@defai.digital/cli 13.1.16 → 13.2.0

package/dist/commands/setup.js

@@ -1,54 +1,22 @@
 /**
- * Setup command - Interactive setup wizard for AutomatosX
+ * Setup command - Global setup wizard for AutomatosX
+ *
+ * Creates global configuration with detected providers.
+ * For per-project initialization (MCP registration), use `ax init`.
  *
  * Features:
  * - Provider detection
- * - Configuration creation
+ * - Global configuration creation
  * - Non-interactive mode for CI
  */
 import { exec } from 'node:child_process';
 import { promisify } from 'node:util';
-import { mkdir, writeFile, readFile, access } from 'node:fs/promises';
-import { join } from 'node:path';
 import { createConfigStore, initConfigDirectory, } from '@defai.digital/config-domain';
-import { DEFAULT_CONFIG, KNOWN_PROVIDERS, PROVIDER_DEFAULTS, DATA_DIR_NAME, CONFIG_FILENAME, TIMEOUT_SETUP_ADD, TIMEOUT_SETUP_REMOVE, TIMEOUT_HEALTH_CHECK, TIMEOUT_WORKFLOW_STEP, DEFAULT_SCHEMA_VERSION, ITERATE_MAX_DEFAULT, ITERATE_TIMEOUT_DEFAULT, } from '@defai.digital/contracts';
-import { CONTEXT_DIRECTORY } from '@defai.digital/context-domain';
-import { PROVIDER_CHECKS, checkProviderCLI, } from './doctor.js';
+import { DEFAULT_CONFIG, KNOWN_PROVIDERS, PROVIDER_DEFAULTS, TIMEOUT_HEALTH_CHECK, TIMEOUT_WORKFLOW_STEP, } from '@defai.digital/contracts';
 const execAsync = promisify(exec);
 // ============================================================================
 // Constants
 // ============================================================================
-// ============================================================================
-// MCP Constants
-// ============================================================================
-/** MCP server name registered with provider CLIs */
-const MCP_SERVER_NAME = 'automatosx';
-/** MCP subcommands */
-const MCP_COMMANDS = {
-    add: 'mcp add',
-    remove: 'mcp remove',
-    serverArgs: 'mcp server',
-};
-/** MCP command flags for different formats */
-const MCP_FLAGS = {
-    /** Claude uses -s local for user-scope config */
-    claudeScope: '-s local',
-    /** ax-wrapper uses -c for command */
-    command: '-c',
-    /** ax-wrapper uses -a for arguments */
-    args: '-a',
-};
-/** Pattern to detect successful MCP server addition in output */
-const MCP_SUCCESS_PATTERN = /Added MCP server|server.*added|successfully added/i;
-// ============================================================================
-// CLI Constants
-// ============================================================================
-/** Fallback CLI command when binary path cannot be determined */
-const CLI_FALLBACK_COMMAND = 'ax';
-/** Node.js executable for running scripts */
-const NODE_EXECUTABLE = 'node';
-/** Conventions file name in context directory */
-const CONVENTIONS_FILENAME = 'conventions.md';
 /** Provider name display width for aligned output */
 const PROVIDER_DISPLAY_WIDTH = 10;
 /** Default error message when error type is unknown */
@@ -59,8 +27,6 @@ const STDERR_REDIRECT = '2>&1';
 const SEMVER_PATTERN = /(\d+\.\d+\.\d+)/;
 /** Platform-specific command to find executables */
 const WHICH_COMMAND = process.platform === 'win32' ? 'where' : 'which';
-/** JSON formatting indentation */
-const JSON_INDENT = 2;
 /** Exit codes for CLI commands */
 const EXIT_CODE = {
     SUCCESS: 0,
@@ -71,11 +37,6 @@ const CONFIG_SCOPE = {
     GLOBAL: 'global',
     LOCAL: 'local',
 };
-/** Health check status values */
-const HEALTH_STATUS = {
-    PASS: 'pass',
-    FAIL: 'fail',
-};
 /** CLI argument flags */
 const CLI_FLAGS = {
     force: ['--force', '-f'],
@@ -83,7 +44,6 @@ const CLI_FLAGS = {
     silent: ['--silent', '-s'],
     local: ['--local', '-l'],
     global: ['--global', '-g'],
-    skipProject: ['--skip-project', '--no-project'],
 };
 /** Terminal color codes */
 const COLORS = {
@@ -102,258 +62,6 @@ const ICONS = {
     warn: `${COLORS.yellow}\u26A0${COLORS.reset}`,
     arrow: `${COLORS.cyan}\u2192${COLORS.reset}`,
 };
-/** MCP configuration for each provider (null = provider doesn't support MCP) */
-const PROVIDER_MCP_CONFIGS = {
-    claude: { cliName: 'claude', format: 'claude' },
-    gemini: { cliName: 'gemini', format: 'standard' },
-    codex: { cliName: 'codex', format: 'standard' },
-    qwen: { cliName: 'qwen', format: 'standard' },
-    glm: { cliName: 'ax-glm', format: 'ax-wrapper' },
-    grok: { cliName: 'ax-grok', format: 'ax-wrapper' },
-    'ax-cli': null, // ax-cli doesn't support MCP yet
-};
-/**
- * Get the absolute path to the CLI binary.
- * Uses process.argv[1] which works for both global and local installations.
- */
-function getCLIBinaryPath() {
-    const binaryPath = process.argv[1];
-    return binaryPath || CLI_FALLBACK_COMMAND;
-}
-/**
- * Check if a path is absolute (Unix or Windows style)
- */
-function isAbsolutePath(filePath) {
-    return filePath.startsWith('/') || filePath.includes('\\');
-}
-/**
- * Build the MCP server command parts based on binary path.
- * Returns { executable, arguments } for use in MCP add commands.
- */
-function buildMCPServerCommand(binaryPath) {
-    if (isAbsolutePath(binaryPath)) {
-        return { executable: NODE_EXECUTABLE, arguments: `"${binaryPath}" ${MCP_COMMANDS.serverArgs}` };
-    }
-    return { executable: binaryPath, arguments: MCP_COMMANDS.serverArgs };
-}
-/**
- * Get the CLI command to add AutomatosX MCP server for a provider.
- * Uses provider's native CLI to ensure proper formatting and validation.
- */
-function buildMCPAddCommand(providerId) {
-    const mcpConfig = PROVIDER_MCP_CONFIGS[providerId];
-    if (!mcpConfig)
-        return null;
-    const binaryPath = getCLIBinaryPath();
-    const { executable, arguments: execArgs } = buildMCPServerCommand(binaryPath);
-    const { cliName, format } = mcpConfig;
-    switch (format) {
-        case 'standard':
-            return `${cliName} ${MCP_COMMANDS.add} ${MCP_SERVER_NAME} ${executable} ${execArgs}`;
-        case 'claude':
-            return `${cliName} ${MCP_COMMANDS.add} ${MCP_SERVER_NAME} ${MCP_FLAGS.claudeScope} ${executable} ${execArgs}`;
-        case 'ax-wrapper': {
-            const command = isAbsolutePath(binaryPath) ? NODE_EXECUTABLE : CLI_FALLBACK_COMMAND;
-            const commandArgs = isAbsolutePath(binaryPath) ? `${binaryPath} ${MCP_COMMANDS.serverArgs}` : MCP_COMMANDS.serverArgs;
-            return `${cliName} ${MCP_COMMANDS.add} ${MCP_SERVER_NAME} ${MCP_FLAGS.command} ${command} ${MCP_FLAGS.args} ${commandArgs}`;
-        }
-        default:
-            return null;
-    }
-}
-/**
- * Get the CLI command to remove MCP server for a provider.
- */
-function buildMCPRemoveCommand(providerId) {
-    const mcpConfig = PROVIDER_MCP_CONFIGS[providerId];
-    if (!mcpConfig)
-        return null;
-    const scopeFlag = mcpConfig.format === 'claude' ? ` ${MCP_FLAGS.claudeScope}` : '';
-    return `${mcpConfig.cliName} ${MCP_COMMANDS.remove} ${MCP_SERVER_NAME}${scopeFlag}`;
-}
-/**
- * Get the settings file path for ax-wrapper providers.
- * ax-glm and ax-grok store configs in .ax-glm/ and .ax-grok/ directories.
- */
-function getAxWrapperSettingsPath(cliName) {
-    // For project-local config, use current working directory
-    return join(process.cwd(), `.${cliName}`, 'settings.json');
-}
-/**
- * Configure MCP for ax-wrapper providers by writing config file directly.
- * This is needed because ax-wrapper CLIs default to 'content-length' framing,
- * but automatosx MCP server uses 'ndjson' framing (MCP SDK default).
- */
-async function configureAxWrapperMCP(cliName) {
-    const binaryPath = getCLIBinaryPath();
-    const settingsPath = getAxWrapperSettingsPath(cliName);
-    const settingsDir = join(process.cwd(), `.${cliName}`);
-    try {
-        // Ensure settings directory exists
-        await mkdir(settingsDir, { recursive: true });
-        // Read existing config or create new one
-        let existingConfig = { mcpServers: {} };
-        try {
-            const content = await readFile(settingsPath, 'utf-8');
-            existingConfig = JSON.parse(content);
-            if (!existingConfig.mcpServers) {
-                existingConfig.mcpServers = {};
-            }
-        }
-        catch {
-            // File doesn't exist or is invalid - use empty config
-        }
-        // Build args based on binary path
-        const args = isAbsolutePath(binaryPath)
-            ? [binaryPath, 'mcp', 'server']
-            : ['mcp', 'server'];
-        const command = isAbsolutePath(binaryPath) ? NODE_EXECUTABLE : binaryPath;
-        // Add automatosx MCP server config with ndjson framing
-        existingConfig.mcpServers[MCP_SERVER_NAME] = {
-            name: MCP_SERVER_NAME,
-            transport: {
-                type: 'stdio',
-                command,
-                args,
-                env: {},
-                framing: 'ndjson',
-            },
-        };
-        // Write updated config
-        await writeFile(settingsPath, JSON.stringify(existingConfig, null, JSON_INDENT) + '\n');
-        return { success: true, skipped: false };
-    }
-    catch (err) {
-        return {
-            success: false,
-            skipped: false,
-            error: err instanceof Error ? err.message : FALLBACK_ERROR_MESSAGE,
-        };
-    }
-}
-/**
- * Check if command output indicates successful MCP server addition.
- * Some providers output success message even when validation times out.
- */
-function isMCPAdditionSuccessful(commandOutput) {
-    return MCP_SUCCESS_PATTERN.test(commandOutput);
-}
-/**
- * Extract clean error message from exec error.
- */
-function extractErrorMessage(rawError) {
-    if (rawError.includes('Command failed')) {
-        return rawError.split('\n').pop() || rawError;
-    }
-    return rawError;
-}
-/**
- * Configure MCP for a detected provider.
- *
- * For ax-wrapper providers (ax-glm, ax-grok):
- * - Write config file directly with ndjson framing (required for MCP SDK compatibility)
- *
- * For other providers:
- * - Use native CLI commands (remove-then-add for clean state)
- */
-async function configureMCPForProvider(providerId) {
-    const mcpConfig = PROVIDER_MCP_CONFIGS[providerId];
-    if (!mcpConfig) {
-        return { success: true, skipped: true };
-    }
-    // For ax-wrapper providers, write config file directly with ndjson framing
-    // This is needed because ax-wrapper CLIs default to 'content-length' framing,
-    // but automatosx MCP server uses 'ndjson' framing (MCP SDK default)
-    if (mcpConfig.format === 'ax-wrapper') {
-        return configureAxWrapperMCP(mcpConfig.cliName);
-    }
-    const addCommand = buildMCPAddCommand(providerId);
-    const removeCommand = buildMCPRemoveCommand(providerId);
-    if (!addCommand) {
-        return { success: true, skipped: true };
-    }
-    try {
-        // Step 1: Remove existing config for clean state (ignore if not exists)
-        if (removeCommand) {
-            try {
-                await execAsync(`${removeCommand} ${STDERR_REDIRECT}`, { timeout: TIMEOUT_SETUP_REMOVE });
-            }
-            catch {
-                // Server might not exist - that's expected
-            }
-        }
-        // Step 2: Add MCP server using provider's native CLI
-        const { stdout, stderr } = await execAsync(`${addCommand} ${STDERR_REDIRECT}`, { timeout: TIMEOUT_SETUP_ADD });
-        const commandOutput = `${stdout}${stderr}`;
-        if (isMCPAdditionSuccessful(commandOutput)) {
-            return { success: true, skipped: false };
-        }
-        return { success: true, skipped: false };
-    }
-    catch (err) {
-        // Node's exec error includes stdout/stderr as properties
-        const execResult = err;
-        const errorMsg = execResult.message || FALLBACK_ERROR_MESSAGE;
-        const fullOutput = `${execResult.stdout || ''}${execResult.stderr || ''}${errorMsg}`;
-        // Check if server was added despite command failure (validation timeout)
-        if (isMCPAdditionSuccessful(fullOutput)) {
-            return { success: true, skipped: false };
-        }
-        return {
-            success: false,
-            skipped: false,
-            error: extractErrorMessage(errorMsg),
-        };
-    }
-}
-/**
- * Use ax doctor logic to check which provider CLIs are installed
- * This ensures consistent detection between 'ax doctor' and 'ax setup'
- */
-async function getInstalledProviderCLIs() {
-    const results = new Map();
-    // Run doctor-style checks for all providers
-    for (const provider of PROVIDER_CHECKS) {
-        const checkResult = await checkProviderCLI(provider);
-        results.set(provider.id, checkResult);
-    }
-    return results;
-}
-/**
- * Configure MCP for all detected providers using their native CLI commands.
- *
- * Uses 'ax doctor' check logic to determine which CLIs are installed.
- * Only configures MCP for providers that pass the doctor check.
- */
-async function configureMCPForAllProviders() {
-    const result = {
-        configured: [],
-        skipped: [],
-        notInstalled: [],
-        failed: [],
-    };
-    const installedProviders = await getInstalledProviderCLIs();
-    for (const [providerId, healthCheck] of installedProviders) {
-        if (healthCheck.status === HEALTH_STATUS.FAIL) {
-            result.notInstalled.push(providerId);
-            continue;
-        }
-        const configResult = await configureMCPForProvider(providerId);
-        if (configResult.skipped) {
-            result.skipped.push(providerId);
-        }
-        else if (configResult.success) {
-            result.configured.push(providerId);
-        }
-        else {
-            result.failed.push({
-                providerId,
-                error: configResult.error || FALLBACK_ERROR_MESSAGE,
-            });
-        }
-    }
-    return result;
-}
 // ============================================================================
 // Provider Detection
 // ============================================================================
@@ -416,121 +124,48 @@ async function detectAllProviders() {
     const results = await Promise.all(KNOWN_PROVIDERS.map((id) => detectProvider(id)));
     return results;
 }
-// ============================================================================
-// Project Structure Creation
-// ============================================================================
-/**
- * Template for project conventions file
- */
-const CONVENTIONS_TEMPLATE = `# Project Conventions
-
-## Code Style
-<!-- Describe your coding standards -->
-- Example: Use TypeScript strict mode
-- Example: Prefer functional components over class components
-- Example: Use named exports over default exports
-
-## Architecture
-<!-- Describe your project structure -->
-- Example: Domain-driven design with packages/core/*/
-- Example: Contract-first: all types in packages/contracts/
-- Example: No circular dependencies between packages
-
-## Testing
-<!-- Describe testing practices -->
-- Example: Use vitest for unit tests
-- Example: Co-locate tests with source: *.test.ts
-- Example: Mock external dependencies, not internal modules
-
-## Naming Conventions
-<!-- Describe naming conventions -->
-- Example: Use camelCase for variables and functions
-- Example: Use PascalCase for types and classes
-- Example: Prefix interfaces with I (e.g., IUserService)
-`;
-/**
- * Template for project config.json
- */
-const PROJECT_CONFIG_TEMPLATE = {
-    version: DEFAULT_SCHEMA_VERSION,
-    iterate: {
-        maxIterations: ITERATE_MAX_DEFAULT,
-        maxTimeMs: ITERATE_TIMEOUT_DEFAULT,
-        autoConfirm: false,
-    },
-};
-/**
- * Creates the .automatosx/ project structure
- */
-async function createProjectStructure(projectDir, force) {
-    const created = [];
-    const skipped = [];
-    const automatosxDir = join(projectDir, DATA_DIR_NAME);
-    const contextDir = join(automatosxDir, CONTEXT_DIRECTORY);
-    const configPath = join(automatosxDir, CONFIG_FILENAME);
-    const conventionsPath = join(contextDir, CONVENTIONS_FILENAME);
-    // Create data directory
-    try {
-        await mkdir(automatosxDir, { recursive: true });
-    }
-    catch {
-        // Directory may already exist
-    }
-    // Create context directory
-    try {
-        await mkdir(contextDir, { recursive: true });
-    }
-    catch {
-        // Directory may already exist
-    }
-    // Create project config.json
-    const configExists = await fileExists(configPath);
-    if (!configExists || force) {
-        await writeFile(configPath, JSON.stringify(PROJECT_CONFIG_TEMPLATE, null, JSON_INDENT) + '\n');
-        created.push(`${DATA_DIR_NAME}/${CONFIG_FILENAME}`);
-    }
-    else {
-        skipped.push(`${DATA_DIR_NAME}/${CONFIG_FILENAME} (already exists)`);
-    }
-    // Create conventions template
-    const conventionsExists = await fileExists(conventionsPath);
-    if (!conventionsExists || force) {
-        await writeFile(conventionsPath, CONVENTIONS_TEMPLATE);
-        created.push(`${DATA_DIR_NAME}/${CONTEXT_DIRECTORY}/${CONVENTIONS_FILENAME}`);
-    }
-    else {
-        skipped.push(`${DATA_DIR_NAME}/${CONTEXT_DIRECTORY}/${CONVENTIONS_FILENAME} (already exists)`);
-    }
-    return { created, skipped };
-}
-/**
- * Check if a file exists
- */
-async function fileExists(path) {
-    try {
-        await access(path);
-        return true;
-    }
-    catch {
-        return false;
-    }
-}
 /**
  * Runs the setup process
  */
 async function runSetup(options) {
     const configStore = createConfigStore();
     const configFilePath = configStore.getPath(options.scope);
+    // Detect providers first (needed for comparison)
+    const allProviders = await detectAllProviders();
+    const availableProviders = allProviders.filter((provider) => provider.detected);
+    const detectedProviderIds = new Set(availableProviders.map((p) => p.providerId));
     // Check if config already exists
     const configExists = await configStore.exists(options.scope);
     if (configExists && !options.force) {
-        throw new Error(`Configuration already exists at ${configFilePath}. Use --force to overwrite.`);
+        // Read existing config and compare
+        const existingConfig = await configStore.read(options.scope);
+        const existingProviderIds = new Set(Object.keys(existingConfig?.providers ?? {}).filter((id) => existingConfig?.providers[id]?.enabled));
+        // Find differences
+        const newProviders = [...detectedProviderIds].filter((id) => !existingProviderIds.has(id));
+        const removedProviders = [...existingProviderIds].filter((id) => !detectedProviderIds.has(id));
+        // If no changes, return "up to date"
+        if (newProviders.length === 0 && removedProviders.length === 0) {
+            return {
+                success: true,
+                config: existingConfig,
+                providers: allProviders,
+                configPath: configFilePath,
+                alreadyUpToDate: true,
+            };
+        }
+        // Changes detected but no --force flag
+        return {
+            success: true,
+            config: existingConfig,
+            providers: allProviders,
+            configPath: configFilePath,
+            alreadyUpToDate: false,
+            newProvidersDetected: newProviders,
+            removedProviders: removedProviders,
+        };
     }
     // Initialize directory
     await initConfigDirectory(options.scope);
-    // Detect providers
-    const allProviders = await detectAllProviders();
-    const availableProviders = allProviders.filter((provider) => provider.detected);
     // Build providers config record
     const providersConfig = {};
     for (const provider of availableProviders) {
@@ -577,7 +212,6 @@ function parseSetupArgs(args) {
     let nonInteractive = false;
     let silent = false;
     let scope = CONFIG_SCOPE.GLOBAL;
-    let skipProjectStructure = false;
     for (const arg of args) {
         if (matchesFlag(arg, CLI_FLAGS.force)) {
             force = true;
@@ -587,8 +221,8 @@ function parseSetupArgs(args) {
         }
         else if (matchesFlag(arg, CLI_FLAGS.silent)) {
             silent = true;
-            nonInteractive = true; // Silent implies non-interactive
-            force = true; // Silent implies force (use defaults, overwrite if exists)
+            nonInteractive = true;
+            force = true;
         }
         else if (matchesFlag(arg, CLI_FLAGS.local)) {
             scope = CONFIG_SCOPE.LOCAL;
@@ -596,11 +230,8 @@ function parseSetupArgs(args) {
         else if (matchesFlag(arg, CLI_FLAGS.global)) {
             scope = CONFIG_SCOPE.GLOBAL;
         }
-        else if (matchesFlag(arg, CLI_FLAGS.skipProject)) {
-            skipProjectStructure = true;
-        }
     }
-    return { force, nonInteractive, silent, scope, skipProjectStructure };
+    return { force, nonInteractive, silent, scope };
 }
 /**
  * Formats provider detection result for display.
@@ -613,6 +244,12 @@ function formatProviderResult(detection) {
 }
 /**
  * Setup command handler
+ *
+ * Global setup for AutomatosX:
+ * 1. Detects installed provider CLIs
+ * 2. Creates global configuration
+ *
+ * For per-project initialization (MCP registration), use `ax init`.
  */
 export async function setupCommand(args, options) {
     const setupOptions = parseSetupArgs(args);
@@ -633,62 +270,104 @@ export async function setupCommand(args, options) {
             outputLines.push(`  ${ICONS.check} Node.js: ${process.version}`);
             outputLines.push('');
         }
-        // Step 2: Detect providers
+        // Step 2 & 3: Detect providers and create/check configuration
         if (showOutput) {
-            outputLines.push(`${COLORS.bold}Step 2: Provider Detection${COLORS.reset}`);
+            outputLines.push(`${COLORS.bold}Step 2: Provider Detection & Configuration${COLORS.reset}`);
         }
-        const detectedProviders = await detectAllProviders();
+        const setupResult = await runSetup(setupOptions);
+        const detectedProviders = setupResult.providers;
         if (showOutput) {
             for (const provider of detectedProviders) {
                 outputLines.push(formatProviderResult(provider));
             }
             outputLines.push('');
         }
-        // Step 3: Create configuration
-        if (showOutput) {
-            outputLines.push(`${COLORS.bold}Step 3: Creating Configuration${COLORS.reset}`);
-        }
-        const setupResult = await runSetup(setupOptions);
-        if (showOutput) {
-            outputLines.push(`  ${ICONS.check} Configuration saved to: ${setupResult.configPath}`);
-            outputLines.push('');
-        }
-        // Step 4: Create project structure (unless skipped)
-        let projectStructure;
-        if (!setupOptions.skipProjectStructure) {
+        // Handle idempotent cases
+        if (setupResult.alreadyUpToDate) {
             if (showOutput) {
-                outputLines.push(`${COLORS.bold}Step 4: Project Structure${COLORS.reset}`);
+                outputLines.push(`${ICONS.check} Configuration is up to date at: ${setupResult.configPath}`);
+                outputLines.push('');
+                outputLines.push(`${COLORS.bold}Summary${COLORS.reset}`);
+                outputLines.push(`  No changes needed - providers match existing configuration`);
+                outputLines.push('');
+                outputLines.push(`${COLORS.bold}Next Steps${COLORS.reset}`);
+                outputLines.push(`  1. Run ${COLORS.cyan}ax doctor${COLORS.reset} to verify providers are working`);
+                outputLines.push(`  2. Run ${COLORS.cyan}ax init${COLORS.reset} in your project directory to register MCP`);
+                outputLines.push('');
             }
-            projectStructure = await createProjectStructure(process.cwd(), setupOptions.force);
+            if (isJsonFormat) {
+                return {
+                    success: true,
+                    message: undefined,
+                    data: {
+                        success: true,
+                        configPath: setupResult.configPath,
+                        alreadyUpToDate: true,
+                        providers: {
+                            detected: detectedProviders
+                                .filter((provider) => provider.detected)
+                                .map((provider) => provider.providerId),
+                            enabled: Object.keys(setupResult.config.providers).filter((id) => setupResult.config.providers[id]?.enabled),
+                        },
+                        defaultProvider: setupResult.config.defaultProvider,
+                        version: setupResult.config.version,
+                    },
+                    exitCode: EXIT_CODE.SUCCESS,
+                };
+            }
+            return {
+                success: true,
+                message: outputLines.join('\n'),
+                data: undefined,
+                exitCode: EXIT_CODE.SUCCESS,
+            };
+        }
+        // Changes detected but no --force
+        if (setupResult.newProvidersDetected || setupResult.removedProviders) {
             if (showOutput) {
-                for (const filePath of projectStructure.created) {
-                    outputLines.push(`  ${ICONS.check} Created ${filePath}`);
+                outputLines.push(`${ICONS.warn} Configuration exists but providers have changed:`);
+                if (setupResult.newProvidersDetected && setupResult.newProvidersDetected.length > 0) {
+                    outputLines.push(`  ${COLORS.green}+ New:${COLORS.reset} ${setupResult.newProvidersDetected.join(', ')}`);
                 }
-                for (const filePath of projectStructure.skipped) {
-                    outputLines.push(`  ${ICONS.warn} Skipped ${filePath}`);
+                if (setupResult.removedProviders && setupResult.removedProviders.length > 0) {
+                    outputLines.push(`  ${COLORS.red}- Removed:${COLORS.reset} ${setupResult.removedProviders.join(', ')}`);
                 }
                 outputLines.push('');
+                outputLines.push(`Run ${COLORS.cyan}ax setup --force${COLORS.reset} to update configuration.`);
+                outputLines.push('');
             }
+            if (isJsonFormat) {
+                return {
+                    success: true,
+                    message: undefined,
+                    data: {
+                        success: true,
+                        configPath: setupResult.configPath,
+                        alreadyUpToDate: false,
+                        changesDetected: {
+                            newProviders: setupResult.newProvidersDetected,
+                            removedProviders: setupResult.removedProviders,
+                        },
+                        providers: {
+                            detected: detectedProviders
+                                .filter((provider) => provider.detected)
+                                .map((provider) => provider.providerId),
+                            enabled: Object.keys(setupResult.config.providers).filter((id) => setupResult.config.providers[id]?.enabled),
+                        },
+                    },
+                    exitCode: EXIT_CODE.SUCCESS,
+                };
+            }
+            return {
+                success: true,
+                message: outputLines.join('\n'),
+                data: undefined,
+                exitCode: EXIT_CODE.SUCCESS,
+            };
         }
-        // Step 5: Configure MCP for all detected providers
-        if (showOutput) {
-            outputLines.push(`${COLORS.bold}Step 5: MCP Configuration${COLORS.reset}`);
-            outputLines.push(`  ${COLORS.dim}Using 'ax doctor' check to verify installed CLIs...${COLORS.reset}`);
-        }
-        const mcpResult = await configureMCPForAllProviders();
+        // Normal setup (new configuration created)
         if (showOutput) {
-            for (const providerId of mcpResult.configured) {
-                outputLines.push(`  ${ICONS.check} ${providerId}: AutomatosX MCP configured`);
-            }
-            for (const providerId of mcpResult.notInstalled) {
-                outputLines.push(`  ${COLORS.dim}  - ${providerId}: CLI not installed, skipped${COLORS.reset}`);
-            }
-            for (const { providerId, error } of mcpResult.failed) {
-                outputLines.push(`  ${ICONS.warn} ${providerId}: ${error}`);
-            }
-            if (mcpResult.configured.length === 0 && mcpResult.failed.length === 0 && mcpResult.notInstalled.length === 0) {
-                outputLines.push(`  ${ICONS.warn} No providers detected for MCP configuration`);
-            }
+            outputLines.push(`${ICONS.check} Configuration saved to: ${setupResult.configPath}`);
             outputLines.push('');
         }
         if (showOutput) {
@@ -701,15 +380,10 @@ export async function setupCommand(args, options) {
             if (setupResult.config.defaultProvider !== undefined) {
                 outputLines.push(`  Default provider: ${setupResult.config.defaultProvider}`);
             }
-            if (projectStructure !== undefined) {
-                outputLines.push(`  Project files created: ${projectStructure.created.length}`);
-            }
-            outputLines.push(`  MCP configured: ${mcpResult.configured.length} provider(s)`);
             outputLines.push('');
             outputLines.push(`${COLORS.bold}Next Steps${COLORS.reset}`);
-            outputLines.push(`  1. Run ${COLORS.cyan}ax doctor${COLORS.reset} to verify installation`);
-            outputLines.push(`  2. Edit ${COLORS.cyan}${DATA_DIR_NAME}/${CONTEXT_DIRECTORY}/${CONVENTIONS_FILENAME}${COLORS.reset} to add your project conventions`);
-            outputLines.push(`  3. Run ${COLORS.cyan}ax call --iterate <provider> "task"${COLORS.reset} to use iterate mode`);
+            outputLines.push(`  1. Run ${COLORS.cyan}ax doctor${COLORS.reset} to verify providers are working`);
+            outputLines.push(`  2. Run ${COLORS.cyan}ax init${COLORS.reset} in your project directory to register MCP`);
             outputLines.push('');
         }
         if (isJsonFormat) {
@@ -720,23 +394,13 @@ export async function setupCommand(args, options) {
                     success: true,
                     configPath: setupResult.configPath,
                     providers: {
-                        detected: detectedProviders.filter((provider) => provider.detected).map((provider) => provider.providerId),
-                        enabled: Object.keys(setupResult.config.providers).filter(id => setupResult.config.providers[id]?.enabled),
+                        detected: detectedProviders
+                            .filter((provider) => provider.detected)
+                            .map((provider) => provider.providerId),
+                        enabled: Object.keys(setupResult.config.providers).filter((id) => setupResult.config.providers[id]?.enabled),
                     },
                     defaultProvider: setupResult.config.defaultProvider,
                     version: setupResult.config.version,
-                    projectStructure: projectStructure !== undefined
-                        ? {
-                            created: projectStructure.created,
-                            skipped: projectStructure.skipped,
-                        }
-                        : undefined,
-                    mcpConfiguration: {
-                        configured: mcpResult.configured,
-                        skipped: mcpResult.skipped,
-                        notInstalled: mcpResult.notInstalled,
-                        failed: mcpResult.failed,
-                    },
                 },
                 exitCode: EXIT_CODE.SUCCESS,
             };