refactor: update import paths to use .js extensions and reorganize Sk…

.gitignore

@@ -31,7 +31,16 @@ packages/desktop/electron.vite.config.*.mjs
 test-output*.txt
 client-tests.txt
 desktop-test.txt
+h-test.txt
+test-fallback.txt
 
 # Compiled JS artifacts leaked into src directories
 packages/infra/src/*.js
 packages/infra/src/*.d.ts
+
+# TypeScript dist-test build artifacts
+dist-test/ 
+
+# Desktop sub-package residual workspace files
+packages/desktop/pnpm-lock.yaml  
+packages/desktop/pnpm-workspace.yaml 

packages/codingcode/package.json

@@ -2,11 +2,46 @@
   "name": "@codingcode/core",
   "version": "0.1.0",
   "type": "module",
-  "main": "./src/index.ts",
+  "main": "./src/layer.ts",
   "exports": {
-    ".": "./src/index.ts",
-    "./client/http": "./src/client/http/index.ts",
-    "./client/types": "./src/client/types.ts"
+    ".": "./src/layer.ts",
+    "./agent/agent": "./src/agent/agent.ts",
+    "./agent/todo": "./src/agent/todo.ts",
+    "./agent/prompt": "./src/agent/prompt.ts",
+    "./session/store": "./src/session/store.ts",
+    "./session/io": "./src/session/io.ts",
+    "./session/messages": "./src/session/messages.ts",
+    "./core/path": "./src/core/path.ts",
+    "./core/workspace": "./src/core/workspace.ts",
+    "./core/error": "./src/core/error.ts",
+    "./core/result": "./src/core/result.ts",
+    "./core/types": "./src/core/types.ts",
+    "./context/context": "./src/context/context.ts",
+    "./context/config": "./src/context/config.ts",
+    "./hooks/registry": "./src/hooks/registry.ts",
+    "./tools/executor": "./src/tools/executor.ts",
+    "./tools/tool-search-service": "./src/tools/tool-search-service.ts",
+    "./mcp/client": "./src/mcp/client.ts",
+    "./mcp/types": "./src/mcp/types.ts",
+    "./skills/types": "./src/skills/types.ts",
+    "./approval/types": "./src/approval/types.ts",
+    "./approval/async-confirm": "./src/approval/async-confirm.ts",
+    "./server/create": "./src/server/index.ts",
+    "./server/adapter": "./src/server/adapter.ts",
+    "./server/port-discovery": "./src/server/port-discovery.ts",
+    "./client/types": "./src/client/types.ts",
+    "./client/direct": "./src/client/direct.ts",
+    "./client/http": "./src/client/http.ts",
+    "./client/http-clients": "./src/client/http/index.ts",
+    "./client/direct-clients": "./src/client/direct/index.ts",
+    "./checkpoint/checkpoint-service": "./src/checkpoint/checkpoint-service.ts",
+    "./checkpoint/shadow-git": "./src/checkpoint/shadow-git.ts",
+    "./checkpoint/ledger": "./src/checkpoint/ledger.ts",
+    "./checkpoint/bootstrap": "./src/checkpoint/bootstrap.ts",
+    "./subagent/registry": "./src/subagent/registry.ts",
+    "./subagent/loader": "./src/subagent/loader.ts",
+    "./llm/factory": "./src/llm/factory.ts",
+    "./layer": "./src/layer.ts"
   },
   "dependencies": {
     "@ai-sdk/deepseek": "^2.0.35",

packages/codingcode/src/agent/agent.ts

@@ -1,6 +1,6 @@
 import { Effect } from 'effect';
 import { z } from 'zod';
 import { appendFileSync } from 'fs';
 import type { Message, ToolCall } from '../core/types.js';
 import { AgentError } from '../core/error.js';
 import { Result } from '../core/result.js';
@@ -16,14 +16,14 @@
 import { getContextConfig } from '../context/config.js';
 import { sharedTodoStore } from './todo.js';
 import { HookService } from '../hooks/registry.js';
-import { SkillService } from '../skills/index.js';
+import { SkillService } from '../skills/service.js';
 import { McpService } from '../mcp/index.js';
 import { loadMemoryForPrompt, flushSessionToMemory } from '../memory/index.js';
-import { createLogger } from '@codingcode/infra';
-import type { AgentProfile } from '../subagent/registry';
+import { createLogger } from '@codingcode/infra/logger';
+import type { AgentProfile } from '../subagent/registry.js';
 import { resolveSubagentEnabled, resolveAgentDisabled } from '../subagent/registry.js';
-import type { ToolVisibilityPolicy } from '../tools/types';
-import { ProjectRuntimeService } from '../runtime/project-runtime';
+import type { ToolVisibilityPolicy } from '../tools/types.js';
+import { ProjectRuntimeService } from '../runtime/project-runtime.js';
 import { createDispatchAgentTool } from '../tools/domains/subagent/dispatch.js';
 import { findModel, createClient } from '../llm/factory.js';
 import { STATIC_BUILTIN_TOOLS } from '../tools/providers.js';

packages/codingcode/src/agent/build-tools.ts

@@ -1,7 +1,7 @@
-import type { ToolDescription } from '../tools/types';
-import type { AgentProfile } from '../subagent/registry';
-import type { ToolVisibilityPolicy } from '../tools/types';
-import type { ToolSearchService } from '../tools/tool-search-service';
+import type { ToolDescription } from '../tools/types.js';
+import type { AgentProfile } from '../subagent/registry.js';
+import type { ToolVisibilityPolicy } from '../tools/types.js';
+import type { ToolSearchService } from '../tools/tool-search-service.js';
 
 export function buildToolsForAgent(
   resolveTools: (input: {

packages/codingcode/src/approval/async-confirm.ts

@@ -1,5 +1,5 @@
 import { Effect, Deferred } from 'effect';
-import type { ConfirmResult } from './confirmation';
+import type { ConfirmResult } from './confirmation.js';
 
 interface PendingEntry {
   deferred: Deferred.Deferred<ConfirmResult, never>;

packages/codingcode/src/approval/confirmation.ts

@@ -1,7 +1,7 @@
 import * as readline from 'node:readline';
 import { Effect } from 'effect';
-import type { PermissionRule } from './types';
-import { ApprovalWaitService } from './async-confirm';
+import type { PermissionRule } from './types.js';
+import { ApprovalWaitService } from './async-confirm.js';
 
 export type ConfirmResult =
   | { type: 'allow' }

packages/codingcode/src/approval/index.ts

@@ -1,10 +1,10 @@
 import { Effect } from 'effect';
-import { HookService } from '../hooks/registry';
-import type { PermissionMode, PermissionRule, ApprovalDecision } from './types';
-import { createRuleEngine, type RuleEngine } from './rule-engine';
-import { DEFAULT_DENY_RULES, READONLY_TOOL_NAMES, DESTRUCTIVE_TOOL_NAMES } from './presets';
-import { runPipeline, type PipelineHooks } from './pipeline';
-import { ApprovalWaitService, hasEmitter } from './async-confirm';
+import { HookService } from '../hooks/registry.js';
+import type { PermissionMode, PermissionRule, ApprovalDecision } from './types.js';
+import { createRuleEngine, type RuleEngine } from './rule-engine.js';
+import { DEFAULT_DENY_RULES, READONLY_TOOL_NAMES, DESTRUCTIVE_TOOL_NAMES } from './presets.js';
+import { runPipeline, type PipelineHooks } from './pipeline.js';
+import { ApprovalWaitService, hasEmitter } from './async-confirm.js';
 
 // Module-level singleton so all callers (HTTP routes, direct client, service) share the same state.
 let _globalPermissionMode: PermissionMode = 'default';

packages/codingcode/src/approval/pipeline.ts

@@ -1,8 +1,8 @@
 import { Effect } from 'effect';
-import type { ApprovalDecision, PermissionMode, PermissionRule, ToolCallRequest } from './types';
-import type { RuleEngine } from './rule-engine';
-import { userConfirm, userConfirmAsync } from './confirmation';
-import type { ApprovalWaitService } from './async-confirm';
+import type { ApprovalDecision, PermissionMode, PermissionRule, ToolCallRequest } from './types.js';
+import type { RuleEngine } from './rule-engine.js';
+import { userConfirm, userConfirmAsync } from './confirmation.js';
+import type { ApprovalWaitService } from './async-confirm.js';
 
 export interface PipelineHooks {
   /** Emit decision from PreToolUse hooks (Layer 4). Returns first non-null HookDecision or null. */

packages/codingcode/src/approval/presets.ts

@@ -1,4 +1,4 @@
-import type { PermissionRule } from './types';
+import type { PermissionRule } from './types.js';
 
 export const DEFAULT_DENY_RULES: PermissionRule[] = [
   {

packages/codingcode/src/approval/rule-engine.ts

@@ -1,4 +1,4 @@
-import type { PermissionRule, RuleAction, ApprovalDecision } from './types';
+import type { PermissionRule, RuleAction, ApprovalDecision } from './types.js';
 
 /**
  * Convert a simple glob pattern to a RegExp.

packages/codingcode/src/checkpoint/checkpoint-service.ts

@@ -1,7 +1,8 @@
 import { Effect } from 'effect';
 import { existsSync, readFileSync, writeFileSync, unlinkSync } from 'fs';
 import { join, dirname, resolve } from 'path';
-import { ShadowGit, normalizePath } from './shadow-git.js';
+import { ShadowGit } from './shadow-git.js';
+import { normalizePath } from '../core/path.js';
 import { Ledger } from './ledger.js';
 import { bootstrapCheckpoint } from './bootstrap.js';
 import { HookService } from '../hooks/registry.js';

packages/codingcode/src/checkpoint/shadow-git.ts

@@ -12,8 +12,6 @@ import { homedir } from 'os';
 import { join } from 'path';
 import { normalizePath, encodeProjectPath } from '../core/path.js';
 
-export { normalizePath } from '../core/path.js';
-
 const PROJECT_BASE = join(homedir(), '.codingcode', 'project');
 const NULL_DEVICE = process.platform === 'win32' ? 'NUL' : '/dev/null';
 
@@ -75,14 +73,9 @@ export class ShadowGit {
 
   commit(message: string): string {
     this.init();
-    // Add all tracked & untracked files (respecting exclude rules)
-    const lsResult = this.run('ls-files', '-m', '-o', '--exclude-standard');
-    const files = lsResult.stdout.trim().split(/\r?\n/).filter(Boolean);
-    if (files.length > 0) {
-      const addResult = this.run('add', ...files);
-      if (addResult.status !== 0) {
-        throw new Error(`ShadowGit add failed: ${addResult.stderr}`);
-      }
+    const addResult = this.run('add', '-A');
+    if (addResult.status !== 0) {
+      throw new Error(`ShadowGit add failed: ${addResult.stderr}`);
     }
     const result = this.run('commit', '--allow-empty', '-m', message);
     if (result.status !== 0) throw new Error(`ShadowGit commit failed: ${result.stderr}`);

packages/codingcode/src/client/direct.ts

@@ -10,8 +10,6 @@ import type { PermissionMode } from '../approval/types.js';
 import type { StreamChunk, AgentClient } from './types.js';
 import { createDirectClients } from './direct/index.js';
 
-export type { StreamChunk, AgentClient } from './types.js';
-
 export async function* agentEventToStreamChunk(
   source: AsyncGenerator<AgentEvent, any, unknown>
 ): AsyncGenerator<StreamChunk, void, unknown> {

packages/codingcode/src/client/direct/index.ts

@@ -3,8 +3,6 @@ import { createDirectSessionClient, type SessionClient } from './sessions.js';
 import { createDirectModelClient, type ModelClient } from './models.js';
 import { createDirectSettingsClient, type SettingsClient } from './settings.js';
 
-export type { AgentRuntimeClient, SessionClient, ModelClient, SettingsClient };
-
 export interface DirectClients {
   agent: AgentRuntimeClient;
   sessions: SessionClient;

packages/codingcode/src/client/direct/settings.ts

@@ -1,7 +1,7 @@
 import { Effect } from 'effect';
 import { McpService } from '../../mcp/index.js';
 import type { McpServerConfig, McpStatus } from '../../mcp/types.js';
-import { SkillService } from '../../skills/index.js';
+import { SkillService } from '../../skills/service.js';
 import { getGlobalPermissionMode, setGlobalPermissionMode } from '../../approval/index.js';
 import type { PermissionMode } from '../../approval/types.js';
 import type { AgentProfile } from '../../subagent/registry.js';
@@ -9,7 +9,7 @@
 import {
   loadMcpConfig,
   writeMcpConfig,
   resolveMcpDisabled,
   setGlobalMcpDisabledState,
   setProjectMcpDisabledState,
   resetProjectMcpDisabledState,
@@ -37,7 +37,7 @@
 import {
   loadHookConfigs,
   writeHookConfigs,
   resolveHookDisabled,
   setGlobalHookDisabledState,
   setProjectHookDisabledState,
   resetProjectHookDisabledState,

packages/codingcode/src/client/http.ts

@@ -2,16 +2,6 @@ import type { AgentClient, StreamChunk } from './types.js';
 import { parseSseStream } from './sse.js';
 import { createHttpClients } from './http/index.js';
 
-export type { AgentClient, StreamChunk } from './types.js';
-export { createHttpClients } from './http/index.js';
-export type {
-  HttpClients,
-  AgentRuntimeClient,
-  SessionClient,
-  ModelClient,
-  SettingsClient,
-} from './http/index.js';
-
 export async function createHttpClient(serverUrl: string): Promise<AgentClient> {
   let currentSessionId: string | undefined;
   const clients = createHttpClients(serverUrl);

packages/codingcode/src/context/config.ts

@@ -1,7 +1,7 @@
 import { getConfig } from '../core/workspace.js';
-import type { ContextConfig } from '@codingcode/infra';
+import type { ContextConfig } from '@codingcode/infra/config';
 
-export type { ContextConfig } from '@codingcode/infra';
+export type { ContextConfig } from '@codingcode/infra/config';
 
 export function getContextConfig(): ContextConfig {
   return getConfig().context;

packages/codingcode/src/core/workspace.ts

@@ -2,7 +2,7 @@ import { existsSync, statSync } from 'fs';
 import { resolve } from 'path';
 import { AgentError } from './error.js';
 import { encodeProjectPath } from './path.js';
-import { type AppConfig, DEFAULT_CONFIG } from '@codingcode/infra';
+import { type AppConfig, DEFAULT_CONFIG } from '@codingcode/infra/config';
 
 let installRoot = process.cwd();
 let workspaceCwd = process.cwd();

packages/codingcode/src/hooks/registry.ts

@@ -1,7 +1,7 @@
 import { Effect } from 'effect';
-import { resolveHookConfigs, resolveHookDisabled } from './config';
-import { executeHookCommand, executeDecisionHookCommand, isHookRuntimeEnabled } from './executor';
-import { createLogger } from '@codingcode/infra';
+import { resolveHookConfigs, resolveHookDisabled } from './config.js';
+import { executeHookCommand, executeDecisionHookCommand, isHookRuntimeEnabled } from './executor.js';
+import { createLogger } from '@codingcode/infra/logger';
 
 const logger = createLogger();
 
@@ -53,7 +53,7 @@
 let entryCounter = 0;
 
 export class HookService extends Effect.Service<HookService>()('HookService', {
   effect: Effect.gen(function* () {
     const globalHooks = new Map<HookPoint, HandlerEntry[]>();
     const hooksByProject = new Map<ProjectPath, Map<HookPoint, HandlerEntry[]>>();
     const hooksBySession = new Map<SessionId, Map<HookPoint, HandlerEntry[]>>();

packages/codingcode/src/layer.ts

@@ -1,18 +1,18 @@
 import { Layer } from 'effect';
-import { AgentService } from './agent/agent';
-import { SessionService } from './session/store';
-import { ContextService } from './context/context';
-import { HookService } from './hooks/registry';
-import { McpService } from './mcp/index';
-import { SkillService } from './skills/index';
-import { ApprovalService } from './approval/index';
-import { ApprovalWaitService } from './approval/async-confirm';
-import { ToolExecutorService } from './tools/executor';
-import { CheckpointService } from './checkpoint/checkpoint-service';
-import { ToolSearchService } from './tools/tool-search-service';
-import { SubagentRegistry } from './subagent/registry';
-import { ProjectRuntimeService } from './runtime/project-runtime';
-import { SchedulerService } from './scheduler/service';
+import { AgentService } from './agent/agent.js';
+import { SessionService } from './session/store.js';
+import { ContextService } from './context/context.js';
+import { HookService } from './hooks/registry.js';
+import { McpService } from './mcp/index.js';
+import { SkillService } from './skills/service.js';
+import { ApprovalService } from './approval/index.js';
+import { ApprovalWaitService } from './approval/async-confirm.js';
+import { ToolExecutorService } from './tools/executor.js';
+import { CheckpointService } from './checkpoint/checkpoint-service.js';
+import { ToolSearchService } from './tools/tool-search-service.js';
+import { SubagentRegistry } from './subagent/registry.js';
+import { ProjectRuntimeService } from './runtime/project-runtime.js';
+import { SchedulerService } from './scheduler/service.js';
 
 export const AgentLayer = AgentService.Default;
 export const SessionLayer = SessionService.Default;