fraim-framework 2.0.78 → 2.0.81

package/README.md

@@ -233,6 +233,34 @@ npm install -g fraim-framework
 fraim setup  # Complete setup with IDE configuration
 ```
 
+The setup command supports three modes:
+
+**Conversational Mode**: AI workflows only, no platform integration required
+```bash
+fraim setup --key=<your-fraim-key>
+# Select "Conversational Mode" when prompted
+```
+
+**Integrated Mode**: Single platform for both code hosting and issue tracking
+```bash
+fraim setup --key=<your-fraim-key>
+# Select "Integrated Mode" when prompted
+# Choose platform: GitHub, Azure DevOps, or GitLab
+```
+
+**Split Mode**: Separate platforms for code hosting and issue tracking
+```bash
+fraim setup --key=<your-fraim-key>
+# Select "Split Mode" when prompted
+# Choose code repository platform: GitHub, Azure DevOps, or GitLab
+# Choose issue tracking platform: GitHub, Azure DevOps, GitLab, or Jira
+```
+
+Common Split mode combinations:
+- GitHub (code) + Jira (issues)
+- GitLab (code) + Jira (issues)
+- Azure DevOps (code) + GitHub (issues)
+
 ### **🔧 Additional Commands**
 
 After initial setup, you can use these commands:
@@ -244,6 +272,12 @@ fraim add-ide --ide antigravity     # Configure Gemini Antigravity
 fraim add-ide --all                 # Configure all detected IDEs
 fraim add-ide --list                # List supported IDEs
 
+# Add platform integrations to existing setup
+fraim setup --github                # Add GitHub integration
+fraim setup --ado                   # Add Azure DevOps integration
+fraim setup --gitlab                # Add GitLab integration
+fraim setup --jira                  # Add Jira integration
+
 # Project initialization
 fraim init-project                  # Initialize FRAIM in current project
 
@@ -255,7 +289,51 @@ fraim doctor                        # Diagnose configuration issues
 fraim sync                          # Sync latest workflows and rules
 ```
 
-**💡 Pro Tip**: Use `fraim add-ide` when you install a new IDE after initial setup. It reuses your existing FRAIM and GitHub keys, making it much faster than running full setup again.
+**💡 Pro Tip**: Use `fraim add-ide` when you install a new IDE after initial setup. It reuses your existing FRAIM and platform tokens, making it much faster than running full setup again.
+
+### **🔧 Jira Integration Setup**
+
+FRAIM uses the official Model Context Protocol (MCP) server for Jira integration. The setup command automatically configures the correct format.
+
+**Jira API Token Requirements**:
+1. Go to https://id.atlassian.com/manage-profile/security/api-tokens
+2. Click "Create API token"
+3. Give it a name (e.g., "FRAIM Integration")
+4. Copy the token (starts with ATATT3...)
+5. Use this token during `fraim setup`
+
+**Correct MCP Configuration** (automatically generated):
+```json
+{
+  "jira": {
+    "command": "uvx",
+    "args": ["mcp-atlassian"],
+    "env": {
+      "JIRA_URL": "https://mycompany.atlassian.net",
+      "JIRA_USERNAME": "user@mycompany.com",
+      "JIRA_API_TOKEN": "your-token-here"
+    }
+  }
+}
+```
+
+**⚠️ Common Issues**:
+- **Old package name**: If you see `@modelcontextprotocol/server-jira` in your config, this package doesn't exist. Run `fraim setup --jira` to update to the correct `mcp-atlassian` package.
+- **Token format**: Jira API tokens typically start with `ATATT3`. If your token doesn't match this format, verify you created an API token (not a personal access token).
+- **First run slow**: The first time `uvx` runs the Jira MCP server, it downloads the package. This is normal and only happens once.
+
+**Troubleshooting**:
+```bash
+# Test Jira MCP connection
+fraim test-mcp
+
+# Reconfigure Jira integration
+fraim setup --jira
+
+# Check configuration
+cat ~/.kiro/settings/mcp.json  # For Kiro IDE
+cat ~/Library/Application\ Support/Claude/claude_desktop_config.json  # For Claude Desktop (macOS)
+```
 
 
 ## 🌟 **Why FRAIM is the Future**

package/bin/fraim-mcp.js

@@ -1,4 +1,4 @@
-#!/usr/bin/env node
+#!/usr/bin/env node
 
 /**
  * FRAIM MCP Server - Smart Entry Point

package/bin/fraim.js

@@ -1,4 +1,4 @@
-#!/usr/bin/env node
+#!/usr/bin/env node
 
 /**
  * FRAIM Framework CLI Entry Point

package/dist/src/cli/commands/add-ide.js

@@ -9,12 +9,12 @@ const chalk_1 = __importDefault(require("chalk"));
 const prompts_1 = __importDefault(require("prompts"));
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
-const os_1 = __importDefault(require("os"));
 const ide_detector_1 = require("../setup/ide-detector");
 const mcp_config_generator_1 = require("../setup/mcp-config-generator");
 const codex_local_config_1 = require("../setup/codex-local-config");
+const script_sync_utils_1 = require("../utils/script-sync-utils");
 const loadGlobalConfig = () => {
-    const globalConfigPath = path_1.default.join(os_1.default.homedir(), '.fraim', 'config.json');
+    const globalConfigPath = path_1.default.join((0, script_sync_utils_1.getUserFraimDir)(), 'config.json');
     if (!fs_1.default.existsSync(globalConfigPath)) {
         return null;
     }
@@ -25,7 +25,8 @@ const loadGlobalConfig = () => {
             githubToken: config.tokens?.github || config.githubToken, // Support both old and new format
             gitlabToken: config.tokens?.gitlab,
             jiraToken: config.tokens?.jira,
-            mode: config.mode
+            mode: config.mode,
+            jiraConfig: config.jiraConfig
         };
     }
     catch (e) {
@@ -77,7 +78,7 @@ const promptForGitHubToken = async (isConversationalMode = false) => {
     return tokenResponse.token;
 };
 const saveGitHubTokenToConfig = (githubToken) => {
-    const globalConfigPath = path_1.default.join(os_1.default.homedir(), '.fraim', 'config.json');
+    const globalConfigPath = path_1.default.join((0, script_sync_utils_1.getUserFraimDir)(), 'config.json');
     if (fs_1.default.existsSync(globalConfigPath)) {
         try {
             const config = JSON.parse(fs_1.default.readFileSync(globalConfigPath, 'utf8'));
@@ -97,7 +98,7 @@ const saveGitHubTokenToConfig = (githubToken) => {
     }
 };
 exports.saveGitHubTokenToConfig = saveGitHubTokenToConfig;
-const configureIDEMCP = async (ide, fraimKey, tokens) => {
+const configureIDEMCP = async (ide, fraimKey, tokens, jiraConfig) => {
     const configPath = (0, ide_detector_1.expandPath)(ide.configPath);
     console.log(chalk_1.default.blue(`🔧 Configuring ${ide.name}...`));
     // Create backup if config exists
@@ -114,10 +115,11 @@ const configureIDEMCP = async (ide, fraimKey, tokens) => {
     }
     let existingConfig = {};
     let existingMCPServers = {};
+    const serversKey = ide.configType === 'vscode' ? 'servers' : 'mcpServers';
     if (fs_1.default.existsSync(configPath) && ide.configFormat === 'json') {
         try {
             existingConfig = JSON.parse(fs_1.default.readFileSync(configPath, 'utf8'));
-            existingMCPServers = existingConfig.mcpServers || {};
+            existingMCPServers = existingConfig[serversKey] || {};
             console.log(chalk_1.default.gray(`  📋 Found existing config with ${Object.keys(existingMCPServers).length} MCP servers`));
         }
         catch (e) {
@@ -131,7 +133,7 @@ const configureIDEMCP = async (ide, fraimKey, tokens) => {
             existingTomlContent = fs_1.default.readFileSync(configPath, 'utf8');
             console.log(chalk_1.default.gray(`  📋 Found existing TOML config`));
         }
-        const newTomlContent = (0, mcp_config_generator_1.generateMCPConfig)(ide.configType, fraimKey, tokens);
+        const newTomlContent = (0, mcp_config_generator_1.generateMCPConfig)(ide.configType, fraimKey, tokens, jiraConfig);
         const serversToAdd = ['fraim', 'git', 'github', 'gitlab', 'jira', 'playwright'];
         const mergeResult = (0, mcp_config_generator_1.mergeTomlMCPServers)(existingTomlContent, newTomlContent, serversToAdd);
         fs_1.default.writeFileSync(configPath, mergeResult.content);
@@ -146,9 +148,9 @@ const configureIDEMCP = async (ide, fraimKey, tokens) => {
         });
     }
     else {
-        // Handle JSON format
-        const newConfig = (0, mcp_config_generator_1.generateMCPConfig)(ide.configType, fraimKey, tokens);
-        const newMCPServers = newConfig.mcpServers || {};
+        // For JSON configs - intelligent merging
+        const newConfig = (0, mcp_config_generator_1.generateMCPConfig)(ide.configType, fraimKey, tokens, jiraConfig);
+        const newMCPServers = newConfig[serversKey] || newConfig.mcpServers || {};
         // Merge MCP servers intelligently
         const mergedMCPServers = { ...existingMCPServers };
         const addedServers = [];
@@ -166,7 +168,7 @@ const configureIDEMCP = async (ide, fraimKey, tokens) => {
         const mergedConfig = {
             ...existingConfig,
             ...newConfig,
-            mcpServers: mergedMCPServers
+            [serversKey]: mergedMCPServers
         };
         // Write updated config
         fs_1.default.writeFileSync(configPath, JSON.stringify(mergedConfig, null, 2));
@@ -322,7 +324,7 @@ const runAddIDE = async (options) => {
     };
     for (const ide of idesToConfigure) {
         try {
-            await configureIDEMCP(ide, globalConfig.fraimKey, platformTokens);
+            await configureIDEMCP(ide, globalConfig.fraimKey, platformTokens, globalConfig.jiraConfig);
             results.successful.push(ide.name);
         }
         catch (error) {
@@ -355,7 +357,7 @@ const runAddIDE = async (options) => {
 exports.runAddIDE = runAddIDE;
 exports.addIDECommand = new commander_1.Command('add-ide')
     .description('Add FRAIM configuration to additional IDEs')
-    .option('--ide <name>', 'Configure specific IDE (claude, antigravity, kiro, cursor, vscode, codex, windsurf)')
+    .option('--ide <name>', 'Configure specific IDE (claude, claude-code, antigravity, kiro, cursor, vscode, codex, windsurf)')
     .option('--all', 'Configure all detected IDEs')
     .option('--list', 'List all supported IDEs and their detection status')
     .action(exports.runAddIDE);

package/dist/src/cli/commands/setup.js

@@ -9,12 +9,12 @@ const chalk_1 = __importDefault(require("chalk"));
 const prompts_1 = __importDefault(require("prompts"));
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
-const os_1 = __importDefault(require("os"));
 const token_validator_1 = require("../setup/token-validator");
 const auto_mcp_setup_1 = require("../setup/auto-mcp-setup");
 const version_utils_1 = require("../utils/version-utils");
 const platform_detection_1 = require("../utils/platform-detection");
 const init_project_1 = require("./init-project");
+const script_sync_utils_1 = require("../utils/script-sync-utils");
 const promptForFraimKey = async () => {
     console.log(chalk_1.default.blue('🔑 FRAIM Key Setup'));
     console.log('FRAIM requires a valid API key to access workflows and features.\n');
@@ -78,7 +78,12 @@ const promptForMode = async () => {
             {
                 title: 'Integrated Mode',
                 value: 'integrated',
-                description: 'Full platform integration with GitHub/ADO for issue tracking and PRs'
+                description: 'Single platform for both code hosting and issue tracking'
+            },
+            {
+                title: 'Split Mode',
+                value: 'split',
+                description: 'Separate platforms for code hosting and issue tracking (e.g., GitHub + Jira)'
             },
             {
                 title: 'Conversational Mode',
@@ -97,6 +102,11 @@ const promptForMode = async () => {
         console.log(chalk_1.default.gray('  You can use FRAIM workflows without platform credentials.'));
         console.log(chalk_1.default.gray('  Platform features (issues, PRs) will be unavailable.\n'));
     }
+    else if (response.mode === 'split') {
+        console.log(chalk_1.default.blue('\n✓ Split mode selected'));
+        console.log(chalk_1.default.gray('  You can use different platforms for code hosting and issue tracking.'));
+        console.log(chalk_1.default.gray('  For example: GitHub for code + Jira for issues.\n'));
+    }
     else {
         console.log(chalk_1.default.blue('\n✓ Integrated mode selected'));
         console.log(chalk_1.default.gray('  Full platform integration will be available.\n'));
@@ -140,6 +150,49 @@ const promptForPlatforms = async () => {
     console.log();
     return platforms;
 };
+const promptForCodeRepository = async () => {
+    console.log(chalk_1.default.blue('\n📦 Code Repository Platform'));
+    console.log(chalk_1.default.gray('Select the platform for code hosting:\n'));
+    const response = await (0, prompts_1.default)({
+        type: 'select',
+        name: 'platform',
+        message: 'Select code repository platform',
+        choices: [
+            { title: 'GitHub', value: 'github' },
+            { title: 'Azure DevOps', value: 'ado' },
+            { title: 'GitLab', value: 'gitlab' }
+        ],
+        initial: 0
+    });
+    if (!response.platform) {
+        console.log(chalk_1.default.yellow('\nℹ️  No platform selected, defaulting to GitHub'));
+        return 'github';
+    }
+    console.log(chalk_1.default.blue(`\n✓ Code repository: ${response.platform === 'github' ? 'GitHub' : response.platform === 'ado' ? 'Azure DevOps' : 'GitLab'}\n`));
+    return response.platform;
+};
+const promptForIssueTracking = async () => {
+    console.log(chalk_1.default.blue('\n🎫 Issue Tracking Platform'));
+    console.log(chalk_1.default.gray('Select the platform for issue tracking:\n'));
+    const response = await (0, prompts_1.default)({
+        type: 'select',
+        name: 'platform',
+        message: 'Select issue tracking platform',
+        choices: [
+            { title: 'GitHub', value: 'github' },
+            { title: 'Azure DevOps', value: 'ado' },
+            { title: 'GitLab', value: 'gitlab' },
+            { title: 'Jira', value: 'jira' }
+        ],
+        initial: 0
+    });
+    if (!response.platform) {
+        console.log(chalk_1.default.yellow('\nℹ️  No platform selected, defaulting to GitHub'));
+        return 'github';
+    }
+    console.log(chalk_1.default.blue(`\n✓ Issue tracking: ${response.platform === 'github' ? 'GitHub' : response.platform === 'ado' ? 'Azure DevOps' : response.platform === 'gitlab' ? 'GitLab' : 'Jira'}\n`));
+    return response.platform;
+};
 const promptForADOToken = async () => {
     console.log(chalk_1.default.blue('\n🔧 Azure DevOps Integration Setup'));
     console.log('FRAIM requires an Azure DevOps Personal Access Token for ADO integration.\n');
@@ -226,29 +279,71 @@ const promptForGitLabToken = async () => {
     console.log(chalk_1.default.green('GitLab token received\n'));
     return tokenResponse.token;
 };
-const promptForJiraToken = async () => {
+const promptForJiraCredentials = async () => {
     console.log(chalk_1.default.blue('\nJira Integration Setup'));
-    console.log('FRAIM requires a Jira API token for Jira MCP integration.\n');
+    console.log('FRAIM requires Jira credentials for MCP integration.\n');
+    // Prompt for base URL
+    const urlResponse = await (0, prompts_1.default)({
+        type: 'text',
+        name: 'baseUrl',
+        message: 'Enter your Jira base URL (e.g., https://company.atlassian.net)',
+        validate: (value) => {
+            if (!value)
+                return 'Jira base URL is required';
+            // Basic URL validation
+            try {
+                new URL(value.startsWith('http') ? value : `https://${value}`);
+                return true;
+            }
+            catch {
+                return 'Please enter a valid URL';
+            }
+        }
+    });
+    if (!urlResponse.baseUrl) {
+        throw new Error('Jira base URL is required');
+    }
+    // Prompt for email
+    const emailResponse = await (0, prompts_1.default)({
+        type: 'text',
+        name: 'email',
+        message: 'Enter your Jira account email',
+        validate: (value) => {
+            if (!value)
+                return 'Jira email is required';
+            if (!value.includes('@'))
+                return 'Please enter a valid email address';
+            return true;
+        }
+    });
+    if (!emailResponse.email) {
+        throw new Error('Jira email is required');
+    }
+    // Prompt for API token
     const tokenResponse = await (0, prompts_1.default)({
         type: 'password',
         name: 'token',
         message: 'Enter your Jira API token',
         validate: (value) => {
             if (!value)
-                return 'Jira token is required';
+                return 'Jira API token is required';
             if (!(0, token_validator_1.isValidTokenFormat)(value, 'jira'))
                 return 'Please enter a valid Jira token';
             return true;
         }
     });
     if (!tokenResponse.token) {
-        throw new Error('Jira token is required');
+        throw new Error('Jira API token is required');
     }
-    console.log(chalk_1.default.green('Jira token received\n'));
-    return tokenResponse.token;
+    console.log(chalk_1.default.green('Jira credentials received\n'));
+    return {
+        baseUrl: urlResponse.baseUrl,
+        email: emailResponse.email,
+        token: tokenResponse.token
+    };
 };
-const saveGlobalConfig = (fraimKey, mode, tokens) => {
-    const globalConfigDir = path_1.default.join(os_1.default.homedir(), '.fraim');
+const saveGlobalConfig = (fraimKey, mode, tokens, jiraConfig) => {
+    const globalConfigDir = (0, script_sync_utils_1.getUserFraimDir)();
     const globalConfigPath = path_1.default.join(globalConfigDir, 'config.json');
     if (!fs_1.default.existsSync(globalConfigDir)) {
         fs_1.default.mkdirSync(globalConfigDir, { recursive: true });
@@ -272,6 +367,10 @@ const saveGlobalConfig = (fraimKey, mode, tokens) => {
             ...(existingConfig.tokens || {}),
             ...tokens
         },
+        jiraConfig: jiraConfig && (jiraConfig.baseUrl || jiraConfig.email) ? {
+            ...(existingConfig.jiraConfig || {}),
+            ...jiraConfig
+        } : existingConfig.jiraConfig,
         configuredAt: new Date().toISOString(),
         userPreferences: {
             autoSync: true,
@@ -284,11 +383,12 @@ const saveGlobalConfig = (fraimKey, mode, tokens) => {
 const runSetup = async (options) => {
     console.log(chalk_1.default.blue('🚀 Welcome to FRAIM! Let\'s get you set up.\n'));
     // Determine if this is an update (adding platforms to existing setup)
-    const globalConfigPath = path_1.default.join(os_1.default.homedir(), '.fraim', 'config.json');
+    const globalConfigPath = path_1.default.join((0, script_sync_utils_1.getUserFraimDir)(), 'config.json');
     const isUpdate = fs_1.default.existsSync(globalConfigPath) && (options.github || options.ado || options.gitlab || options.jira);
     let fraimKey;
     let mode;
     const tokens = {};
+    let jiraConfig = {};
     if (isUpdate) {
         // Update existing setup - add platforms
         console.log(chalk_1.default.blue('📝 Updating existing FRAIM configuration...\n'));
@@ -413,7 +513,7 @@ const runSetup = async (options) => {
                 }
             }
         }
-        // Get Jira token if needed
+        // Get Jira credentials if needed
         if (needJira && !tokens.jira) {
             if (options.jiraToken) {
                 if (!(0, token_validator_1.isValidTokenFormat)(options.jiraToken, 'jira')) {
@@ -421,13 +521,28 @@ const runSetup = async (options) => {
                     process.exit(1);
                 }
                 tokens.jira = options.jiraToken;
+                // Use provided URL and email if available, otherwise prompt
+                if (options.jiraUrl && options.jiraEmail) {
+                    jiraConfig.baseUrl = options.jiraUrl;
+                    jiraConfig.email = options.jiraEmail;
+                    console.log(chalk_1.default.green('✅ Jira credentials received\n'));
+                }
+                else {
+                    console.log(chalk_1.default.yellow('⚠️  Jira token provided but missing URL or email'));
+                    const jiraCredentials = await promptForJiraCredentials();
+                    jiraConfig.baseUrl = jiraCredentials.baseUrl;
+                    jiraConfig.email = jiraCredentials.email;
+                }
             }
             else {
                 try {
-                    tokens.jira = await promptForJiraToken();
+                    const jiraCredentials = await promptForJiraCredentials();
+                    tokens.jira = jiraCredentials.token;
+                    jiraConfig.baseUrl = jiraCredentials.baseUrl;
+                    jiraConfig.email = jiraCredentials.email;
                 }
                 catch (e) {
-                    console.log(chalk_1.default.red('Failed to get Jira token'));
+                    console.log(chalk_1.default.red('Failed to get Jira credentials'));
                     process.exit(1);
                 }
             }
@@ -441,12 +556,171 @@ const runSetup = async (options) => {
             console.log(chalk_1.default.cyan('   fraim setup --jira\n'));
         }
     }
+    else if (mode === 'split') {
+        // Split mode: separate platforms for code repository and issue tracking
+        console.log(chalk_1.default.blue('\n🔀 Split Mode Configuration'));
+        console.log(chalk_1.default.gray('Configure separate platforms for code hosting and issue tracking.\n'));
+        // Get code repository platform
+        const codeRepoPlatform = await promptForCodeRepository();
+        // Get code repository token
+        if (codeRepoPlatform === 'github' && !tokens.github) {
+            if (options.githubToken) {
+                if (!(0, token_validator_1.isValidTokenFormat)(options.githubToken, 'github')) {
+                    console.log(chalk_1.default.red('❌ Invalid GitHub token format'));
+                    process.exit(1);
+                }
+                console.log(chalk_1.default.blue('🔍 Validating GitHub token...'));
+                const isValid = await (0, token_validator_1.validateGitHubToken)(options.githubToken);
+                if (!isValid) {
+                    console.log(chalk_1.default.red('❌ Invalid GitHub token'));
+                    process.exit(1);
+                }
+                tokens.github = options.githubToken;
+                console.log(chalk_1.default.green('✅ GitHub token validated\n'));
+            }
+            else {
+                try {
+                    tokens.github = await (0, auto_mcp_setup_1.promptForGitHubToken)();
+                }
+                catch (e) {
+                    process.exit(1);
+                }
+            }
+        }
+        else if (codeRepoPlatform === 'ado' && !tokens.ado) {
+            if (options.adoToken) {
+                tokens.ado = options.adoToken;
+                console.log(chalk_1.default.green('✅ Azure DevOps token received\n'));
+            }
+            else {
+                try {
+                    tokens.ado = await promptForADOToken();
+                }
+                catch (e) {
+                    console.log(chalk_1.default.red('❌ Failed to get Azure DevOps token'));
+                    process.exit(1);
+                }
+            }
+        }
+        else if (codeRepoPlatform === 'gitlab' && !tokens.gitlab) {
+            if (options.gitlabToken) {
+                if (!(0, token_validator_1.isValidTokenFormat)(options.gitlabToken, 'gitlab')) {
+                    console.log(chalk_1.default.red('Invalid GitLab token format'));
+                    process.exit(1);
+                }
+                tokens.gitlab = options.gitlabToken;
+            }
+            else {
+                try {
+                    tokens.gitlab = await promptForGitLabToken();
+                }
+                catch (e) {
+                    console.log(chalk_1.default.red('Failed to get GitLab token'));
+                    process.exit(1);
+                }
+            }
+        }
+        // Get issue tracking platform
+        const issueTrackingPlatform = await promptForIssueTracking();
+        // Get issue tracking token (if different from code repo)
+        if (issueTrackingPlatform === 'github' && !tokens.github) {
+            if (options.githubToken) {
+                if (!(0, token_validator_1.isValidTokenFormat)(options.githubToken, 'github')) {
+                    console.log(chalk_1.default.red('❌ Invalid GitHub token format'));
+                    process.exit(1);
+                }
+                console.log(chalk_1.default.blue('🔍 Validating GitHub token...'));
+                const isValid = await (0, token_validator_1.validateGitHubToken)(options.githubToken);
+                if (!isValid) {
+                    console.log(chalk_1.default.red('❌ Invalid GitHub token'));
+                    process.exit(1);
+                }
+                tokens.github = options.githubToken;
+                console.log(chalk_1.default.green('✅ GitHub token validated\n'));
+            }
+            else {
+                try {
+                    tokens.github = await (0, auto_mcp_setup_1.promptForGitHubToken)();
+                }
+                catch (e) {
+                    process.exit(1);
+                }
+            }
+        }
+        else if (issueTrackingPlatform === 'ado' && !tokens.ado) {
+            if (options.adoToken) {
+                tokens.ado = options.adoToken;
+                console.log(chalk_1.default.green('✅ Azure DevOps token received\n'));
+            }
+            else {
+                try {
+                    tokens.ado = await promptForADOToken();
+                }
+                catch (e) {
+                    console.log(chalk_1.default.red('❌ Failed to get Azure DevOps token'));
+                    process.exit(1);
+                }
+            }
+        }
+        else if (issueTrackingPlatform === 'gitlab' && !tokens.gitlab) {
+            if (options.gitlabToken) {
+                if (!(0, token_validator_1.isValidTokenFormat)(options.gitlabToken, 'gitlab')) {
+                    console.log(chalk_1.default.red('Invalid GitLab token format'));
+                    process.exit(1);
+                }
+                tokens.gitlab = options.gitlabToken;
+            }
+            else {
+                try {
+                    tokens.gitlab = await promptForGitLabToken();
+                }
+                catch (e) {
+                    console.log(chalk_1.default.red('Failed to get GitLab token'));
+                    process.exit(1);
+                }
+            }
+        }
+        else if (issueTrackingPlatform === 'jira' && !tokens.jira) {
+            if (options.jiraToken) {
+                if (!(0, token_validator_1.isValidTokenFormat)(options.jiraToken, 'jira')) {
+                    console.log(chalk_1.default.red('Invalid Jira token format'));
+                    process.exit(1);
+                }
+                tokens.jira = options.jiraToken;
+                // Use provided URL and email if available, otherwise prompt
+                if (options.jiraUrl && options.jiraEmail) {
+                    jiraConfig.baseUrl = options.jiraUrl;
+                    jiraConfig.email = options.jiraEmail;
+                    console.log(chalk_1.default.green('✅ Jira credentials received\n'));
+                }
+                else {
+                    console.log(chalk_1.default.yellow('⚠️  Jira token provided but missing URL or email'));
+                    const jiraCredentials = await promptForJiraCredentials();
+                    jiraConfig.baseUrl = jiraCredentials.baseUrl;
+                    jiraConfig.email = jiraCredentials.email;
+                }
+            }
+            else {
+                try {
+                    const jiraCredentials = await promptForJiraCredentials();
+                    tokens.jira = jiraCredentials.token;
+                    jiraConfig.baseUrl = jiraCredentials.baseUrl;
+                    jiraConfig.email = jiraCredentials.email;
+                }
+                catch (e) {
+                    console.log(chalk_1.default.red('Failed to get Jira credentials'));
+                    process.exit(1);
+                }
+            }
+        }
+        console.log(chalk_1.default.green(`\n✅ Split mode configured: ${codeRepoPlatform} (code) + ${issueTrackingPlatform} (issues)\n`));
+    }
     else {
         console.log(chalk_1.default.gray('ℹ️  Conversational mode: No platform tokens needed\n'));
     }
     // Save global configuration
     console.log(chalk_1.default.blue('💾 Saving global configuration...'));
-    saveGlobalConfig(fraimKey, mode, tokens);
+    saveGlobalConfig(fraimKey, mode, tokens, jiraConfig);
     // Configure MCP servers (only on initial setup)
     if (!isUpdate) {
         console.log(chalk_1.default.blue('\n🔌 Configuring MCP servers...'));
@@ -462,7 +736,7 @@ const runSetup = async (options) => {
             console.log(chalk_1.default.gray('   FRAIM workflows will work, but GitHub-specific features will be unavailable\n'));
         }
         try {
-            await (0, auto_mcp_setup_1.autoConfigureMCP)(fraimKey, mcpTokens, options.ide ? [options.ide] : undefined);
+            await (0, auto_mcp_setup_1.autoConfigureMCP)(fraimKey, mcpTokens, options.ide ? [options.ide] : undefined, jiraConfig);
         }
         catch (e) {
             console.log(chalk_1.default.yellow('⚠️  MCP configuration encountered issues'));
@@ -508,6 +782,8 @@ exports.setupCommand = new commander_1.Command('setup')
     .option('--ado-token <token>', 'Azure DevOps Personal Access Token')
     .option('--gitlab-token <token>', 'GitLab Personal Access Token')
     .option('--jira-token <token>', 'Jira API token')
+    .option('--jira-url <url>', 'Jira base URL (e.g., https://company.atlassian.net)')
+    .option('--jira-email <email>', 'Jira account email')
     .option('--github', 'Add/update GitHub integration')
     .option('--ado', 'Add/update Azure DevOps integration')
     .option('--gitlab', 'Add/update GitLab integration')

package/dist/src/cli/commands/test-mcp.js

@@ -8,8 +8,8 @@ const commander_1 = require("commander");
 const chalk_1 = __importDefault(require("chalk"));
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
-const os_1 = __importDefault(require("os"));
 const ide_detector_1 = require("../setup/ide-detector");
+const script_sync_utils_1 = require("../utils/script-sync-utils");
 const testIDEConfig = async (ide) => {
     const result = {
         ide: ide.name,
@@ -57,7 +57,7 @@ const testIDEConfig = async (ide) => {
     return result;
 };
 const checkGlobalSetup = () => {
-    const globalConfigPath = path_1.default.join(os_1.default.homedir(), '.fraim', 'config.json');
+    const globalConfigPath = path_1.default.join((0, script_sync_utils_1.getUserFraimDir)(), 'config.json');
     return fs_1.default.existsSync(globalConfigPath);
 };
 const runTestMCP = async () => {