ai-nexus 1.3.21 → 1.4.1

package/README.ko.md

@@ -136,6 +136,8 @@ alwaysApply: false
 
 개별 룰 파일들이 단일 `AGENTS.md` 파일로 자동 병합되며, 세션 시작 시 로드됩니다. 동적 로딩 없음.
 
+> **Codex 사용자: 필요한 룰만 선택하세요.** 모든 룰이 매 세션마다 로딩되므로, 너무 많이 설치하면 토큰이 낭비됩니다. 대화형 설치 마법사(`npx ai-nexus install`)에서 필요한 카테고리와 파일만 선택하세요. 권장 시작 세트: `rules/essential.md`, `rules/commit.md`, `rules/security.md`.
+
 ---
 
 ## 명령어
@@ -199,35 +201,13 @@ description: 이 룰을 로드할 시점 (시맨틱 라우터가 사용)
 
 ---
 
-## 설치 모드
-
-### Symlink (기본값)
-
-```bash
-npx ai-nexus install
-```
-
-- 룰이 소스에 링크 → `update`로 즉시 동기화
-- 룰을 직접 수정 불가 (소스에서 수정)
-
-### Copy
-
-```bash
-npx ai-nexus install --copy
-```
-
-- 룰이 독립적인 복사본
-- 로컬에서 자유롭게 수정 가능
-- `update`는 새 파일만 추가, 기존 파일 덮어쓰지 않음
-
----
-
-## 로컬 우선
+## 업데이트 & 로컬 우선
 
-사용자의 커스터마이징은 항상 안전합니다:
+룰은 독립적인 복사본으로 설치됩니다. 사용자의 커스터마이징은 항상 안전합니다:
 
 - **기존 파일은 절대 덮어쓰지 않음** (install, update 모두)
 - 소스에서 새 파일만 추가
+- `npx ai-nexus update`로 최신 패키지의 새 룰을 동기화
 - `--force`로 강제 덮어쓰기 (백업 먼저!)
 
 ```bash
@@ -238,6 +218,8 @@ npx ai-nexus update
 npx ai-nexus update --force
 ```
 
+> **symlink 모드에서 마이그레이션?** `npx ai-nexus update`만 실행하면 symlink이 자동으로 복사본으로 변환됩니다.
+
 ---
 
 ## 디렉토리 구조
@@ -251,8 +233,8 @@ npx ai-nexus update --force
 .claude/                      # Claude Code
 ├── hooks/semantic-router.cjs
 ├── settings.json
-├── rules/          → .ai-nexus/config/rules
-└── commands/       → .ai-nexus/config/commands
+├── rules/                    # .ai-nexus/config/rules에서 복사
+└── commands/                 # .ai-nexus/config/commands에서 복사
 
 .cursor/rules/                # Cursor (.mdc 파일)
 ├── essential.mdc
@@ -272,7 +254,6 @@ npx ai-nexus install
 # 선택: Claude Code, Cursor
 # 선택: rules, commands, hooks, settings
 # 템플릿: React/Next.js
-# 모드: symlink
 ```
 
 ### 팀 설정

package/README.md

@@ -136,6 +136,8 @@ After conversion, **Cursor's built-in semantic search** handles rule filtering
 
 Individual rule files are aggregated into a single `AGENTS.md` file, which is loaded at session start. No dynamic loading.
 
+> **Codex users: select only the rules you need.** Since all rules are loaded every session, installing too many wastes tokens. Use the interactive wizard (`npx ai-nexus install`) to pick only relevant categories and files. Recommended starting set: `rules/essential.md`, `rules/commit.md`, `rules/security.md`.
+
 ---
 
 ## Commands
@@ -199,35 +201,13 @@ Your rule content...
 
 ---
 
-## Installation Modes
-
-### Symlink (default)
-
-```bash
-npx ai-nexus install
-```
-
-- Rules link to source → `update` syncs instantly
-- Cannot edit rules directly (edit source instead)
-
-### Copy
-
-```bash
-npx ai-nexus install --copy
-```
-
-- Rules are independent copies
-- Can edit locally
-- `update` only adds new files, never overwrites
-
----
-
-## Local Priority
+## Update & Local Priority
 
-Your customizations are always safe:
+Rules are installed as independent copies. Your customizations are always safe:
 
 - **Existing files are never overwritten** during install or update
 - Only new files from source are added
+- `npx ai-nexus update` syncs new rules from the latest package
 - Use `--force` to override (backup first!)
 
 ```bash
@@ -238,6 +218,8 @@ npx ai-nexus update
 npx ai-nexus update --force
 ```
 
+> **Migrating from symlink mode?** Just run `npx ai-nexus update` — symlinks are automatically converted to copies.
+
 ---
 
 ## Directory Structure
@@ -251,8 +233,8 @@ npx ai-nexus update --force
 .claude/                      # Claude Code
 ├── hooks/semantic-router.cjs
 ├── settings.json
-├── rules/          → .ai-nexus/config/rules
-└── commands/       → .ai-nexus/config/commands
+├── rules/                    # Copied from .ai-nexus/config/rules
+└── commands/                 # Copied from .ai-nexus/config/commands
 
 .cursor/rules/                # Cursor (.mdc files)
 ├── essential.mdc
@@ -272,7 +254,6 @@ npx ai-nexus install
 # Select: Claude Code, Cursor
 # Select: rules, commands, hooks, settings
 # Template: React/Next.js
-# Mode: symlink
 ```
 
 ### Team Setup

package/bin/ai-rules.cjs

@@ -16,7 +16,6 @@ program
   .command('init')
   .description('Initialize rules in current project (.claude/, .codex/)')
   .option('--rules <url>', 'Git repository URL for rules (e.g., github.com/org/my-rules)')
-  .option('--copy', 'Copy files instead of symlink')
   .option('-q, --quick', 'Quick mode (skip interactive wizard)')
   .option('-y, --yes', 'Skip prompts and use defaults')
   .action(async (options) => {
@@ -33,7 +32,6 @@ program
   .command('install')
   .description('Install rules globally (~/.claude/, ~/.codex/)')
   .option('--rules <url>', 'Git repository URL for rules')
-  .option('--copy', 'Copy files instead of symlink')
   .option('-q, --quick', 'Quick mode (skip interactive wizard)')
   .action(async (options) => {
     if (options.quick || options.rules) {

package/dist/commands/doctor.js

@@ -15,15 +15,14 @@ export async function doctor() {
             status: 'ok',
             message: `Found ${install.scope} installation at ${install.configPath}`,
         });
-        // Check mode
         const metaPath = path.join(install.configPath, 'meta.json');
         if (fs.existsSync(metaPath)) {
             try {
-                const meta = JSON.parse(fs.readFileSync(metaPath, 'utf8'));
+                JSON.parse(fs.readFileSync(metaPath, 'utf8'));
                 results.push({
-                    name: 'Mode',
+                    name: 'Metadata',
                     status: 'ok',
-                    message: `${meta.mode} mode`,
+                    message: 'meta.json valid',
                 });
             }
             catch {
@@ -84,7 +83,7 @@ export async function doctor() {
                     name: dir.label,
                     status: 'warn',
                     message: `Missing: ${missing.join(', ')}`,
-                    fix: 'Run: ai-nexus install --copy',
+                    fix: 'Run: ai-nexus install',
                 });
             }
         }

package/dist/commands/init-interactive.js

@@ -5,7 +5,7 @@ import { createRequire } from 'module';
 import inquirer from 'inquirer';
 import chalk from 'chalk';
 import ora from 'ora';
-import { getTargetDir, getConfigPath, ensureDir, createSymlink, scanDir, computeFileHashes, aggregateToAgentsMd, } from '../utils/files.js';
+import { getTargetDir, getConfigPath, ensureDir, scanDir, computeFileHashes, aggregateToAgentsMd, } from '../utils/files.js';
 import { scanConfigDir } from '../utils/config-scanner.js';
 // Convert .md to .mdc format for Cursor
 function convertToMdc(content, filename) {
@@ -135,30 +135,11 @@ export async function initInteractive() {
             choices: TEMPLATES,
         },
     ]);
-    // Step 6: Select install method
-    const { method } = await inquirer.prompt([
-        {
-            type: 'list',
-            name: 'method',
-            message: 'Select install method',
-            choices: [
-                {
-                    name: '🔗 symlink (auto-update via ai-nexus update)',
-                    value: 'symlink',
-                },
-                {
-                    name: '📄 copy (independent copy)',
-                    value: 'copy',
-                },
-            ],
-        },
-    ]);
-    // Step 7: Confirmation
+    // Step 6: Confirmation
     console.log(chalk.cyan('\n📋 Installation Summary\n'));
     console.log(chalk.gray('─'.repeat(40)));
     console.log(`   Scope: ${scope === 'global' ? 'Global (~/)' : 'Project (./)'}`);
     console.log(`   Tools: ${tools.join(', ')}`);
-    console.log(`   Method: ${method === 'symlink' ? 'symlink' : 'copy'}`);
     console.log(`   Template: ${template || 'None'}`);
     console.log(`   Categories:`);
     let totalFiles = 0;
@@ -190,7 +171,6 @@ export async function initInteractive() {
             categories,
             selectedFiles,
             template,
-            method,
         });
         spinner.succeed('Installation complete!');
     }
@@ -212,16 +192,12 @@ export async function initInteractive() {
     if (tools.includes('cursor')) {
         console.log(`   Cursor: ${path.join(targetDir, '.cursor/rules')}`);
     }
-    console.log(`   Mode: ${method}`);
     if (template) {
         console.log(`   Template: ${template}`);
     }
     console.log(chalk.gray('─'.repeat(40)));
     // Next steps
     console.log(chalk.cyan('\n📋 Next Steps:\n'));
-    if (method === 'symlink') {
-        console.log(chalk.white('  1. Run "ai-nexus update" to sync latest rules'));
-    }
     const hasApiKey = !!(process.env.ANTHROPIC_API_KEY || process.env.OPENAI_API_KEY);
     if (!hasApiKey && tools.includes('claude') && categories.includes('hooks')) {
         console.log(chalk.white('  2. Enable AI-powered rule selection (optional):'));
@@ -235,7 +211,7 @@ export async function initInteractive() {
     console.log();
 }
 async function install(selections) {
-    const { scope, tools, categories, selectedFiles, template, method } = selections;
+    const { scope, tools, categories, selectedFiles, template } = selections;
     const targetDir = getTargetDir(scope);
     const aiRulesDir = getConfigPath(scope);
     const configDir = path.join(aiRulesDir, 'config');
@@ -298,42 +274,36 @@ async function install(selections) {
             const targetPath = path.join(toolDir, category);
             if (!fs.existsSync(sourceDir))
                 continue;
-            // Local priority: skip if directory exists and is not a symlink
+            // Local priority: skip if directory already exists
             if (fs.existsSync(targetPath)) {
                 try {
                     const stat = fs.lstatSync(targetPath);
-                    if (!stat.isSymbolicLink()) {
+                    if (stat.isSymbolicLink()) {
+                        // Remove existing symlink to replace with copy
+                        fs.unlinkSync(targetPath);
+                    }
+                    else {
                         // Existing directory - only add new files
-                        if (method === 'copy') {
-                            const files = scanDir(sourceDir);
-                            for (const [rel, content] of Object.entries(files)) {
-                                const dest = path.join(targetPath, rel);
-                                if (!fs.existsSync(dest)) {
-                                    ensureDir(path.dirname(dest));
-                                    fs.writeFileSync(dest, content);
-                                }
+                        const files = scanDir(sourceDir);
+                        for (const [rel, content] of Object.entries(files)) {
+                            const dest = path.join(targetPath, rel);
+                            if (!fs.existsSync(dest)) {
+                                ensureDir(path.dirname(dest));
+                                fs.writeFileSync(dest, content);
                             }
                         }
                         continue;
                     }
-                    // Symlink - remove and recreate
-                    fs.unlinkSync(targetPath);
                 }
                 catch {
                     // Ignore errors
                 }
             }
-            if (method === 'symlink') {
-                createSymlink(sourceDir, targetPath);
-            }
-            else {
-                // Copy mode
-                const files = scanDir(sourceDir);
-                for (const [rel, content] of Object.entries(files)) {
-                    const dest = path.join(targetPath, rel);
-                    ensureDir(path.dirname(dest));
-                    fs.writeFileSync(dest, content);
-                }
+            const files = scanDir(sourceDir);
+            for (const [rel, content] of Object.entries(files)) {
+                const dest = path.join(targetPath, rel);
+                ensureDir(path.dirname(dest));
+                fs.writeFileSync(dest, content);
             }
         }
         // Install hooks for Claude Code
@@ -386,16 +356,15 @@ async function install(selections) {
             }
         }
     }
-    // Save metadata (compute file hashes for copy mode conflict detection)
+    // Save metadata
     const claudeDir = path.join(targetDir, '.claude');
     const meta = {
         version: require(path.join(PACKAGE_ROOT, 'package.json')).version,
-        mode: method,
         tools,
         template,
         sources: [{ name: 'builtin', type: 'builtin' }],
         selectedFiles,
-        ...(method === 'copy' ? { fileHashes: computeFileHashes(claudeDir) } : {}),
+        fileHashes: computeFileHashes(claudeDir),
         createdAt: new Date().toISOString(),
         updatedAt: new Date().toISOString(),
     };

package/dist/commands/init.d.ts

@@ -1,7 +1,6 @@
 interface InitOptions {
     scope: 'project' | 'global';
     rules?: string;
-    copy?: boolean;
 }
 export declare function init(options: InitOptions): Promise<void>;
 export {};

package/dist/commands/init.js

@@ -3,17 +3,16 @@ import path from 'path';
 import { fileURLToPath } from 'url';
 import { createRequire } from 'module';
 import chalk from 'chalk';
-import { getTargetDir, getConfigPath, ensureDir, createSymlink, scanDir, computeFileHashes, } from '../utils/files.js';
+import { getTargetDir, getConfigPath, ensureDir, scanDir, computeFileHashes, } from '../utils/files.js';
 import { cloneRepo, getRepoName, normalizeGitUrl } from '../utils/git.js';
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 const PACKAGE_ROOT = path.resolve(__dirname, '../..');
 const require = createRequire(import.meta.url);
 export async function init(options) {
-    const { scope, rules: rulesUrl, copy: copyMode } = options;
+    const { scope, rules: rulesUrl } = options;
     const targetDir = getTargetDir(scope);
     const aiRulesDir = getConfigPath(scope);
     const configDir = path.join(aiRulesDir, 'config');
-    const mode = copyMode ? 'copy' : 'symlink';
     console.log(chalk.bold(`\n  ai-nexus ${scope === 'global' ? 'global' : 'project'} setup\n`));
     // Create .ai-nexus directory
     ensureDir(aiRulesDir);
@@ -66,35 +65,30 @@ export async function init(options) {
         if (!fs.existsSync(sourceDir))
             continue;
         const fileCount = countFiles(sourceDir);
-        // Local priority: skip if directory exists and is not a symlink
+        // Local priority: skip if directory already exists
         if (fs.existsSync(targetPath)) {
             try {
                 const stat = fs.lstatSync(targetPath);
-                if (!stat.isSymbolicLink()) {
+                if (stat.isSymbolicLink()) {
+                    // Remove existing symlink to replace with copy
+                    fs.unlinkSync(targetPath);
+                }
+                else {
                     results.push({ name: category, action: 'skipped', fileCount });
                     continue;
                 }
-                // Remove existing symlink to recreate
-                fs.unlinkSync(targetPath);
             }
             catch {
                 // Ignore errors
             }
         }
-        if (mode === 'symlink') {
-            createSymlink(sourceDir, targetPath);
-            results.push({ name: category, action: 'symlink', fileCount });
-        }
-        else {
-            // Copy mode
-            const files = scanDir(sourceDir);
-            for (const [rel, content] of Object.entries(files)) {
-                const dest = path.join(targetPath, rel);
-                ensureDir(path.dirname(dest));
-                fs.writeFileSync(dest, content);
-            }
-            results.push({ name: category, action: 'copied', fileCount });
+        const files = scanDir(sourceDir);
+        for (const [rel, content] of Object.entries(files)) {
+            const dest = path.join(targetPath, rel);
+            ensureDir(path.dirname(dest));
+            fs.writeFileSync(dest, content);
         }
+        results.push({ name: category, action: 'copied', fileCount });
     }
     // Install hooks
     const hooksSourceDir = path.join(configDir, 'hooks');
@@ -132,22 +126,20 @@ export async function init(options) {
     // Save metadata
     const meta = {
         version: require(path.join(PACKAGE_ROOT, 'package.json')).version,
-        mode,
         sources,
-        ...(mode === 'copy' ? { fileHashes: computeFileHashes(claudeDir) } : {}),
+        fileHashes: computeFileHashes(claudeDir),
         createdAt: new Date().toISOString(),
         updatedAt: new Date().toISOString(),
     };
     fs.writeFileSync(path.join(aiRulesDir, 'meta.json'), JSON.stringify(meta, null, 2));
     // Print structured summary
-    printSummary(claudeDir, mode, results);
+    printSummary(claudeDir, results);
 }
-function printSummary(claudeDir, mode, results) {
+function printSummary(claudeDir, results) {
     const installed = results.filter(r => r.action !== 'skipped');
     const skipped = results.filter(r => r.action === 'skipped');
     console.log(chalk.green.bold('\n  Setup complete!\n'));
-    console.log(`  Location: ${claudeDir}`);
-    console.log(`  Mode:     ${mode}\n`);
+    console.log(`  Location: ${claudeDir}\n`);
     // Installed items
     if (installed.length > 0) {
         console.log(chalk.bold('  Installed:'));

package/dist/commands/update.js

@@ -26,10 +26,40 @@ export async function update(options = {}) {
         process.exit(1);
     }
     const meta = JSON.parse(fs.readFileSync(metaPath, 'utf8'));
-    console.log(`   Mode: ${meta.mode}`);
     console.log(`   Sources: ${meta.sources.map(s => s.name).join(', ')}\n`);
-    // Update external sources
+    const configDir = path.join(configPath, 'config');
+    const targetDir = scope === 'global' ? os.homedir() : process.cwd();
+    const claudeDir = path.join(targetDir, '.claude');
+    // Migrate from symlink if needed
+    if (meta.mode === 'symlink') {
+        migrateFromSymlink(claudeDir, meta, metaPath);
+    }
     let hasChanges = false;
+    // Step 1: Sync new builtin files to .ai-nexus/config/
+    const builtinConfigDir = path.join(PACKAGE_ROOT, 'config');
+    const categories = ['rules', 'commands', 'skills', 'agents', 'contexts', 'hooks'];
+    let builtinAdded = 0;
+    for (const category of categories) {
+        const srcDir = path.join(builtinConfigDir, category);
+        if (!fs.existsSync(srcDir))
+            continue;
+        const destDir = path.join(configDir, category);
+        ensureDir(destDir);
+        const srcFiles = scanDir(srcDir);
+        for (const [rel, content] of Object.entries(srcFiles)) {
+            const dest = path.join(destDir, rel);
+            if (!fs.existsSync(dest)) {
+                ensureDir(path.dirname(dest));
+                fs.writeFileSync(dest, content);
+                builtinAdded++;
+            }
+        }
+    }
+    if (builtinAdded > 0) {
+        console.log(chalk.green(`   + ${builtinAdded} new builtin files synced`));
+        hasChanges = true;
+    }
+    // Step 2: Update external sources and re-merge new files
     const sourcesDir = path.join(configPath, 'sources');
     for (const source of meta.sources) {
         if (source.type === 'external' && source.url) {
@@ -44,50 +74,47 @@ export async function update(options = {}) {
                 else {
                     console.log(`      - Already up to date`);
                 }
-            }
-        }
-    }
-    // Sync config to .claude/
-    const configDir = path.join(configPath, 'config');
-    const targetDir = scope === 'global'
-        ? os.homedir()
-        : process.cwd();
-    const claudeDir = path.join(targetDir, '.claude');
-    if (meta.mode === 'symlink') {
-        // Sync new builtin files to ~/.ai-nexus/config/
-        const builtinConfigDir = path.join(PACKAGE_ROOT, 'config');
-        const categories = ['rules', 'commands', 'skills', 'agents', 'contexts', 'hooks'];
-        let addedCount = 0;
-        for (const category of categories) {
-            const srcDir = path.join(builtinConfigDir, category);
-            if (!fs.existsSync(srcDir))
-                continue;
-            const destDir = path.join(configDir, category);
-            ensureDir(destDir);
-            const srcFiles = scanDir(srcDir);
-            for (const [rel, content] of Object.entries(srcFiles)) {
-                const dest = path.join(destDir, rel);
-                if (!fs.existsSync(dest)) {
-                    ensureDir(path.dirname(dest));
-                    fs.writeFileSync(dest, content);
-                    addedCount++;
+                // Re-merge new files from external source to config
+                const externalConfigDir = fs.existsSync(path.join(repoPath, 'config'))
+                    ? path.join(repoPath, 'config')
+                    : repoPath;
+                let extAdded = 0;
+                for (const category of categories) {
+                    const srcCat = path.join(externalConfigDir, category);
+                    if (!fs.existsSync(srcCat))
+                        continue;
+                    const destCat = path.join(configDir, category);
+                    ensureDir(destCat);
+                    const srcFiles = scanDir(srcCat);
+                    for (const [rel, content] of Object.entries(srcFiles)) {
+                        const prefixed = `${source.name}-${path.basename(rel)}`;
+                        const destRel = path.join(path.dirname(rel), prefixed);
+                        const dest = path.join(destCat, destRel === prefixed ? prefixed : destRel);
+                        if (!fs.existsSync(dest)) {
+                            ensureDir(path.dirname(dest));
+                            fs.writeFileSync(dest, content);
+                            extAdded++;
+                        }
+                    }
+                }
+                if (extAdded > 0) {
+                    console.log(chalk.green(`      + ${extAdded} new files from ${source.name}`));
+                    hasChanges = true;
                 }
             }
         }
-        if (addedCount > 0) {
-            console.log(chalk.green(`   + ${addedCount} new files added`));
-            hasChanges = true;
-        }
     }
-    if (meta.mode === 'copy') {
-        // Copy mode: compare and update files
-        const sourceFiles = scanDir(configDir);
-        const installedFiles = scanDir(claudeDir);
-        const diff = compareConfigs(sourceFiles, installedFiles);
-        if (diff.added.length === 0 && diff.modified.length === 0 && diff.removed.length === 0) {
+    // Step 3: Compare .ai-nexus/config vs .claude/ and sync
+    const sourceFiles = scanDir(configDir);
+    const installedFiles = scanDir(claudeDir);
+    const diff = compareConfigs(sourceFiles, installedFiles);
+    if (diff.added.length === 0 && diff.modified.length === 0 && diff.removed.length === 0) {
+        if (!hasChanges) {
             console.log('\n✅ Already up to date!\n');
             return;
         }
+    }
+    else {
         console.log('\n   Changes detected:');
         if (diff.added.length > 0)
             console.log(chalk.green(`   + ${diff.added.length} new files`));
@@ -95,113 +122,128 @@ export async function update(options = {}) {
             console.log(chalk.yellow(`   ~ ${diff.modified.length} modified files`));
         if (diff.removed.length > 0)
             console.log(chalk.red(`   - ${diff.removed.length} removed in source`));
-        // Determine which files to update
-        const filesToAdd = diff.added;
-        let filesToUpdate;
-        let filesToRemove = [];
-        if (options.force) {
-            // Force mode: update everything, but warn about user-edited files
-            const userEdited = detectUserEdits(diff.modified, claudeDir, meta.fileHashes);
-            if (userEdited.length > 0) {
-                console.log(chalk.red(`\n   WARNING: ${userEdited.length} file(s) have local edits that will be overwritten:`));
-                for (const f of userEdited) {
-                    console.log(chalk.red(`     - ${f}`));
-                }
-                const { proceed } = await inquirer.prompt([
-                    {
-                        type: 'confirm',
-                        name: 'proceed',
-                        message: 'Overwrite these user-edited files?',
-                        default: false,
-                    },
-                ]);
-                if (!proceed) {
-                    filesToUpdate = diff.modified.filter(f => !userEdited.includes(f));
-                }
-                else {
-                    filesToUpdate = diff.modified;
-                }
+    }
+    // Determine which files to update
+    const filesToAdd = diff.added;
+    let filesToUpdate;
+    let filesToRemove = [];
+    if (options.force) {
+        const userEdited = detectUserEdits(diff.modified, claudeDir, meta.fileHashes);
+        if (userEdited.length > 0) {
+            console.log(chalk.red(`\n   WARNING: ${userEdited.length} file(s) have local edits that will be overwritten:`));
+            for (const f of userEdited) {
+                console.log(chalk.red(`     - ${f}`));
+            }
+            const { proceed } = await inquirer.prompt([
+                {
+                    type: 'confirm',
+                    name: 'proceed',
+                    message: 'Overwrite these user-edited files?',
+                    default: false,
+                },
+            ]);
+            if (!proceed) {
+                filesToUpdate = diff.modified.filter(f => !userEdited.includes(f));
             }
             else {
                 filesToUpdate = diff.modified;
             }
-            filesToRemove = diff.removed;
         }
-        else if (options.addOnly) {
-            // Add-only mode: only add new files
-            filesToUpdate = [];
-            filesToRemove = [];
+        else {
+            filesToUpdate = diff.modified;
         }
-        else if (options.interactive && diff.modified.length > 0) {
-            // Interactive mode: ask for each modified file
-            console.log(chalk.cyan('\n   Modified files (choose which to overwrite):\n'));
-            const { selectedFiles } = await inquirer.prompt([
+        filesToRemove = diff.removed;
+    }
+    else if (options.addOnly) {
+        filesToUpdate = [];
+        filesToRemove = [];
+    }
+    else if (options.interactive && diff.modified.length > 0) {
+        console.log(chalk.cyan('\n   Modified files (choose which to overwrite):\n'));
+        const { selectedFiles } = await inquirer.prompt([
+            {
+                type: 'checkbox',
+                name: 'selectedFiles',
+                message: 'Select files to overwrite',
+                choices: diff.modified.map(f => ({
+                    name: f,
+                    value: f,
+                    checked: false,
+                })),
+            },
+        ]);
+        filesToUpdate = selectedFiles;
+        if (diff.removed.length > 0) {
+            const { removeFiles } = await inquirer.prompt([
                 {
-                    type: 'checkbox',
-                    name: 'selectedFiles',
-                    message: 'Select files to overwrite',
-                    choices: diff.modified.map(f => ({
-                        name: f,
-                        value: f,
-                        checked: false,
-                    })),
+                    type: 'confirm',
+                    name: 'removeFiles',
+                    message: `Remove ${diff.removed.length} files that no longer exist in source?`,
+                    default: false,
                 },
             ]);
-            filesToUpdate = selectedFiles;
-            if (diff.removed.length > 0) {
-                const { removeFiles } = await inquirer.prompt([
-                    {
-                        type: 'confirm',
-                        name: 'removeFiles',
-                        message: `Remove ${diff.removed.length} files that no longer exist in source?`,
-                        default: false,
-                    },
-                ]);
-                filesToRemove = removeFiles ? diff.removed : [];
-            }
+            filesToRemove = removeFiles ? diff.removed : [];
         }
-        else {
-            // Default: add new files, skip modified, keep removed
-            // (merge mode)
-            filesToUpdate = [];
-            filesToRemove = [];
-            if (diff.modified.length > 0) {
-                console.log(chalk.gray(`\n   Skipping ${diff.modified.length} modified files (use --force to overwrite)`));
-            }
-        }
-        // Apply changes
-        let addedCount = 0;
-        let updatedCount = 0;
-        let removedCount = 0;
-        for (const rel of filesToAdd) {
-            const src = path.join(configDir, rel);
-            const dest = path.join(claudeDir, rel);
-            ensureDir(path.dirname(dest));
-            fs.copyFileSync(src, dest);
-            addedCount++;
+    }
+    else {
+        filesToUpdate = [];
+        filesToRemove = [];
+        if (diff.modified.length > 0) {
+            console.log(chalk.gray(`\n   Skipping ${diff.modified.length} modified files (use --force to overwrite)`));
         }
-        for (const rel of filesToUpdate) {
-            const src = path.join(configDir, rel);
-            const dest = path.join(claudeDir, rel);
-            ensureDir(path.dirname(dest));
-            fs.copyFileSync(src, dest);
-            updatedCount++;
+    }
+    // Apply changes
+    let addedCount = 0;
+    let updatedCount = 0;
+    let removedCount = 0;
+    for (const rel of filesToAdd) {
+        const src = path.join(configDir, rel);
+        const dest = path.join(claudeDir, rel);
+        ensureDir(path.dirname(dest));
+        fs.copyFileSync(src, dest);
+        addedCount++;
+    }
+    for (const rel of filesToUpdate) {
+        const src = path.join(configDir, rel);
+        const dest = path.join(claudeDir, rel);
+        ensureDir(path.dirname(dest));
+        fs.copyFileSync(src, dest);
+        updatedCount++;
+    }
+    for (const rel of filesToRemove) {
+        const dest = path.join(claudeDir, rel);
+        if (fs.existsSync(dest)) {
+            fs.unlinkSync(dest);
+            removedCount++;
         }
-        for (const rel of filesToRemove) {
-            const dest = path.join(claudeDir, rel);
-            if (fs.existsSync(dest)) {
-                fs.unlinkSync(dest);
-                removedCount++;
+    }
+    if (addedCount > 0 || updatedCount > 0 || removedCount > 0) {
+        console.log('\n   Applied:');
+        if (addedCount > 0)
+            console.log(chalk.green(`   + ${addedCount} files added`));
+        if (updatedCount > 0)
+            console.log(chalk.yellow(`   ~ ${updatedCount} files updated`));
+        if (removedCount > 0)
+            console.log(chalk.red(`   - ${removedCount} files removed`));
+        hasChanges = true;
+    }
+    // Step 4: Sync hooks to .claude/hooks/ (new files only)
+    const hooksConfigDir = path.join(configDir, 'hooks');
+    const hooksTargetDir = path.join(claudeDir, 'hooks');
+    if (fs.existsSync(hooksConfigDir)) {
+        ensureDir(hooksTargetDir);
+        let hooksAdded = 0;
+        const hookFiles = scanDir(hooksConfigDir);
+        for (const [rel, content] of Object.entries(hookFiles)) {
+            const dest = path.join(hooksTargetDir, rel);
+            if (!fs.existsSync(dest)) {
+                ensureDir(path.dirname(dest));
+                fs.writeFileSync(dest, content);
+                hooksAdded++;
             }
         }
-        if (addedCount > 0 || updatedCount > 0 || removedCount > 0) {
-            console.log('\n   Applied:');
-            if (addedCount > 0)
-                console.log(chalk.green(`   + ${addedCount} files added`));
-            if (updatedCount > 0)
-                console.log(chalk.yellow(`   ~ ${updatedCount} files updated`));
-            if (removedCount > 0)
-                console.log(chalk.red(`   - ${removedCount} files removed`));
+        if (hooksAdded > 0) {
+            console.log(chalk.green(`   + ${hooksAdded} new hooks added`));
             hasChanges = true;
         }
     }
@@ -231,11 +273,10 @@ export async function update(options = {}) {
             hasChanges = true;
         }
     }
-    // Update metadata (refresh file hashes for copy mode)
+    // Update metadata
     meta.updatedAt = new Date().toISOString();
-    if (meta.mode === 'copy') {
-        meta.fileHashes = computeFileHashes(claudeDir);
-    }
+    delete meta.mode; // remove deprecated field
+    meta.fileHashes = computeFileHashes(claudeDir);
     fs.writeFileSync(metaPath, JSON.stringify(meta, null, 2));
     if (hasChanges) {
         console.log('\n✅ Update complete!\n');
@@ -244,6 +285,44 @@ export async function update(options = {}) {
         console.log('\n✅ Already up to date!\n');
     }
 }
+function migrateFromSymlink(claudeDir, meta, metaPath) {
+    console.log(chalk.yellow('   ⚡ Migrating from symlink to copy mode...\n'));
+    const categories = ['rules', 'commands', 'skills', 'agents', 'contexts'];
+    let migrated = 0;
+    for (const category of categories) {
+        const targetPath = path.join(claudeDir, category);
+        if (!fs.existsSync(targetPath))
+            continue;
+        try {
+            const stat = fs.lstatSync(targetPath);
+            if (!stat.isSymbolicLink())
+                continue;
+            // Read files through symlink before removing it
+            const files = scanDir(targetPath);
+            // Remove symlink
+            fs.unlinkSync(targetPath);
+            // Create directory and copy files
+            ensureDir(targetPath);
+            for (const [rel, content] of Object.entries(files)) {
+                const dest = path.join(targetPath, rel);
+                ensureDir(path.dirname(dest));
+                fs.writeFileSync(dest, content);
+            }
+            migrated++;
+        }
+        catch {
+            // Skip on error
+        }
+    }
+    // Update meta
+    delete meta.mode;
+    meta.fileHashes = computeFileHashes(claudeDir);
+    meta.updatedAt = new Date().toISOString();
+    fs.writeFileSync(metaPath, JSON.stringify(meta, null, 2));
+    if (migrated > 0) {
+        console.log(chalk.green(`   ✓ Migrated ${migrated} symlinks to copies\n`));
+    }
+}
 function detectUserEdits(modifiedFiles, claudeDir, savedHashes) {
     if (!savedHashes)
         return [];

package/dist/types.d.ts

@@ -5,7 +5,7 @@ export interface MetaSource {
 }
 export interface DotrulesMeta {
     version: string;
-    mode: 'symlink' | 'copy';
+    mode?: 'symlink' | 'copy';
     sources: MetaSource[];
     tools?: string[];
     template?: string | null;

package/dist/utils/files.d.ts

@@ -14,7 +14,6 @@ export declare function getTargetDir(scope: 'project' | 'global'): string;
 export declare function getConfigPath(scope: 'project' | 'global'): string;
 export declare function ensureDir(dir: string): void;
 export declare function copyFile(src: string, dest: string): void;
-export declare function createSymlink(target: string, linkPath: string): void;
 /**
  * Aggregate rule files into a single AGENTS.md content string.
  * If selectedFiles is provided, only those files are included.

package/dist/utils/files.js

@@ -76,13 +76,6 @@ export function copyFile(src, dest) {
     ensureDir(path.dirname(dest));
     fs.copyFileSync(src, dest);
 }
-export function createSymlink(target, linkPath) {
-    ensureDir(path.dirname(linkPath));
-    if (fs.existsSync(linkPath)) {
-        fs.rmSync(linkPath, { recursive: true });
-    }
-    fs.symlinkSync(target, linkPath);
-}
 const AGENTS_CATEGORIES = ['rules', 'commands', 'skills', 'agents', 'contexts'];
 const CATEGORY_LABELS = {
     rules: 'Rules',
@@ -94,6 +87,25 @@ const CATEGORY_LABELS = {
 function stripFrontmatter(content) {
     return content.replace(/^---\r?\n[\s\S]*?\r?\n---\r?\n*/, '').trim();
 }
+/**
+ * Collect all .md files from a category directory, including SKILL.md in subdirectories.
+ */
+function collectMdFiles(catDir) {
+    const files = [];
+    const entries = fs.readdirSync(catDir, { withFileTypes: true });
+    for (const entry of entries) {
+        if (entry.isFile() && entry.name.endsWith('.md')) {
+            files.push(entry.name);
+        }
+        else if (entry.isDirectory()) {
+            const skillMd = path.join(catDir, entry.name, 'SKILL.md');
+            if (fs.existsSync(skillMd)) {
+                files.push(path.join(entry.name, 'SKILL.md'));
+            }
+        }
+    }
+    return files;
+}
 /**
  * Aggregate rule files into a single AGENTS.md content string.
  * If selectedFiles is provided, only those files are included.
@@ -112,8 +124,7 @@ export function aggregateToAgentsMd(configDir, selectedFiles) {
             files = selectedFiles[category];
         }
         else {
-            // Scan all .md files in the category directory
-            files = fs.readdirSync(catDir).filter(f => f.endsWith('.md'));
+            files = collectMdFiles(catDir);
         }
         if (files.length === 0)
             continue;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ai-nexus",
-  "version": "1.3.21",
+  "version": "1.4.1",
   "description": "Unified rule manager for Claude Code, Cursor, and Codex - write once, use everywhere, save tokens",
   "main": "dist/index.js",
   "bin": {