@tonycasey/lisa 2.2.0 → 2.5.5

package/dist/lib/cli.js

@@ -1,623 +1,81 @@
 #!/usr/bin/env node
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.runScan = exports.TEMPLATE_ROOT = exports.DEFAULT_GROUP = exports.DEFAULT_ENDPOINT = exports.createDefaultServices = void 0;
-exports.initCommand = initCommand;
-exports.doctorCommand = doctorCommand;
-exports.upCommand = upCommand;
-exports.downCommand = downCommand;
-exports.cleanupPreviousInstall = cleanupPreviousInstall;
+exports.runScan = exports.TEMPLATE_ROOT = exports.DEFAULT_GROUP = exports.DEFAULT_ENDPOINT = exports.cleanupPreviousInstall = exports.createDefaultServices = exports.downCommand = exports.upCommand = exports.doctorCommand = exports.initCommand = void 0;
 const commander_1 = require("commander");
 const child_process_1 = require("child_process");
 const fs_extra_1 = __importDefault(require("fs-extra"));
 const path_1 = __importDefault(require("path"));
 const chalk_1 = __importDefault(require("chalk"));
-const prompts_1 = require("@inquirer/prompts");
 const services_1 = require("./services");
 Object.defineProperty(exports, "createDefaultServices", { enumerable: true, get: function () { return services_1.createDefaultServices; } });
 const scanner_1 = require("./scanner");
 Object.defineProperty(exports, "runScan", { enumerable: true, get: function () { return scanner_1.runScan; } });
 const infrastructure_1 = require("./infrastructure");
-// Templates are copied into dist/project by postbuild; resolve relative to compiled file.
-const TEMPLATE_ROOT = path_1.default.join(__dirname, '..', 'project');
-exports.TEMPLATE_ROOT = TEMPLATE_ROOT;
-// Bundled hooks and plugins are in dist/hooks and dist/opencode
-const BUNDLED_HOOKS_ROOT = path_1.default.join(__dirname, '..', 'hooks');
-const BUNDLED_OPENCODE_ROOT = path_1.default.join(__dirname, '..', 'opencode');
-// Read version from package.json (works in both dev and dist)
-const PACKAGE_JSON_PATH = path_1.default.join(__dirname, '..', '..', 'package.json');
-const VERSION = fs_extra_1.default.existsSync(PACKAGE_JSON_PATH)
-    ? fs_extra_1.default.readJsonSync(PACKAGE_JSON_PATH).version
-    : '0.0.0';
-const DEFAULT_ENDPOINT = 'http://localhost:8010/mcp/';
-exports.DEFAULT_ENDPOINT = DEFAULT_ENDPOINT;
-const ZEP_CLOUD_ENDPOINT = 'https://api.getzep.com/mcp/';
-/**
- * Get project name from package.json or directory name.
- * Used as the default group ID for memory storage.
- */
-function getProjectName() {
-    try {
-        const pkgPath = path_1.default.join(process.cwd(), 'package.json');
-        if (fs_extra_1.default.existsSync(pkgPath)) {
-            const pkg = fs_extra_1.default.readJsonSync(pkgPath);
-            if (pkg.name) {
-                // Remove scope prefix if present (e.g., @tonycasey/lisa -> lisa)
-                return pkg.name.replace(/^@[^/]+\//, '');
-            }
-        }
-    }
-    catch {
-        // Ignore errors reading package.json
-    }
-    // Fall back to directory name
-    return path_1.default.basename(process.cwd());
-}
-const DEFAULT_GROUP = getProjectName();
-exports.DEFAULT_GROUP = DEFAULT_GROUP;
+const di_1 = require("./infrastructure/di");
+const requests_1 = require("./application/mediator/requests");
+const cli_1 = require("./infrastructure/cli");
+const domain_1 = require("./domain");
+const services_2 = require("./infrastructure/services");
+const commands_1 = require("./commands");
+Object.defineProperty(exports, "doctorCommand", { enumerable: true, get: function () { return commands_1.doctorCommand; } });
+Object.defineProperty(exports, "initCommand", { enumerable: true, get: function () { return commands_1.initCommand; } });
+Object.defineProperty(exports, "cleanupPreviousInstall", { enumerable: true, get: function () { return commands_1.cleanupPreviousInstall; } });
+Object.defineProperty(exports, "upCommand", { enumerable: true, get: function () { return commands_1.upCommand; } });
+Object.defineProperty(exports, "downCommand", { enumerable: true, get: function () { return commands_1.downCommand; } });
+Object.defineProperty(exports, "TEMPLATE_ROOT", { enumerable: true, get: function () { return commands_1.TEMPLATE_ROOT; } });
+Object.defineProperty(exports, "DEFAULT_ENDPOINT", { enumerable: true, get: function () { return commands_1.DEFAULT_ENDPOINT; } });
+Object.defineProperty(exports, "DEFAULT_GROUP", { enumerable: true, get: function () { return commands_1.DEFAULT_GROUP; } });
 // Create CLI logger (console disabled by default to avoid interfering with CLI output)
 const cliLogger = (0, infrastructure_1.createLogger)({
     enableConsole: process.env.LOG_CONSOLE === 'true',
     enableFile: process.env.LOG_FILE !== 'false',
 });
-/**
- * Create a symlink with Windows fallback.
- * On Windows, tries junction first, then falls back to directory copy.
- * Records copy fallbacks for later sync.
- */
-async function createSymlink(target, link, cwd) {
-    const isWindows = process.platform === 'win32';
-    const projectRoot = cwd || process.cwd();
-    // Skip if link already exists (use lstat to detect symlinks even if target doesn't exist)
-    try {
-        await fs_extra_1.default.lstat(link);
-        return; // Link exists (symlink, junction, or regular file/dir)
-    }
-    catch {
-        // Link doesn't exist, proceed with creation
-    }
-    // Calculate relative path from link to target (for Unix symlinks)
-    const linkDir = path_1.default.dirname(link);
-    const relativeTarget = path_1.default.relative(linkDir, target);
-    try {
-        if (isWindows) {
-            // Windows junctions require absolute paths
-            const absoluteTarget = path_1.default.resolve(target);
-            // Try junction first (doesn't require admin rights)
-            await fs_extra_1.default.symlink(absoluteTarget, link, 'junction');
-        }
-        else {
-            // Unix: standard symlink with relative path
-            await fs_extra_1.default.symlink(relativeTarget, link, 'dir');
-        }
-    }
-    catch (err) {
-        const error = err;
-        if (isWindows && (error.code === 'EPERM' || error.code === 'ENOENT' || error.code === 'EINVAL')) {
-            // Junction failed, fall back to copy
-            console.warn(chalk_1.default.yellow(`  Symlink failed, copying directory instead: ${path_1.default.basename(link)}`));
-            await fs_extra_1.default.copy(target, link);
-            // Record that we used copy (for future sync)
-            await recordCopyFallback(projectRoot, link, target);
-        }
-        else {
-            throw err;
-        }
-    }
-}
-/**
- * Track directories that were copied instead of linked.
- * Used by `lisa sync` to keep copies up to date.
- */
-async function recordCopyFallback(projectRoot, link, target) {
-    const fallbackFile = path_1.default.join(projectRoot, '.lisa', '.copy-fallbacks.json');
-    let existing = { copies: [] };
-    try {
-        existing = await fs_extra_1.default.readJson(fallbackFile);
-    }
-    catch {
-        // File doesn't exist yet, use default
-    }
-    // Store relative paths
-    const relLink = path_1.default.relative(projectRoot, link);
-    const relTarget = path_1.default.relative(projectRoot, target);
-    // Check if already recorded
-    if (!existing.copies.some(c => c.link === relLink)) {
-        existing.copies.push({ link: relLink, target: relTarget, createdAt: new Date().toISOString() });
-        await fs_extra_1.default.ensureDir(path_1.default.dirname(fallbackFile));
-        await fs_extra_1.default.writeJson(fallbackFile, existing, { spaces: 2 });
-    }
-}
-/**
- * Clean up previous Lisa installation before upgrade.
- * - Removes scripts/** JS files from skill directories (old format)
- * - Backs up existing SKILL.md files to SKILL.md.backup
- * - Removes common/ and shared/ directories (now bundled)
- *
- * @param skillsDir - Path to skills directory
- * @param verbose - If true, logs detailed information about each operation
- */
-async function cleanupPreviousInstall(skillsDir, verbose = false) {
-    const backedUp = [];
-    const removed = [];
-    if (!await fs_extra_1.default.pathExists(skillsDir)) {
-        if (verbose) {
-            console.log(chalk_1.default.gray(`  [cleanup] Skills directory does not exist: ${skillsDir}`));
-        }
-        return { backedUp, removed };
-    }
-    if (verbose) {
-        console.log(chalk_1.default.cyan(`  [cleanup] Scanning skills directory: ${skillsDir}`));
-    }
-    const skillDirs = await fs_extra_1.default.readdir(skillsDir);
-    for (const skillName of skillDirs) {
-        const skillPath = path_1.default.join(skillsDir, skillName);
-        const stat = await fs_extra_1.default.stat(skillPath);
-        if (!stat.isDirectory())
-            continue;
-        // Remove common/ and shared/ directories (now bundled into CLI)
-        if (skillName === 'common' || skillName === 'shared') {
-            if (verbose) {
-                console.log(chalk_1.default.yellow(`  [cleanup] Removing bundled directory: ${skillName}/`));
-            }
-            await fs_extra_1.default.remove(skillPath);
-            removed.push(skillPath);
-            continue;
-        }
-        // Backup existing SKILL.md files
-        const skillMdPath = path_1.default.join(skillPath, 'SKILL.md');
-        if (await fs_extra_1.default.pathExists(skillMdPath)) {
-            const backupPath = path_1.default.join(skillPath, 'SKILL.md.backup');
-            if (verbose) {
-                console.log(chalk_1.default.gray(`  [cleanup] Backing up: ${skillName}/SKILL.md -> SKILL.md.backup`));
-            }
-            await fs_extra_1.default.copy(skillMdPath, backupPath, { overwrite: true });
-            backedUp.push(skillMdPath);
-        }
-        // Remove scripts/ directory with all JS files
-        const scriptsDir = path_1.default.join(skillPath, 'scripts');
-        if (await fs_extra_1.default.pathExists(scriptsDir)) {
-            // Find and remove all .js files in scripts/
-            const scriptFiles = await fs_extra_1.default.readdir(scriptsDir);
-            for (const file of scriptFiles) {
-                if (file.endsWith('.js')) {
-                    const filePath = path_1.default.join(scriptsDir, file);
-                    if (verbose) {
-                        console.log(chalk_1.default.yellow(`  [cleanup] Removing old script: ${skillName}/scripts/${file}`));
-                    }
-                    await fs_extra_1.default.remove(filePath);
-                    removed.push(filePath);
-                }
-            }
-            // Remove scripts/ directory if empty
-            const remainingFiles = await fs_extra_1.default.readdir(scriptsDir);
-            if (remainingFiles.length === 0) {
-                if (verbose) {
-                    console.log(chalk_1.default.gray(`  [cleanup] Removing empty directory: ${skillName}/scripts/`));
-                }
-                await fs_extra_1.default.remove(scriptsDir);
-                removed.push(scriptsDir);
-            }
-            else if (verbose) {
-                console.log(chalk_1.default.gray(`  [cleanup] Keeping ${skillName}/scripts/ (contains ${remainingFiles.length} non-JS files)`));
-            }
-        }
-    }
-    return { backedUp, removed };
-}
-// Interactive prompt functions
-async function promptDeploymentMode() {
-    return await (0, prompts_1.select)({
-        message: 'How would you like to configure storage?',
-        choices: [
-            {
-                name: 'Set up later (scaffold project, configure storage later)',
-                value: 'skip',
-            },
-            {
-                name: 'Local Docker (runs Neo4j + MCP server locally)',
-                value: 'local',
-            },
-            {
-                name: 'Zep Cloud (managed storage service)',
-                value: 'zep-cloud',
-            },
-        ],
-    });
-}
-async function promptZepCloudConfig() {
-    const zepApiKey = await (0, prompts_1.password)({
-        message: 'Zep API Key:',
-        validate: (val) => val.length > 0 || 'API key is required',
-    });
-    const zepProjectId = await (0, prompts_1.input)({
-        message: 'Zep Project ID:',
-        validate: (val) => val.length > 0 || 'Project ID is required',
-    });
-    return {
-        zepApiKey,
-        zepProjectId,
-        endpoint: ZEP_CLOUD_ENDPOINT,
-    };
-}
-async function promptGroupId() {
-    const projectName = path_1.default.basename(process.cwd());
-    return await (0, prompts_1.input)({
-        message: 'Group ID:',
-        default: projectName,
-    });
-}
-async function promptCliSupport() {
-    const choices = await (0, prompts_1.checkbox)({
-        message: 'Which CLI tools do you want to support?',
-        choices: [
-            {
-                name: 'Claude Code (Anthropic)',
-                value: 'claude-code',
-                checked: true,
-            },
-            {
-                name: 'OpenCode (open source)',
-                value: 'opencode',
-                checked: true,
-            },
-        ],
-    });
-    // Default to both if none selected
-    if (choices.length === 0) {
-        return ['claude-code', 'opencode'];
-    }
-    return choices;
-}
-async function initCommand(opts, services) {
-    const force = Boolean(opts.force);
-    const verbose = opts.verbose !== false; // Default to true
-    const cwd = opts.cwd;
-    let config;
-    let cliSupport;
-    // Determine if we need interactive prompts
-    const hasExplicitMode = opts.mode !== undefined;
-    const skipPrompts = opts.yes || hasExplicitMode;
-    if (skipPrompts) {
-        // Non-interactive mode - use provided options or defaults
-        const mode = opts.mode || 'local';
-        config = {
-            mode,
-            endpoint: opts.endpoint || (mode === 'zep-cloud' ? ZEP_CLOUD_ENDPOINT : DEFAULT_ENDPOINT),
-            groupId: opts.group || process.env.GRAPHITI_GROUP_ID || DEFAULT_GROUP,
-            zepApiKey: opts.zepApiKey,
-            zepProjectId: opts.zepProjectId,
-        };
-        // Default to both CLIs if not specified
-        cliSupport = opts.cliSupport || ['claude-code', 'opencode'];
-    }
-    else {
-        // Interactive mode - prompt user
-        const mode = await promptDeploymentMode();
-        let modeConfig;
-        if (mode === 'zep-cloud') {
-            modeConfig = await promptZepCloudConfig();
-        }
-        else {
-            modeConfig = { endpoint: DEFAULT_ENDPOINT };
-        }
-        const groupId = await promptGroupId();
-        // Prompt for CLI support
-        cliSupport = await promptCliSupport();
-        config = {
-            mode,
-            endpoint: modeConfig.endpoint || DEFAULT_ENDPOINT,
-            groupId,
-            ...modeConfig,
-        };
-    }
-    const includeDocker = opts.includeDocker !== false && config.mode !== 'zep-cloud' && config.mode !== 'skip';
-    const supportClaudeCode = cliSupport.includes('claude-code');
-    const supportOpenCode = cliSupport.includes('opencode');
-    const replacements = {
-        GRAPHITI_ENDPOINT: config.endpoint,
-        GRAPHITI_GROUP: config.groupId,
-        GRAPHITI_GROUP_ID: config.groupId,
-        PROJECT_NAME: config.groupId,
-    };
-    const lisaDir = path_1.default.join(cwd, '.lisa');
-    const skillsDir = path_1.default.join(lisaDir, 'skills');
-    const rulesDir = path_1.default.join(lisaDir, 'rules');
-    const claudeDir = path_1.default.join(cwd, '.claude');
-    const composeDest = path_1.default.join(cwd, 'docker-compose.graphiti.yml');
-    const copies = [];
-    // Create .env from template on first install only (preserve user customizations)
-    const envDest = path_1.default.join(lisaDir, '.env');
-    if (!await fs_extra_1.default.pathExists(envDest)) {
-        await fs_extra_1.default.ensureDir(lisaDir);
-        copies.push(services.templateCopier.copy('.lisa/.env.template', envDest, replacements, false // Never force overwrite - preserves user customizations
-        ));
-    }
-    // Clean up previous installation if upgrading
-    // This removes old scripts/** JS files and backs up existing SKILL.md files
-    if (await fs_extra_1.default.pathExists(skillsDir)) {
-        if (verbose) {
-            console.log(chalk_1.default.cyan('\nUpgrade cleanup:'));
-        }
-        const cleanup = await cleanupPreviousInstall(skillsDir, verbose);
-        if (cleanup.backedUp.length > 0) {
-            console.log(chalk_1.default.cyan(`  Backed up ${cleanup.backedUp.length} existing SKILL.md file(s)`));
-        }
-        if (cleanup.removed.length > 0) {
-            console.log(chalk_1.default.cyan(`  Removed ${cleanup.removed.length} old script file(s)/director(ies)`));
-        }
-        if (verbose && cleanup.backedUp.length === 0 && cleanup.removed.length === 0) {
-            console.log(chalk_1.default.gray('  No cleanup needed (fresh install or already upgraded)'));
-        }
-    }
-    // Skill scaffolding (model-neutral) - copy only SKILL.md files and cache dirs
-    // Scripts are accessed via subcommands (lisa memory, lisa tasks, etc.)
-    // SKILL.md files are always overwritten (we back them up above), other files respect force flag
-    const skillsSrc = path_1.default.join(TEMPLATE_ROOT, '.lisa', 'skills');
-    await fs_extra_1.default.ensureDir(skillsDir);
-    copies.push(fs_extra_1.default.copy(skillsSrc, skillsDir, {
-        overwrite: true, // Always overwrite SKILL.md files (they're backed up above)
-        filter: (src) => {
-            const basename = path_1.default.basename(src);
-            const relativePath = path_1.default.relative(skillsSrc, src);
-            // Always include the root skills directory
-            if (relativePath === '')
-                return true;
-            // Include skill directories (memory, tasks, jira, git, lisa, prompt, init-review)
-            // but exclude shared/, common/, scripts/
-            if (relativePath.includes('shared') || relativePath.includes('common'))
-                return false;
-            if (relativePath.includes('scripts'))
-                return false;
-            // Include SKILL.md files and cache directories
-            if (basename === 'SKILL.md' || basename === 'SKILL.local.md')
-                return true;
-            if (basename === 'cache' || basename === '.gitkeep')
-                return true;
-            // Include directories that might contain the above
-            return fs_extra_1.default.statSync(src).isDirectory();
-        }
-    }));
-    // Rules scaffolding (shared)
-    copies.push(services.templateCopier.copy('.lisa/rules/shared/clean-architecture.md', path_1.default.join(rulesDir, 'shared', 'clean-architecture.md'), replacements, force));
-    copies.push(services.templateCopier.copy('.lisa/rules/shared/code-quality-rules.md', path_1.default.join(rulesDir, 'shared', 'code-quality-rules.md'), replacements, force));
-    copies.push(services.templateCopier.copy('.lisa/rules/shared/testing-principles.md', path_1.default.join(rulesDir, 'shared', 'testing-principles.md'), replacements, force));
-    // Rules scaffolding (typescript)
-    copies.push(services.templateCopier.copy('.lisa/rules/typescript/coding-standards.md', path_1.default.join(rulesDir, 'typescript', 'coding-standards.md'), replacements, force));
-    copies.push(services.templateCopier.copy('.lisa/rules/typescript/testing.md', path_1.default.join(rulesDir, 'typescript', 'testing.md'), replacements, force));
-    copies.push(services.templateCopier.copy('.lisa/rules/typescript/typescript-config-guide.md', path_1.default.join(rulesDir, 'typescript', 'typescript-config-guide.md'), replacements, force));
-    // Claude Code scaffolding (hooks and settings) - only if Claude Code is selected
-    if (supportClaudeCode) {
-        copies.push(services.templateCopier.copy('.claude/config.js', path_1.default.join(claudeDir, 'config.js'), replacements, force));
-        // Copy bundled hooks (these are pre-bundled with all dependencies)
-        const hooksDir = path_1.default.join(claudeDir, 'hooks');
-        await fs_extra_1.default.ensureDir(hooksDir);
-        const bundledHooks = ['session-start.js', 'session-stop.js', 'user-prompt-submit.js'];
-        for (const hook of bundledHooks) {
-            const src = path_1.default.join(BUNDLED_HOOKS_ROOT, hook);
-            const dest = path_1.default.join(hooksDir, hook);
-            if (await fs_extra_1.default.pathExists(src)) {
-                copies.push(fs_extra_1.default.copy(src, dest, { overwrite: force }));
-            }
-        }
-        // Create symlinks for .claude/skills and .claude/rules
-        // If these are real directories (not symlinks), clean them up first
-        const claudeSkillsLink = path_1.default.join(claudeDir, 'skills');
-        const claudeRulesLink = path_1.default.join(claudeDir, 'rules');
-        // Check if .claude/skills exists as a real directory (not symlink)
-        try {
-            const skillsStat = await fs_extra_1.default.lstat(claudeSkillsLink);
-            if (skillsStat.isDirectory() && !skillsStat.isSymbolicLink()) {
-                // Clean up old scripts in .claude/skills before removing
-                if (verbose) {
-                    console.log(chalk_1.default.cyan('\nConverting .claude/skills from directory to symlink:'));
-                }
-                await cleanupPreviousInstall(claudeSkillsLink, verbose);
-                await fs_extra_1.default.remove(claudeSkillsLink);
-                console.log(chalk_1.default.cyan('  Converted .claude/skills to symlink -> .lisa/skills'));
-            }
-        }
-        catch {
-            // Doesn't exist, will be created as symlink
-        }
-        try {
-            const rulesStat = await fs_extra_1.default.lstat(claudeRulesLink);
-            if (rulesStat.isDirectory() && !rulesStat.isSymbolicLink()) {
-                await fs_extra_1.default.remove(claudeRulesLink);
-                console.log(chalk_1.default.cyan('  Converted .claude/rules to symlink -> .lisa/rules'));
-            }
-        }
-        catch {
-            // Doesn't exist, will be created as symlink
-        }
-        await createSymlink(skillsDir, claudeSkillsLink, cwd);
-        await createSymlink(rulesDir, claudeRulesLink, cwd);
-    }
-    // OpenCode scaffolding - only if OpenCode is selected
-    if (supportOpenCode) {
-        const opencodeDir = path_1.default.join(cwd, '.opencode');
-        const pluginDir = path_1.default.join(opencodeDir, 'plugin');
-        await fs_extra_1.default.ensureDir(pluginDir);
-        // Copy bundled OpenCode plugin
-        const pluginSrc = path_1.default.join(BUNDLED_OPENCODE_ROOT, 'lisa.js');
-        const pluginDest = path_1.default.join(pluginDir, 'lisa.js');
-        if (await fs_extra_1.default.pathExists(pluginSrc)) {
-            copies.push(fs_extra_1.default.copy(pluginSrc, pluginDest, { overwrite: force }));
-        }
-        // Create symlink for .opencode/skills
-        await createSymlink(skillsDir, path_1.default.join(opencodeDir, 'skills'), cwd);
-    }
-    if (includeDocker) {
-        // Choose compose file based on mode
-        const composeTemplate = '.lisa/docker/docker-compose.graphiti.yml';
-        copies.push(services.templateCopier.copy(composeTemplate, composeDest, replacements, force));
-    }
-    await Promise.all(copies);
-    // Build scaffolded directories list
-    const scaffoldedDirs = ['.lisa'];
-    if (supportClaudeCode)
-        scaffoldedDirs.push('.claude');
-    if (supportOpenCode)
-        scaffoldedDirs.push('.opencode');
-    if (includeDocker)
-        scaffoldedDirs.push('Docker assets');
-    console.log(chalk_1.default.green(`Scaffolded ${scaffoldedDirs.join(', ')} into ${cwd}`));
-    console.log(`Mode: ${config.mode}`);
-    console.log(`Endpoint: ${config.endpoint}`);
-    console.log(`Group ID: ${config.groupId}`);
-    console.log(`CLI Support: ${cliSupport.join(', ')}`);
-    // Show skip mode instructions
-    if (config.mode === 'skip') {
-        console.log('');
-        console.log(chalk_1.default.cyan('To configure storage later:'));
-        console.log(chalk_1.default.cyan('  1. Read .lisa/docs/STORAGE_SETUP.md'));
-        console.log(chalk_1.default.cyan('  2. Edit .lisa/.env with your configuration'));
-        console.log(chalk_1.default.cyan('  3. Start a new terminal session'));
-        console.log(chalk_1.default.cyan('  4. Run `lisa doctor` to verify connection'));
-    }
-    // Isolated mode: create .claude/lib structure for non-npm projects
-    if (opts.isolated) {
-        const libDir = path_1.default.join(claudeDir, 'lib');
-        await fs_extra_1.default.ensureDir(libDir);
-        // Create minimal package.json in .claude/lib
-        const libPackageJson = {
-            name: 'claude-lib',
-            version: '1.0.0',
-            private: true,
-            description: 'Lisa support files for Claude Code',
-        };
-        const libPackagePath = path_1.default.join(libDir, 'package.json');
-        if (!await fs_extra_1.default.pathExists(libPackagePath) || force) {
-            await fs_extra_1.default.writeJson(libPackagePath, libPackageJson, { spaces: 2 });
-            console.log(chalk_1.default.green('Created .claude/lib/package.json'));
-        }
-        // Add .claude/lib to .gitignore if not already there
-        const gitignorePath = path_1.default.join(cwd, '.gitignore');
-        if (await fs_extra_1.default.pathExists(gitignorePath)) {
-            let gitignore = await fs_extra_1.default.readFile(gitignorePath, 'utf8');
-            if (!gitignore.includes('.claude/lib/node_modules')) {
-                gitignore += '\n# Lisa support files\n.claude/lib/node_modules/\n';
-                await fs_extra_1.default.writeFile(gitignorePath, gitignore);
-                console.log(chalk_1.default.green('Added .claude/lib/node_modules to .gitignore'));
-            }
-        }
-        console.log('');
-        console.log(chalk_1.default.cyan('Isolated mode: Lisa installed to .claude/lib/'));
-        console.log(chalk_1.default.cyan('Your project root stays clean (no package.json or node_modules).'));
-    }
-}
-async function loadConfig(cwd) {
-    // Read from .env file (legacy/runtime config)
-    const lisaEnv = path_1.default.join(cwd, '.lisa', '.env');
-    const map = {};
-    if (await fs_extra_1.default.pathExists(lisaEnv)) {
-        const raw = await fs_extra_1.default.readFile(lisaEnv, 'utf8');
-        raw.split(/\r?\n/).forEach((line) => {
-            if (!line || line.startsWith('#'))
-                return;
-            const idx = line.indexOf('=');
-            if (idx === -1)
-                return;
-            const key = line.slice(0, idx).trim();
-            map[key] = line.slice(idx + 1).trim();
-        });
-    }
-    // If no .env exists, return null
-    if (Object.keys(map).length === 0) {
-        return null;
-    }
-    return {
-        endpoint: map.GRAPHITI_ENDPOINT || DEFAULT_ENDPOINT,
-        group: map.GRAPHITI_GROUP_ID || DEFAULT_GROUP,
-        mode: map.STORAGE_MODE || 'local',
-        zepApiKey: map.ZEP_API_KEY,
-    };
-}
-async function doctorCommand(opts, services) {
-    const cwd = opts.cwd;
-    // Default compose file location is at project root (deployed by init command)
-    const composeFile = opts.compose || path_1.default.join(cwd, 'docker-compose.graphiti.yml');
-    const config = (await loadConfig(cwd)) ?? { endpoint: undefined, group: undefined, mode: 'local' };
-    const endpoint = opts.endpoint || config.endpoint || DEFAULT_ENDPOINT;
-    const mode = config.mode || 'local';
-    const results = [];
-    // Show current mode
-    results.push(chalk_1.default.cyan(`Mode: ${mode}`));
-    results.push(chalk_1.default.cyan(`Group: ${config.group || DEFAULT_GROUP}`));
-    results.push('');
-    // Mode-specific checks
-    if (mode === 'zep-cloud') {
-        // Zep Cloud mode - no local Docker needed
-        results.push(chalk_1.default.yellow('Zep Cloud mode - no local Docker required'));
-        results.push('');
-        // Get API key from config or environment for Zep Cloud authentication
-        const zepApiKey = config.zepApiKey || process.env.ZEP_API_KEY;
-        if (!zepApiKey) {
-            results.push(chalk_1.default.yellow('Warning: ZEP_API_KEY not configured (required for Zep Cloud)'));
-        }
-        try {
-            await services.mcp.ping(endpoint, { apiKey: zepApiKey });
-            results.push(chalk_1.default.green(`Zep MCP reachable at ${endpoint}`));
-        }
-        catch (err) {
-            const message = err instanceof Error ? err.message : String(err);
-            results.push(chalk_1.default.red(`Zep MCP check failed at ${endpoint}: ${message}`));
-        }
-    }
-    else if (mode === 'skip') {
-        // Skip mode - memory/tasks not configured
-        results.push(chalk_1.default.yellow('Skip mode - memory/tasks not configured'));
-        results.push(chalk_1.default.yellow('Run "lisa init" again to configure storage backend'));
-    }
-    else {
-        // Local mode - Docker is needed
-        try {
-            const stdout = await services.docker.version();
-            results.push(chalk_1.default.green(`Docker OK: ${stdout}`));
-        }
-        catch (err) {
-            const message = err instanceof Error ? err.message : String(err);
-            results.push(chalk_1.default.red(`Docker missing or not running: ${message}`));
-        }
-        try {
-            const stdout = await services.docker.composeVersion();
-            results.push(chalk_1.default.green(`Docker Compose OK: ${stdout}`));
-        }
-        catch (err) {
-            const message = err instanceof Error ? err.message : String(err);
-            results.push(chalk_1.default.red(`Docker Compose missing: ${message}`));
-        }
-        if (await fs_extra_1.default.pathExists(composeFile)) {
-            results.push(chalk_1.default.green(`Compose file found: ${composeFile}`));
-        }
-        else {
-            results.push(chalk_1.default.red(`Compose file not found: ${composeFile}`));
-        }
-        try {
-            await services.mcp.ping(endpoint);
-            results.push(chalk_1.default.green(`MCP reachable at ${endpoint}`));
-        }
-        catch (err) {
-            const message = err instanceof Error ? err.message : String(err);
-            results.push(chalk_1.default.red(`MCP check failed at ${endpoint}: ${message}`));
-        }
-    }
-    console.log(results.join('\n'));
-}
-async function upCommand(opts, services) {
-    await services.docker.compose(opts.composeFile, ['up', '-d']);
-}
-async function downCommand(opts, services) {
-    await services.docker.compose(opts.composeFile, ['down']);
-}
+// Command implementations moved to src/lib/commands/
+// - initCommand, cleanupPreviousInstall -> init.ts
+// - doctorCommand -> doctor.ts
+// - upCommand, downCommand -> docker.ts
 const program = new commander_1.Command();
 program
     .name('lisa')
     .description('Lisa remembers everything. Memory for Claude Code and AI assistants.')
-    .version(VERSION);
+    .version(commands_1.VERSION);
 program
     .command('init')
     .description('Scaffold .lisa, .claude/.opencode, and Docker assets')
@@ -643,7 +101,7 @@ program
             opencodeOnly: cmd.opencodeOnly,
             verbose,
         });
-        const services = (0, services_1.createDefaultServices)(TEMPLATE_ROOT);
+        const services = (0, services_1.createDefaultServices)(commands_1.TEMPLATE_ROOT);
         // Determine CLI support from flags
         let cliSupport;
         if (cmd.claudeOnly && !cmd.opencodeOnly) {
@@ -656,7 +114,7 @@ program
             cliSupport = ['claude-code', 'opencode'];
         }
         // If neither flag is set, cliSupport remains undefined and prompts will be shown
-        await initCommand({
+        await (0, commands_1.initCommand)({
             endpoint: cmd.endpoint,
             group: cmd.group,
             force: cmd.force,
@@ -689,7 +147,7 @@ program
     .option('-v, --verbose', 'Show detailed logging (default: true)', true)
     .option('-q, --quiet', 'Suppress detailed logging')
     .action(async (cmd) => {
-    const services = (0, services_1.createDefaultServices)(TEMPLATE_ROOT);
+    const services = (0, services_1.createDefaultServices)(commands_1.TEMPLATE_ROOT);
     const verbose = cmd.verbose && !cmd.quiet;
     // Determine CLI support from flags
     let cliSupport;
@@ -702,7 +160,7 @@ program
     else if (cmd.claudeOnly && cmd.opencodeOnly) {
         cliSupport = ['claude-code', 'opencode'];
     }
-    await initCommand({
+    await (0, commands_1.initCommand)({
         endpoint: cmd.endpoint,
         group: cmd.group,
         force: cmd.force,
@@ -723,8 +181,8 @@ program
     .option('-c, --compose <file>', 'Compose file', 'docker-compose.graphiti.yml')
     .action(async (cmd) => {
     const composeFile = path_1.default.resolve(process.cwd(), cmd.compose);
-    const services = (0, services_1.createDefaultServices)(TEMPLATE_ROOT);
-    await upCommand({ composeFile }, services);
+    const services = (0, services_1.createDefaultServices)(commands_1.TEMPLATE_ROOT);
+    await (0, commands_1.upCommand)({ composeFile }, services);
 });
 program
     .command('down')
@@ -732,17 +190,25 @@ program
     .option('-c, --compose <file>', 'Compose file', 'docker-compose.graphiti.yml')
     .action(async (cmd) => {
     const composeFile = path_1.default.resolve(process.cwd(), cmd.compose);
-    const services = (0, services_1.createDefaultServices)(TEMPLATE_ROOT);
-    await downCommand({ composeFile }, services);
+    const services = (0, services_1.createDefaultServices)(commands_1.TEMPLATE_ROOT);
+    await (0, commands_1.downCommand)({ composeFile }, services);
 });
 program
     .command('doctor')
-    .description('Validate Docker and MCP connectivity')
+    .description('Validate Lisa configuration and backend connectivity')
     .option('-c, --compose <file>', 'Compose file', 'docker-compose.graphiti.yml')
     .option('-e, --endpoint <url>', 'MCP endpoint override')
+    .option('-v, --verbose', 'Show detailed diagnostics')
+    .option('--json', 'Output results as JSON')
     .action(async (cmd) => {
-    const services = (0, services_1.createDefaultServices)(TEMPLATE_ROOT);
-    await doctorCommand({ cwd: process.cwd(), compose: cmd.compose, endpoint: cmd.endpoint }, services);
+    const services = (0, services_1.createDefaultServices)(commands_1.TEMPLATE_ROOT);
+    await (0, commands_1.doctorCommand)({
+        cwd: process.cwd(),
+        compose: cmd.compose,
+        endpoint: cmd.endpoint,
+        verbose: cmd.verbose,
+        json: cmd.json,
+    }, services);
 });
 program
     .command('scan [path]')
@@ -993,6 +459,17 @@ program
     const scriptPath = path_1.default.join(__dirname, 'skills', 'jira', 'jira.js');
     await spawnAndWait(scriptPath, args);
 });
+// Subcommand: lisa github
+program
+    .command('github')
+    .description('GitHub Issues and Projects operations')
+    .allowUnknownOption()
+    .action(async (_opts, cmd) => {
+    // Pass all arguments after the command to the script
+    const args = cmd.args || [];
+    const scriptPath = path_1.default.join(__dirname, 'skills', 'github', 'github.js');
+    await spawnAndWait(scriptPath, args);
+});
 // Subcommand: lisa prompt
 program
     .command('prompt')
@@ -1033,6 +510,274 @@ program
     const scriptPath = path_1.default.join(__dirname, 'skills', 'lisa', 'compile-skills.js');
     await spawnAndWait(scriptPath, args);
 });
+// Subcommand: lisa issue
+// Wraps gh CLI with auto-labeling capabilities
+const issueCmd = program
+    .command('issue')
+    .description('GitHub issue management with auto-labeling');
+issueCmd
+    .command('create')
+    .description('Create a GitHub issue with automatic label inference')
+    .requiredOption('-t, --title <title>', 'Issue title')
+    .option('-b, --body <body>', 'Issue body')
+    .option('-l, --label <labels...>', 'Explicit labels (skips auto-labeling for type)')
+    .option('--no-auto-label', 'Disable automatic label inference')
+    .option('-y, --yes', 'Skip confirmation, apply inferred labels automatically')
+    .option('--dry-run', 'Show what would be created without creating')
+    .action(async (opts) => {
+    const title = opts.title;
+    const body = opts.body || '';
+    const explicitLabels = opts.label || [];
+    const autoLabel = opts.autoLabel !== false;
+    const skipConfirm = opts.yes || false;
+    const dryRun = opts.dryRun || false;
+    // Collect all labels
+    const allLabels = [...explicitLabels];
+    let inferredLabels = [];
+    let reasons = {};
+    // Auto-label if enabled and no explicit type labels provided
+    if (autoLabel) {
+        const service = (0, services_2.createLabelInferenceService)();
+        const result = service.inferLabels(title, body);
+        inferredLabels = result.labels;
+        reasons = result.reasons;
+        // Filter out labels that conflict with explicit labels
+        const explicitTypes = explicitLabels.filter(l => ['bug', 'enhancement', 'documentation', 'refactor', 'testing'].includes(l));
+        if (explicitTypes.length > 0) {
+            // User specified a type label, don't override it
+            inferredLabels = inferredLabels.filter(l => !['bug', 'enhancement', 'documentation', 'refactor', 'testing'].includes(l));
+        }
+        // Add non-duplicate inferred labels
+        for (const label of inferredLabels) {
+            if (!allLabels.includes(label)) {
+                allLabels.push(label);
+            }
+        }
+    }
+    // Show what will be created
+    console.log(chalk_1.default.bold('Issue to create:'));
+    console.log(`  Title: ${chalk_1.default.cyan(title)}`);
+    if (body) {
+        const bodyPreview = body.length > 100 ? body.slice(0, 100) + '...' : body;
+        console.log(`  Body: ${chalk_1.default.dim(bodyPreview)}`);
+    }
+    console.log('');
+    if (explicitLabels.length > 0) {
+        console.log(chalk_1.default.bold('Explicit labels:'));
+        for (const label of explicitLabels) {
+            console.log(`  ${chalk_1.default.green('+')} ${label}`);
+        }
+        console.log('');
+    }
+    if (inferredLabels.length > 0) {
+        console.log(chalk_1.default.bold('Inferred labels:'));
+        for (const label of inferredLabels) {
+            const reason = reasons[label] || 'Pattern match';
+            console.log(`  ${chalk_1.default.yellow('~')} ${label} ${chalk_1.default.dim(`(${reason})`)}`);
+        }
+        console.log('');
+    }
+    if (allLabels.length > 0) {
+        console.log(chalk_1.default.bold('Final labels:'));
+        console.log(`  ${allLabels.join(', ')}`);
+        console.log('');
+    }
+    if (dryRun) {
+        console.log(chalk_1.default.yellow('Dry run - no issue created'));
+        return;
+    }
+    // Confirm if not skipping
+    if (!skipConfirm && inferredLabels.length > 0) {
+        const { confirm } = await Promise.resolve().then(() => __importStar(require('@inquirer/prompts')));
+        const confirmed = await confirm({
+            message: 'Create issue with these labels?',
+            default: true,
+        });
+        if (!confirmed) {
+            console.log(chalk_1.default.yellow('Cancelled'));
+            return;
+        }
+    }
+    // Build gh command
+    const ghArgs = ['issue', 'create', '--title', title];
+    if (body) {
+        ghArgs.push('--body', body);
+    }
+    for (const label of allLabels) {
+        ghArgs.push('--label', label);
+    }
+    // Execute gh command using spawnSync to avoid shell injection
+    try {
+        const { spawnSync } = await Promise.resolve().then(() => __importStar(require('child_process')));
+        const result = spawnSync('gh', ghArgs, {
+            encoding: 'utf8',
+            stdio: ['inherit', 'pipe', 'inherit'],
+            shell: false,
+        });
+        if (result.error) {
+            throw result.error;
+        }
+        if (result.status !== 0) {
+            throw new Error(`gh exited with code ${result.status}`);
+        }
+        console.log(chalk_1.default.green('Issue created:'), (result.stdout || '').trim());
+    }
+    catch (error) {
+        const message = error instanceof Error ? error.message : String(error);
+        console.error(chalk_1.default.red('Failed to create issue:'), message);
+        process.exit(1);
+    }
+});
+issueCmd
+    .command('labels')
+    .description('Infer labels for content without creating an issue')
+    .requiredOption('-t, --title <title>', 'Issue title to analyze')
+    .option('-b, --body <body>', 'Issue body to analyze')
+    .option('--json', 'Output as JSON')
+    .action((opts) => {
+    const service = (0, services_2.createLabelInferenceService)();
+    const result = service.inferLabels(opts.title, opts.body || '');
+    if (opts.json) {
+        console.log(JSON.stringify(result, null, 2));
+    }
+    else {
+        if (result.labels.length === 0) {
+            console.log(chalk_1.default.yellow('No labels inferred'));
+        }
+        else {
+            console.log(chalk_1.default.bold('Inferred labels:'));
+            for (const label of result.labels) {
+                const reason = result.reasons[label] || 'Pattern match';
+                console.log(`  ${chalk_1.default.green('+')} ${label}`);
+                console.log(`    ${chalk_1.default.dim(reason)}`);
+            }
+            console.log('');
+            console.log(`Confidence: ${(result.confidence * 100).toFixed(0)}%`);
+        }
+    }
+});
+// Subcommand: lisa hook
+// These commands are called by Claude Code via settings.json hooks
+const hookCmd = program
+    .command('hook')
+    .description('Hook commands for Claude Code integration');
+hookCmd
+    .command('session-start')
+    .description('Handle session start event (called by Claude Code)')
+    .action(async () => {
+    let dispose;
+    try {
+        // Read input from Claude Code
+        const input = await (0, cli_1.readJsonFromStdin)();
+        const trigger = (0, cli_1.parseTrigger)(input.source, input.session_type, input.trigger);
+        // Bootstrap container and resolve mediator
+        const bootstrap = await (0, di_1.bootstrapContainer)({
+            projectRoot: input.cwd || process.cwd(),
+            disableLogging: true,
+        });
+        dispose = bootstrap.dispose;
+        const mediator = await bootstrap.container.resolve(di_1.TOKENS.Mediator);
+        // Create and send request
+        const request = new requests_1.SessionStartRequest(trigger, (0, domain_1.toISOTimestamp)(), input.session_id);
+        const result = await mediator.send(request);
+        // Output context to stdout (goes to Claude)
+        const output = {
+            hookSpecificOutput: {
+                hookEventName: 'SessionStart',
+                additionalContext: result.contextContent,
+            },
+        };
+        await (0, cli_1.writeJsonToStdout)(output);
+        // Status message to stderr (shown to user)
+        await (0, cli_1.writeStatus)(result.message);
+    }
+    catch (error) {
+        // On error, still output something to not block session
+        const errorMessage = error instanceof Error ? error.message : String(error);
+        const output = {
+            hookSpecificOutput: {
+                hookEventName: 'SessionStart',
+                additionalContext: `Memory load skipped: ${errorMessage}`,
+            },
+        };
+        await (0, cli_1.writeJsonToStdout)(output);
+        await (0, cli_1.writeStatus)(`Memory load failed: ${errorMessage}`);
+    }
+    finally {
+        if (dispose)
+            await dispose();
+    }
+});
+hookCmd
+    .command('session-stop')
+    .description('Handle session stop event (called by Claude Code)')
+    .action(async () => {
+    let dispose;
+    try {
+        // Read input from Claude Code
+        const input = await (0, cli_1.readJsonFromStdin)();
+        // Bootstrap container and resolve mediator
+        const bootstrap = await (0, di_1.bootstrapContainer)({
+            projectRoot: input.cwd || process.cwd(),
+            disableLogging: true,
+        });
+        dispose = bootstrap.dispose;
+        const mediator = await bootstrap.container.resolve(di_1.TOKENS.Mediator);
+        // Create and send request
+        const request = new requests_1.SessionStopRequest('idle', (0, domain_1.toISOTimestamp)(), input.session_id, input.transcript_path);
+        const result = await mediator.send(request);
+        // Status message to stderr
+        await (0, cli_1.writeStatus)(result.message);
+    }
+    catch (error) {
+        // Silent failure - don't block user
+        const errorMessage = error instanceof Error ? error.message : String(error);
+        await (0, cli_1.writeStatus)(`Session capture failed: ${errorMessage}`);
+    }
+    finally {
+        if (dispose)
+            await dispose();
+    }
+});
+hookCmd
+    .command('user-prompt-submit')
+    .description('Handle user prompt submit event (called by Claude Code)')
+    .action(async () => {
+    let dispose;
+    try {
+        // Read input from Claude Code
+        const input = await (0, cli_1.readJsonFromStdin)();
+        const content = input.prompt || input.content || '';
+        const permissionMode = (input.permission_mode || input.permissionMode || 'default');
+        if (!content) {
+            // No content to process
+            return;
+        }
+        // Bootstrap container and resolve mediator
+        const bootstrap = await (0, di_1.bootstrapContainer)({
+            projectRoot: process.cwd(),
+            disableLogging: true,
+        });
+        dispose = bootstrap.dispose;
+        const mediator = await bootstrap.container.resolve(di_1.TOKENS.Mediator);
+        // Create and send request
+        const request = new requests_1.PromptSubmitRequest(content, (0, domain_1.toISOTimestamp)(), input.session_id, permissionMode);
+        const result = await mediator.send(request);
+        // Output recursion results if in plan mode
+        if (result.recursion?.hasContext) {
+            console.log('\n🔍 Related Context from Memory:\n');
+            console.log(result.recursion.summary);
+            console.log('');
+        }
+    }
+    catch {
+        // Silent failure - don't block user
+    }
+    finally {
+        if (dispose)
+            await dispose();
+    }
+});
 if (require.main === module) {
     program.parseAsync(process.argv).catch((err) => {
         console.error(chalk_1.default.red(err.message));