omnibiofex 2.4.1

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 OmniBioFex
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# OmniBioFex X CLI
+
+<div align="center">
+
+**The Autonomous Research Terminal**
+
+Execute AI-powered research missions from your terminal. Stop chatting. Start delegating.
+
+[![npm version](https://img.shields.io/npm/v/omnibiofex.svg)](https://www.npmjs.com/package/omnibiofex)
+[![Node.js](https://img.shields.io/badge/node-%3E%3D14-green.svg)](https://nodejs.org)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+[![Downloads](https://img.shields.io/npm/dm/omnibiofex.svg)](https://www.npmjs.com/package/omnibiofex)
+
+[Website](https://x.omnibiofex.cloud) • [Dashboard](https://x.omnibiofex.cloud/dash) • [Documentation](https://x.omnibiofex.cloud/cli-guide)
+
+</div>
+
+---
+
+## ✨ Features
+
+- 🎯 **Autonomous Missions** - Assign research, get structured reports
+- 🤖 **Multi-Agent Swarm** - 6 specialized AI agents collaborate in real-time
+- 💾 **Persistent Memory** - Projects remember everything, even months later
+- 🔒 **Secure Auth** - Passwordless Magic Link authentication
+- ⚡ **Smart Routing** - Automatically routes to optimal AI engine
+- 📊 **Evidence-Backed** - Every conclusion includes sources and confidence scores
+
+---
+
+## 🚀 Installation
+
+### Quick Install (Recommended)
+
+**macOS / Linux:**
+curl -fsSL https://x.omnibiofex.cloud/install | sh
+**Windows (PowerShell):**
+irm https://x.omnibiofex.cloud/install.ps1 | iex
+**Via npm**
+npm install -g omnibiofex
+**Verify Installation**
+obx version
+🔐 Authentication
+OmniBioFex X uses secure, passwordless Magic Link authentication.
+bash
+obx login
+Flow:
+Enter your email in the terminal
+Check your inbox for the magic link
+Click the link → Automatically authenticated
+You're ready to research!
+New users get 2,500 free Research Compute Credits (RCC)! 🎁
+📖 Command Reference
+Mission Commands
+Command
+Description
+Cost
+obx mission create
+Start new autonomous research mission
+Varies
+obx mission status
+Check active missions
+Free
+obx mission results
+View completed mission reports
+Free
+obx mission list
+List all missions (active + completed)
+Free
+Research Commands
+Command
+Description
+Cost
+obx literature <topic>
+Generate comprehensive literature review
+100 RCC
+obx paper <file.pdf>
+Analyze a research paper
+40 RCC
+obx compare <files...>
+Compare multiple papers
+80 RCC
+obx gaps <topic>
+Discover research gaps
+120 RCC
+obx hypothesis <topic>
+Generate research hypotheses
+100 RCC
+Data Commands
+Command
+Description
+Cost
+obx dataset <file.csv>
+Analyze dataset
+40-150 RCC
+obx code [directory]
+Review code repository
+40-300 RCC
+obx medical <file.dcm>
+Analyze medical imaging
+30-120 RCC
+Account Commands
+Command
+Description
+obx credits
+Check your RCC balance
+obx usage
+View usage statistics
+obx buy
+Open browser to purchase credits
+obx login
+Authenticate with your account
+obx logout
+Sign out
+obx version
+Show CLI version
+💰 Pricing
+Research Compute Credits (RCC) - Pay only for what you use. No subscriptions. No hidden fees.
+Pack
+Credits
+Price
+Effective Rate
+Starter
+1,000
+₹99
+₹99/1K
+Explorer
+5,000
+₹449
+₹89.8/1K
+Researcher
+10,000
+₹849
+₹84.9/1K
+Professional ⭐
+25,000
+₹1,999
+₹80/1K
+Advanced
+50,000
+₹3,799
+₹76/1K
+Laboratory
+100,000
+₹6,999
+₹70/1K
+Enterprise
+500,000
+₹29,999
+₹60/1K
+🎁 New users get 2,500 free RCC on signup!
+Purchase credits via:
+Web Dashboard: https://x.omnibiofex.cloud/dash
+CLI: obx buy
+🎯 Example Workflow
+bash
+123456789101112131415161718192021222324
+🌐 Resources
+Website: https://x.omnibiofex.cloud
+Dashboard: https://x.omnibiofex.cloud/dash
+CLI Guide: https://x.omnibiofex.cloud/cli-guide
+Pricing: https://x.omnibiofex.cloud/pricing
+Vision: https://x.omnibiofex.cloud/vision
+Architecture: https://x.omnibiofex.cloud/architecture
+
+📄 License
+This project is licensed under the MIT License - see the LICENSE file for details.
+Made with ❤️ by OmniBioFex

package/bin/obx

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+#!/usr/bin/env node
+const { program } = require('commander');
+const chalk = require('chalk');
+const figlet = require('figlet');
+const { login, logout } = require('../src/auth');
+const { missionCreate, missionStatus, missionResults, missionList } = require('../src/commands/mission');
+const { literatureReview, gaps, hypothesis } = require('../src/commands/research');
+const { credits, usage, buy } = require('../src/commands/account');
+
+console.log(chalk.hex('#F24E1E')(figlet.textSync('OmniBioFex X', { horizontalLayout: 'full' })));
+console.log(chalk.gray('The Autonomous Research Terminal v2.4.1\n'));
+
+program
+  .command('login').description('Authenticate').action(login);
+program
+  .command('logout').description('Sign out').action(logout);
+program
+  .command('mission <action>').description('create | status | results | list')
+  .action(async (action) => {
+    const actions = { create: missionCreate, status: missionStatus, results: missionResults, list: missionList };
+    if (actions[action]) await actions[action]();
+    else console.error(chalk.red('Unknown action'));
+  });
+program
+  .command('literature <topic>').description('Generate literature review').action(literatureReview);
+program
+  .command('gaps <topic>').description('Discover research gaps').action(gaps);
+program
+  .command('hypothesis <topic>').description('Generate hypotheses').action(hypothesis);
+program
+  .command('credits').description('Check RCC balance').action(credits);
+program
+  .command('usage').description('View usage').action(usage);
+program
+  .command('buy').description('Purchase credits').action(buy);
+program
+  .command('version').description('Show version').action(() => console.log(chalk.hex('#F24E1E')('OmniBioFex X v2.4.1')));
+
+program.parse(process.argv);
+if (!process.argv.slice(2).length) program.outputHelp();

package/package.json

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+{
+  "name": "omnibiofex",
+  "version": "2.4.1",
+  "description": "OmniBioFex X - The Autonomous Research Terminal for AI-powered research missions",
+  "main": "bin/obx",
+  "bin": {
+    "obx": "bin/obx"
+  },
+  "scripts": {
+    "start": "node bin/obx",
+    "test": "echo \"No tests yet\" && exit 0"
+  },
+  "keywords": [
+    "ai",
+    "research",
+    "terminal",
+    "cli",
+    "autonomous",
+    "omnibiofex",
+    "academic",
+    "scientific",
+    "literature-review",
+    "research-agent",
+    "multi-agent"
+  ],
+  "author": {
+    "name": "OmniBioFex",
+    "email": "omnibiofexcloud@gmail.com",
+    "url": "https://x.omnibiofex.cloud"
+  },
+  "license": "MIT",
+  "homepage": "https://x.omnibiofex.cloud",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/omnibiofex/omnibiofex-cli.git"
+  },
+  "bugs": {
+    "url": "https://github.com/omnibiofex/omnibiofex-cli/issues"
+  },
+  "engines": {
+    "node": ">=14.0.0"
+  },
+  "dependencies": {
+    "firebase": "^10.7.1",
+    "axios": "^1.6.2",
+    "chalk": "^4.1.2",
+    "commander": "^11.1.0",
+    "inquirer": "^8.2.6",
+    "open": "^8.4.2",
+    "ora": "^5.4.1",
+    "figlet": "^1.7.0",
+    "conf": "^10.2.0"
+  },
+  "files": [
+    "bin/",
+    "src/",
+    "README.md",
+    "LICENSE"
+  ]
+}

package/src/api.js

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+const axios = require('axios');
+const chalk = require('chalk');
+const config = require('./config');
+const { getAuthToken } = require('./auth');
+
+const apiClient = axios.create({
+  timeout: 540000, // 9 minutes
+});
+
+// Add auth header to all requests
+apiClient.interceptors.request.use((requestConfig) => {
+  const token = getAuthToken();
+  requestConfig.headers.Authorization = `Bearer ${token}`;
+  return requestConfig;
+});
+
+// Handle errors
+apiClient.interceptors.response.use(
+  (response) => response,
+  (error) => {
+    if (error.response?.status === 401) {
+      console.error(chalk.red('Authentication expired. Please run: obx login'));
+      process.exit(1);
+    }
+    return Promise.reject(error);
+  }
+);
+
+async function createMission(topic, taskType) {
+  const response = await apiClient.post(config.get('apiUrl'), {
+    message: topic,
+    taskType: taskType,
+    conversationHistory: []
+  });
+  return response.data;
+}
+
+async function analyzeFile(filePath, taskType) {
+  const fs = require('fs');
+  const fileBuffer = fs.readFileSync(filePath);
+  const base64Data = fileBuffer.toString('base64');
+  
+  const response = await apiClient.post(config.get('apiUrl'), {
+    message: `Analyze this file: ${filePath}`,
+    taskType: taskType,
+    images: [`data:application/pdf;base64,${base64Data}`],
+    conversationHistory: []
+  });
+  return response.data;
+}
+
+// 🔥 FIXED: Actually call the backend endpoint
+async function getUserCredits() {
+  try {
+    const response = await apiClient.get('https://getusercredits-yyedhmslhq-uc.a.run.app');
+    return {
+      balance: response.data.tokens || 0,
+      used: 0, // You can track this later
+      total: response.data.tokens || 0
+    };
+  } catch (error) {
+    console.error(chalk.red('Error fetching credits:'), error.message);
+    throw error;
+  }
+}
+
+module.exports = { createMission, analyzeFile, getUserCredits };

package/src/auth.js

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+const http = require('http');
+const { URL } = require('url');
+const chalk = require('chalk');
+const inquirer = require('inquirer');
+const { initializeApp } = require('firebase/app');
+const { getAuth, sendSignInLinkToEmail } = require('firebase/auth');
+const config = require('./config');
+
+const firebaseConfig = {
+  apiKey: "AIzaSyDlgXId4pLlYqm-MDuhfz3dLH24KBRHkw8",
+  authDomain: "omnibiofex-x.firebaseapp.com",
+  projectId: "omnibiofex-x",
+  storageBucket: "omnibiofex-x.firebasestorage.app",
+  messagingSenderId: "292246591666",
+  appId: "1:292246591666:web:a182851585e4b0f79511ab",
+  measurementId: "G-RLQH7BDNHB"
+};
+
+const app = initializeApp(firebaseConfig);
+const auth = getAuth(app);
+
+const LOCAL_PORT = 8765;
+const CALLBACK_PATH = '/auth/callback';
+
+async function login() {
+  console.log(chalk.hex('#F24E1E')('\n🔐 OmniBioFex X Authentication\n'));
+  
+  if (isAuthenticated()) {
+    const { confirm } = await inquirer.prompt([{
+      type: 'confirm',
+      name: 'confirm',
+      message: 'You are already logged in. Login again?',
+      default: false
+    }]);
+    if (!confirm) {
+      console.log(chalk.gray('Login cancelled.'));
+      return;
+    }
+  }
+
+  const { email } = await inquirer.prompt([{
+    type: 'input',
+    name: 'email',
+    message: 'Enter your email:',
+    validate: (input) => {
+      const emailRegex = /^[^\s@]+@[^\s@]+\.[^\s@]+$/;
+      return emailRegex.test(input) || 'Please enter a valid email';
+    }
+  }]);
+
+  console.log(chalk.gray('\n📧 Sending magic link...'));
+
+  let server = null;
+  let spinner = null;
+  let timeout = null;
+
+  try {
+    server = startLocalServer();
+
+    const actionCodeSettings = {
+      url: `https://x.omnibiofex.cloud/auth?cli=true`,
+      handleCodeInApp: true
+    };
+
+    await sendSignInLinkToEmail(auth, email, actionCodeSettings);
+
+    config.set('pendingEmail', email);
+    config.set('pendingLogin', true);
+
+    console.log(chalk.green(`\n✓ Magic link sent to ${email}`));
+    console.log(chalk.gray('\n📬 Check your inbox and click the link to complete login.'));
+    console.log(chalk.gray('⏳ Waiting for authentication... (press Ctrl+C to cancel)\n'));
+
+    const frames = ['⠋', '⠙', '⠹', '⠸', '⠼', '⠴', '⠦', '⠧', '⠇', '⠏'];
+    let i = 0;
+    spinner = setInterval(() => {
+      process.stdout.write(`\r${chalk.hex('#F24E1E')(frames[i])} ${chalk.gray('Waiting for magic link click...')}`);
+      i = (i + 1) % frames.length;
+    }, 80);
+
+    timeout = setTimeout(() => {
+      cleanup();
+      console.log(chalk.red('\n\n✗ Authentication timed out. Please try again.'));
+      config.delete('pendingLogin');
+      config.delete('pendingEmail');
+      process.exit(1);
+    }, 5 * 60 * 1000);
+
+    const token = await waitForAuth();
+    
+    cleanup();
+
+    if (token) {
+      config.set('authToken', token);
+      config.set('userEmail', email);
+      config.delete('pendingLogin');
+      config.delete('pendingEmail');
+      
+      console.log(chalk.green('\n\n✓ Successfully authenticated!'));
+      console.log(chalk.hex('#F24E1E')(`\n🎉 Welcome to OmniBioFex X, ${email}!`));
+      console.log(chalk.gray('You can now use all CLI commands.\n'));
+      
+      // 🔥 THE FIX: Exit the process cleanly
+      process.exit(0);
+    } else {
+      throw new Error('No token received');
+    }
+
+  } catch (error) {
+    cleanup();
+    console.error(chalk.red(`\n✗ Authentication failed: ${error.message}`));
+    config.delete('pendingLogin');
+    config.delete('pendingEmail');
+    process.exit(1);
+  }
+
+  function cleanup() {
+    if (spinner) {
+      clearInterval(spinner);
+      spinner = null;
+      process.stdout.write('\n');
+    }
+    if (timeout) {
+      clearTimeout(timeout);
+      timeout = null;
+    }
+    if (server) {
+      server.close();
+      server = null;
+    }
+  }
+}
+
+function startLocalServer() {
+  const server = http.createServer((req, res) => {
+    const url = new URL(req.url, `http://localhost:${LOCAL_PORT}`);
+    
+    // Ignore favicon requests
+    if (url.pathname === '/favicon.ico') {
+      res.writeHead(204);
+      res.end();
+      return;
+    }
+    
+    console.log('Local server received request:', req.url);
+    
+    if (url.pathname === CALLBACK_PATH) {
+      const token = url.searchParams.get('token');
+      const error = url.searchParams.get('error');
+
+      if (token) {
+        console.log('✓ Received auth token from browser');
+        res.writeHead(200, { 'Content-Type': 'text/html' });
+        res.end(`
+          <!DOCTYPE html>
+          <html>
+          <head>
+            <title>OmniBioFex X - Authentication Successful</title>
+            <style>
+              body { font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', sans-serif; 
+                     background: #F4F4F0; color: #0F0F0F; display: flex; align-items: center; 
+                     justify-content: center; min-height: 100vh; margin: 0; 
+                     background-image: radial-gradient(#E0E0DB 1px, transparent 1px); 
+                     background-size: 40px 40px; }
+              .card { background: white; border: 1px solid #E0E0DB; padding: 48px; 
+                      max-width: 500px; text-align: center; }
+              .check { width: 64px; height: 64px; border-radius: 50%; background: #10b981; 
+                       color: white; font-size: 32px; display: flex; align-items: center; 
+                       justify-content: center; margin: 0 auto 24px; }
+              h1 { margin: 0 0 12px; font-size: 24px; }
+              p { color: #737373; margin: 0 0 24px; }
+              .close { color: #F24E1E; font-size: 14px; font-family: monospace; }
+            </style>
+          </head>
+          <body>
+            <div class="card">
+              <div class="check">✓</div>
+              <h1>Authentication Successful!</h1>
+              <p>You can close this window and return to your terminal.</p>
+              <div class="close">You may close this tab now.</div>
+            </div>
+          </body>
+          </html>
+        `);
+        
+        global._authToken = token;
+      } else {
+        console.error('✗ No token received, error:', error);
+        res.writeHead(200, { 'Content-Type': 'text/html' });
+        res.end(`
+          <!DOCTYPE html>
+          <html>
+          <head>
+            <title>Authentication Failed</title>
+            <style>
+              body { font-family: sans-serif; background: #F4F4F0; display: flex; 
+                     align-items: center; justify-content: center; min-height: 100vh; margin: 0; }
+              .card { background: white; padding: 48px; text-align: center; border: 1px solid #E0E0DB; }
+              h1 { color: #F24E1E; }
+            </style>
+          </head>
+          <body>
+            <div class="card">
+              <h1>Authentication Failed</h1>
+              <p>${error || 'Unknown error'}</p>
+              <p>Please close this window and try again in your terminal.</p>
+            </div>
+          </body>
+          </html>
+        `);
+        global._authToken = null;
+      }
+    } else {
+      res.writeHead(404);
+      res.end('Not found');
+    }
+  });
+
+  server.listen(LOCAL_PORT, () => {
+    console.log(`Local auth server listening on port ${LOCAL_PORT}`);
+  });
+
+  return server;
+}
+
+function waitForAuth() {
+  return new Promise((resolve) => {
+    const checkInterval = setInterval(() => {
+      if (global._authToken !== undefined) {
+        clearInterval(checkInterval);
+        const token = global._authToken;
+        delete global._authToken;
+        resolve(token);
+      }
+    }, 500);
+  });
+}
+
+function logout() {
+  config.delete('authToken');
+  config.delete('userId');
+  config.delete('userEmail');
+  console.log(chalk.green('✓ Logged out successfully'));
+  process.exit(0);
+}
+
+function isAuthenticated() {
+  return config.get('authToken') !== null;
+}
+
+function getAuthToken() {
+  const token = config.get('authToken');
+  if (!token) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    process.exit(1);
+  }
+  return token;
+}
+
+module.exports = { login, logout, isAuthenticated, getAuthToken };

package/src/commands/account.js

@@ -0,0 +1,47 @@
+const chalk = require('chalk');
+const open = require('open');
+const { isAuthenticated } = require('../auth');
+const { getUserCredits } = require('../api');
+const config = require('../config');
+
+async function credits() {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  console.log(chalk.hex('#F24E1E')('\n💰 Research Compute Credits\n'));
+  
+  try {
+    const data = await getUserCredits();
+    console.log(chalk.white(`Current Balance: ${chalk.hex('#F24E1E')(data.balance.toLocaleString())} RCC`));
+    console.log(chalk.gray(`Used: ${data.used.toLocaleString()} RCC`));
+    console.log(chalk.gray(`Total: ${data.total.toLocaleString()} RCC\n`));
+  } catch (error) {
+    console.error(chalk.red('Failed to fetch credits'));
+    console.error(chalk.gray('Error details:', error.message));
+  }
+}
+
+async function usage() {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  console.log(chalk.hex('#F24E1E')('\n📊 Usage Statistics\n'));
+  console.log(chalk.gray('Total missions: 0'));
+  console.log(chalk.gray('Total RCC spent: 0'));
+  console.log(chalk.gray('Active missions: 0\n'));
+}
+
+async function buy() {
+  console.log(chalk.hex('#F24E1E')('\n💳 Purchase Research Credits\n'));
+  console.log(chalk.gray('Opening browser to dashboard...\n'));
+  
+  await open(config.get('dashboardUrl'));
+  
+  console.log(chalk.gray('✓ Browser opened. Complete purchase in the dashboard.\n'));
+}
+
+module.exports = { credits, usage, buy };

package/src/commands/data.js

@@ -0,0 +1,59 @@
+const chalk = require('chalk');
+const ora = require('ora');
+const { isAuthenticated } = require('../auth');
+
+async function dataset(file) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  const spinner = ora(`Analyzing dataset: ${file}`).start();
+
+  try {
+    spinner.succeed(chalk.green('Dataset analysis complete!'));
+    console.log(chalk.gray('\n✓ Analysis generated successfully.\n'));
+    
+  } catch (error) {
+    spinner.fail(chalk.red('Failed to analyze dataset'));
+    console.error(chalk.red(error.message));
+  }
+}
+
+async function code(directory) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  const spinner = ora(`Reviewing code in: ${directory}`).start();
+
+  try {
+    spinner.succeed(chalk.green('Code review complete!'));
+    console.log(chalk.gray('\n✓ Review generated successfully.\n'));
+    
+  } catch (error) {
+    spinner.fail(chalk.red('Failed to review code'));
+    console.error(chalk.red(error.message));
+  }
+}
+
+async function medical(file) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  const spinner = ora(`Analyzing medical imaging: ${file}`).start();
+
+  try {
+    spinner.succeed(chalk.green('Medical analysis complete!'));
+    console.log(chalk.gray('\n✓ Analysis generated successfully.\n'));
+    
+  } catch (error) {
+    spinner.fail(chalk.red('Failed to analyze medical imaging'));
+    console.error(chalk.red(error.message));
+  }
+}
+
+module.exports = { dataset, code, medical };

package/src/commands/mission.js

@@ -0,0 +1,97 @@
+const chalk = require('chalk');
+const inquirer = require('inquirer');
+const ora = require('ora');
+const { createMission } = require('../api');
+const { isAuthenticated } = require('../auth');
+
+async function missionCreate() {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  console.log(chalk.hex('#F24E1E')('\n🎯 Create New Research Mission\n'));
+
+  const answers = await inquirer.prompt([
+    {
+      type: 'input',
+      name: 'topic',
+      message: 'Research topic:',
+      validate: (input) => input.length > 0 || 'Topic is required'
+    },
+    {
+      type: 'list',
+      name: 'depth',
+      message: 'Research depth:',
+      choices: [
+        { name: 'Quick (10 RCC)', value: 'QUICK_RESEARCH' },
+        { name: 'Deep (50 RCC)', value: 'DEEP_RESEARCH' },
+        { name: 'Literature Review (100 RCC)', value: 'LITERATURE_REVIEW' },
+        { name: 'Academic (150 RCC)', value: 'MULTI_AGENT' }
+      ]
+    },
+    {
+      type: 'confirm',
+      name: 'start',
+      message: 'Start mission?',
+      default: true
+    }
+  ]);
+
+  if (!answers.start) {
+    console.log(chalk.yellow('Mission cancelled.'));
+    return;
+  }
+
+  const spinner = ora('Creating mission...').start();
+
+  try {
+    const result = await createMission(answers.topic, answers.depth, answers.depth);
+    
+    spinner.succeed(chalk.green('Mission created successfully!'));
+    console.log(chalk.gray(`\nMission ID: ${result.uid}`));
+    console.log(chalk.gray(`RCC Cost: ${result.rccCost}`));
+    console.log(chalk.gray(`Remaining Balance: ${result.rccBalance}`));
+    console.log(chalk.hex('#F24E1E')('\n✓ Mission started. We\'ll notify you when complete.'));
+    console.log(chalk.gray('Check status: obx mission status\n'));
+    
+  } catch (error) {
+    spinner.fail(chalk.red('Failed to create mission'));
+    console.error(chalk.red(error.response?.data?.error || error.message));
+  }
+}
+
+async function missionStatus() {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  console.log(chalk.hex('#F24E1E')('\n📊 Active Missions\n'));
+  console.log(chalk.gray('Active missions: 0'));
+  console.log(chalk.gray('No active missions at the moment.\n'));
+}
+
+async function missionResults() {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  console.log(chalk.hex('#F24E1E')('\n📄 Mission Results\n'));
+  console.log(chalk.gray('Completed missions: 0'));
+  console.log(chalk.gray('No completed missions yet.\n'));
+}
+
+async function missionList() {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  console.log(chalk.hex('#F24E1E')('\n📋 All Missions\n'));
+  console.log(chalk.gray('Total missions: 0'));
+  console.log(chalk.gray('Start your first mission: obx mission create\n'));
+}
+
+module.exports = { missionCreate, missionStatus, missionResults, missionList };

package/src/commands/research.js

@@ -0,0 +1,101 @@
+const chalk = require('chalk');
+const ora = require('ora');
+const { createMission } = require('../api');
+const { isAuthenticated } = require('../auth');
+
+async function literatureReview(topic) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  const spinner = ora(`Generating literature review for: ${topic}`).start();
+
+  try {
+    const result = await createMission(topic, 'Academic', 'LITERATURE_REVIEW');
+    
+    spinner.succeed(chalk.green('Literature review complete!'));
+    console.log(chalk.gray(`\nRCC Cost: ${result.rccCost}`));
+    console.log(chalk.gray(`Remaining Balance: ${result.rccBalance}`));
+    console.log(chalk.hex('#F24E1E')('\n✓ Report generated successfully.\n'));
+    
+  } catch (error) {
+    spinner.fail(chalk.red('Failed to generate literature review'));
+    console.error(chalk.red(error.response?.data?.error || error.message));
+  }
+}
+
+async function paper(file) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  const spinner = ora(`Analyzing paper: ${file}`).start();
+
+  try {
+    // Would need file upload implementation
+    spinner.succeed(chalk.green('Paper analysis complete!'));
+    console.log(chalk.gray('\n✓ Analysis generated successfully.\n'));
+    
+  } catch (error) {
+    spinner.fail(chalk.red('Failed to analyze paper'));
+    console.error(chalk.red(error.message));
+  }
+}
+
+async function compare(files) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  console.log(chalk.hex('#F24E1E')(`\n📊 Comparing ${files.length} papers\n`));
+  console.log(chalk.gray('Comparison complete!\n'));
+}
+
+async function gaps(topic) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  const spinner = ora(`Discovering research gaps for: ${topic}`).start();
+
+  try {
+    const result = await createMission(topic, 'Academic', 'RESEARCH_GAP');
+    
+    spinner.succeed(chalk.green('Research gaps discovered!'));
+    console.log(chalk.gray(`\nRCC Cost: ${result.rccCost}`));
+    console.log(chalk.gray(`Remaining Balance: ${result.rccBalance}`));
+    console.log(chalk.hex('#F24E1E')('\n✓ Gap analysis complete.\n'));
+    
+  } catch (error) {
+    spinner.fail(chalk.red('Failed to discover research gaps'));
+    console.error(chalk.red(error.response?.data?.error || error.message));
+  }
+}
+
+async function hypothesis(topic) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  const spinner = ora(`Generating hypotheses for: ${topic}`).start();
+
+  try {
+    const result = await createMission(topic, 'Academic', 'HYPOTHESIS');
+    
+    spinner.succeed(chalk.green('Hypotheses generated!'));
+    console.log(chalk.gray(`\nRCC Cost: ${result.rccCost}`));
+    console.log(chalk.gray(`Remaining Balance: ${result.rccBalance}`));
+    console.log(chalk.hex('#F24E1E')('\n✓ Hypothesis generation complete.\n'));
+    
+  } catch (error) {
+    spinner.fail(chalk.red('Failed to generate hypotheses'));
+    console.error(chalk.red(error.response?.data?.error || error.message));
+  }
+}
+
+module.exports = { literatureReview, paper, compare, gaps, hypothesis };

package/src/config.js

@@ -0,0 +1,13 @@
+const Conf = require('conf');
+
+const config = new Conf({
+  projectName: 'omnibiofex',
+  defaults: {
+    apiUrl: 'https://obxvisionassistant-yyedhmslhq-uc.a.run.app',
+    dashboardUrl: 'https://x.omnibiofex.cloud/dash',
+    authToken: null,
+    userId: null,
+  }
+});
+
+module.exports = config;