry)}\n`);
-		}
-	}
-
 	saveMessage(message: AppMessage): void {
 		const entry: SessionMessageEntry = {
 			type: "message",
 			timestamp: new Date().toISOString(),
 			message,
 		};
-
+		this.inMemoryEntries.push(entry);
-		if (!this.sessionInitialized) {
+		this._persist(entry);
-			this.pendingEntries.push(entry);
-		} else {
-			this.inMemoryEntries.push(entry);
-			appendFileSync(this.contextFile, `${JSON.stringify(entry)}\n`);
-		}
 	}
 
 	saveThinkingLevelChange(thinkingLevel: string): void {
@@ -297,13 +262,8 @@ export class MomSessionManager {
 			timestamp: new Date().toISOString(),
 			thinkingLevel,
 		};
-
+		this.inMemoryEntries.push(entry);
-		if (!this.sessionInitialized) {
+		this._persist(entry);
-			this.pendingEntries.push(entry);
-		} else {
-			this.inMemoryEntries.push(entry);
-			appendFileSync(this.contextFile, `${JSON.stringify(entry)}\n`);
-		}
 	}
 
 	saveModelChange(provider: string, modelId: string): void {
@@ -313,18 +273,13 @@ export class MomSessionManager {
 			provider,
 			modelId,
 		};
-
+		this.inMemoryEntries.push(entry);
-		if (!this.sessionInitialized) {
+		this._persist(entry);
-			this.pendingEntries.push(entry);
-		} else {
-			this.inMemoryEntries.push(entry);
-			appendFileSync(this.contextFile, `${JSON.stringify(entry)}\n`);
-		}
 	}
 
 	saveCompaction(entry: CompactionEntry): void {
 		this.inMemoryEntries.push(entry);
-		appendFileSync(this.contextFile, `${JSON.stringify(entry)}\n`);
+		this._persist(entry);
 	}
 
 	/** Load session with compaction support */
@@ -349,20 +304,18 @@ export class MomSessionManager {
 		return this.contextFile;
 	}
 
-	/** Check if session should be initialized */
-	shouldInitializeSession(messages: AppMessage[]): boolean {
-		if (this.sessionInitialized) return false;
-		const userMessages = messages.filter((m) => m.role === "user");
-		const assistantMessages = messages.filter((m) => m.role === "assistant");
-		return userMessages.length >= 1 && assistantMessages.length >= 1;
-	}
-
 	/** Reset session (clears context.jsonl) */
 	reset(): void {
-		this.pendingEntries = [];
-		this.inMemoryEntries = [];
-		this.sessionInitialized = false;
 		this.sessionId = uuidv4();
+		this.flushed = false;
+		this.inMemoryEntries = [
+			{
+				type: "session",
+				id: this.sessionId,
+				timestamp: new Date().toISOString(),
+				cwd: this.channelDir,
+			},
+		];
 		// Truncate the context file
 		if (existsSync(this.contextFile)) {
 			writeFileSync(this.contextFile, "");
@@ -370,7 +323,7 @@ export class MomSessionManager {
 	}
 
 	// Compatibility methods for AgentSession
-	isEnabled(): boolean {
+	isPersisted(): boolean {
 		return true;
 	}