proagents 1.6.7 → 1.6.9

package/lib/commands/ai.js

@@ -1,4 +1,4 @@
-import { existsSync, cpSync, mkdirSync, readFileSync, writeFileSync } from 'fs';
+import { existsSync, cpSync, mkdirSync, readFileSync, writeFileSync, rmSync } from 'fs';
 import { join, dirname } from 'path';
 import { fileURLToPath } from 'url';
 import { createInterface } from 'readline';
@@ -49,8 +49,9 @@ export function getPlatformById(id) {
 
 /**
  * Interactive platform selection using readline
+ * @param {string[]} previouslySelected - Previously selected platforms (from interrupted setup)
  */
-export async function selectPlatforms() {
+export async function selectPlatforms(previouslySelected = []) {
   const rl = createInterface({
     input: process.stdin,
     output: process.stdout
@@ -63,12 +64,16 @@ export async function selectPlatforms() {
 
   let index = 1;
   const indexMap = {};
+  const preSelectedIndices = [];
 
   // IDE-based platforms
   console.log(chalk.cyan.bold(`  ${AI_PLATFORMS.ide.label}:`));
   for (const platform of AI_PLATFORMS.ide.platforms) {
-    console.log(chalk.white(`    ${index}. ${platform.name}`) + chalk.gray(` - ${platform.desc}`));
+    const wasSelected = previouslySelected && previouslySelected.includes(platform.id);
+    const marker = wasSelected ? chalk.green(' ✓ (previously selected)') : '';
+    console.log(chalk.white(`    ${index}. ${platform.name}`) + chalk.gray(` - ${platform.desc}`) + marker);
     indexMap[index] = platform.id;
+    if (wasSelected) preSelectedIndices.push(index);
     index++;
   }
 
@@ -77,16 +82,29 @@ export async function selectPlatforms() {
   // Web-based platforms
   console.log(chalk.cyan.bold(`  ${AI_PLATFORMS.web.label}:`));
   for (const platform of AI_PLATFORMS.web.platforms) {
-    console.log(chalk.white(`    ${index}. ${platform.name}`) + chalk.gray(` - ${platform.desc}`));
+    const wasSelected = previouslySelected && previouslySelected.includes(platform.id);
+    const marker = wasSelected ? chalk.green(' ✓ (previously selected)') : '';
+    console.log(chalk.white(`    ${index}. ${platform.name}`) + chalk.gray(` - ${platform.desc}`) + marker);
     indexMap[index] = platform.id;
+    if (wasSelected) preSelectedIndices.push(index);
     index++;
   }
 
   console.log('');
 
-  const answer = await question(chalk.yellow('Your selection (e.g., 1,2,3 or "all"): '));
+  // Show default based on previous selection
+  const defaultHint = preSelectedIndices.length > 0
+    ? `Enter for previous: ${preSelectedIndices.join(',')}`
+    : 'e.g., 1,2,3 or "all"';
+
+  const answer = await question(chalk.yellow(`Your selection (${defaultHint}): `));
   rl.close();
 
+  // If user just pressed enter and we have previous selections, use them
+  if (answer.trim() === '' && preSelectedIndices.length > 0) {
+    return previouslySelected;
+  }
+
   if (answer.toLowerCase() === 'all') {
     return getAllPlatforms().map(p => p.id);
   }
@@ -131,6 +149,46 @@ function extractProagentsSection(content) {
   return null;
 }
 
+/**
+ * Remove only ProAgents section from a file, keep user's original content
+ * Returns: 'deleted' (file removed), 'cleaned' (section removed), 'skipped' (no ProAgents section)
+ */
+function removeProagentsSectionFromFile(filePath) {
+  try {
+    const content = readFileSync(filePath, 'utf-8');
+
+    const startIndex = content.indexOf(PROAGENTS_START);
+    const endIndex = content.indexOf(PROAGENTS_END);
+
+    if (startIndex !== -1 && endIndex !== -1) {
+      // Has ProAgents section - remove it, keep the rest
+      const before = content.substring(0, startIndex).trim();
+      const after = content.substring(endIndex + PROAGENTS_END.length).trim();
+      const remaining = (before + '\n\n' + after).trim();
+
+      if (remaining.length === 0) {
+        // File only had ProAgents content - delete it
+        rmSync(filePath, { force: true });
+        return 'deleted';
+      } else {
+        // File has other content - keep it, remove only ProAgents section
+        writeFileSync(filePath, remaining + '\n');
+        return 'cleaned';
+      }
+    } else {
+      // No ProAgents markers - file was created by ProAgents (not merged)
+      // Check if it's a ProAgents-generated file by looking for ProAgents reference
+      if (content.includes('proagents') || content.includes('ProAgents') || content.includes('.proagents/')) {
+        rmSync(filePath, { force: true });
+        return 'deleted';
+      }
+      return 'skipped';
+    }
+  } catch (error) {
+    return 'skipped';
+  }
+}
+
 /**
  * Merge ProAgents instructions with existing file content
  * - If file doesn't exist: create with ProAgents content
@@ -247,6 +305,51 @@ export function loadPlatformConfig(configPath) {
   }
 }
 
+/**
+ * Check if a file contains ProAgents content
+ */
+function hasProagentsContent(filePath) {
+  try {
+    const content = readFileSync(filePath, 'utf-8');
+    // Check for ProAgents markers or references
+    return content.includes(PROAGENTS_START) ||
+           content.includes('.proagents/') ||
+           content.includes('ProAgents Commands');
+  } catch {
+    return false;
+  }
+}
+
+/**
+ * Detect installed platforms by checking for actual files with ProAgents content
+ * Only counts as installed if the file has ProAgents-related content
+ */
+export function detectInstalledPlatforms(targetDir) {
+  const installed = [];
+
+  for (const platform of getAllPlatforms()) {
+    const filePath = join(targetDir, platform.file);
+    if (existsSync(filePath) && hasProagentsContent(filePath)) {
+      installed.push(platform.id);
+    }
+  }
+
+  return installed;
+}
+
+/**
+ * Get installed platforms - combines config and file detection
+ * Returns platforms that are either in config OR have files present
+ */
+export function getInstalledPlatforms(targetDir, configPath) {
+  const fromConfig = loadPlatformConfig(configPath);
+  const fromFiles = detectInstalledPlatforms(targetDir);
+
+  // Merge both sources, remove duplicates
+  const combined = [...new Set([...fromConfig, ...fromFiles])];
+  return combined;
+}
+
 /**
  * Show available platforms that can be added
  */
@@ -294,7 +397,7 @@ export async function aiAddCommand() {
   const targetDir = process.cwd();
   const proagentsDir = join(targetDir, '.proagents');
   const sourceDir = join(__dirname, '..', '..', '.proagents');
-  const configPath = join(proagentsDir, 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
 
   // Check if proagents is initialized
   if (!existsSync(proagentsDir)) {
@@ -302,8 +405,8 @@ export async function aiAddCommand() {
     return;
   }
 
-  // Load current platforms
-  const currentIds = loadPlatformConfig(configPath);
+  // Detect from both config AND actual files
+  const currentIds = getInstalledPlatforms(targetDir, configPath);
 
   console.log(chalk.bold.blue('\nProAgents - Add AI Platform'));
   console.log(chalk.blue('===========================\n'));
@@ -361,7 +464,7 @@ export async function aiAddCommand() {
   }
 
   console.log(chalk.gray('\nAI instruction files added to project root.'));
-  console.log(chalk.gray('Config updated in .proagents/proagents.config.yaml\n'));
+  console.log(chalk.gray('Config updated in proagents.config.yaml\n'));
 }
 
 /**
@@ -370,9 +473,10 @@ export async function aiAddCommand() {
 export function aiListCommand() {
   const targetDir = process.cwd();
   const proagentsDir = join(targetDir, '.proagents');
-  const configPath = join(proagentsDir, 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
 
-  const currentIds = loadPlatformConfig(configPath);
+  // Detect from both config AND actual files
+  const currentIds = getInstalledPlatforms(targetDir, configPath);
 
   console.log(chalk.bold.blue('\nProAgents - AI Platforms'));
   console.log(chalk.blue('========================\n'));
@@ -387,17 +491,18 @@ export function aiListCommand() {
 export async function aiRemoveCommand() {
   const targetDir = process.cwd();
   const proagentsDir = join(targetDir, '.proagents');
-  const configPath = join(proagentsDir, 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
 
   if (!existsSync(proagentsDir)) {
     console.log(chalk.red('\n✗ ProAgents not initialized.\n'));
     return;
   }
 
-  const currentIds = loadPlatformConfig(configPath);
+  // Detect from both config AND actual files
+  const currentIds = getInstalledPlatforms(targetDir, configPath);
 
   if (currentIds.length === 0) {
-    console.log(chalk.yellow('\nNo AI platforms configured.\n'));
+    console.log(chalk.yellow('\nNo AI platforms installed.\n'));
     return;
   }
 
@@ -443,12 +548,36 @@ export async function aiRemoveCommand() {
     return;
   }
 
-  // Remove from config (don't delete files - user might have customized them)
+  // Remove from config
   const newIds = currentIds.filter(id => !toRemove.includes(id));
   savePlatformConfig(newIds, configPath);
 
-  const removedNames = toRemove.map(id => getPlatformById(id)?.name).filter(Boolean);
-  console.log(chalk.green(`\n✓ Removed from config: ${removedNames.join(', ')}`));
-  console.log(chalk.gray('Note: AI instruction files in project root were not deleted.'));
-  console.log(chalk.gray('You can manually delete them if needed.\n'));
+  // Remove ProAgents sections from AI files (smart removal - keeps user content)
+  const results = { deleted: [], cleaned: [], skipped: [] };
+
+  for (const id of toRemove) {
+    const platform = getPlatformById(id);
+    if (!platform) continue;
+
+    const filePath = join(targetDir, platform.file);
+    if (existsSync(filePath)) {
+      const result = removeProagentsSectionFromFile(filePath);
+      if (result === 'deleted') {
+        results.deleted.push(platform.name);
+      } else if (result === 'cleaned') {
+        results.cleaned.push(platform.name);
+      }
+    }
+  }
+
+  // Show results
+  console.log('');
+  if (results.deleted.length > 0) {
+    console.log(chalk.green(`✓ Removed: ${results.deleted.join(', ')}`));
+  }
+  if (results.cleaned.length > 0) {
+    console.log(chalk.green(`✓ Cleaned ProAgents section from: ${results.cleaned.join(', ')} (kept your custom config)`));
+  }
+
+  console.log(chalk.gray('\nConfig updated in proagents.config.yaml\n'));
 }

package/lib/commands/config.js

@@ -28,12 +28,12 @@ export function configListCommand() {
   // 1. Main Config
   console.log(chalk.cyan.bold('1. Main Configuration'));
   console.log(chalk.gray('   ─────────────────────────────────────────'));
-  const configPath = join(proagentsDir, 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
   if (existsSync(configPath)) {
-    console.log(chalk.green('   ✓ ') + chalk.white('.proagents/proagents.config.yaml'));
+    console.log(chalk.green('   ✓ ') + chalk.white('proagents.config.yaml'));
     console.log(chalk.gray('     Checkpoints, git settings, parallel features, etc.\n'));
   } else {
-    console.log(chalk.yellow('   ○ ') + chalk.white('.proagents/proagents.config.yaml') + chalk.gray(' (not created)\n'));
+    console.log(chalk.yellow('   ○ ') + chalk.white('proagents.config.yaml') + chalk.gray(' (not created)\n'));
   }
 
   // 2. AI Platforms
@@ -184,7 +184,7 @@ export function configListCommand() {
  */
 export function configShowCommand() {
   const targetDir = process.cwd();
-  const configPath = join(targetDir, '.proagents', 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
 
   console.log('\n' + chalk.bold.blue('ProAgents Current Configuration'));
   console.log(chalk.blue('================================\n'));
@@ -198,7 +198,7 @@ export function configShowCommand() {
     const content = readFileSync(configPath, 'utf-8');
     const config = yaml.load(content);
 
-    console.log(chalk.cyan('File: ') + chalk.white('.proagents/proagents.config.yaml\n'));
+    console.log(chalk.cyan('File: ') + chalk.white('proagents.config.yaml\n'));
     console.log(chalk.gray('─────────────────────────────────────────────\n'));
     console.log(content);
   } catch (error) {
@@ -212,7 +212,7 @@ export function configShowCommand() {
  */
 export function configEditCommand() {
   const targetDir = process.cwd();
-  const configPath = join(targetDir, '.proagents', 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
 
   if (!existsSync(configPath)) {
     console.log(chalk.yellow('\nConfig file not found. Run "proagents init" first.\n'));
@@ -220,7 +220,7 @@ export function configEditCommand() {
   }
 
   console.log(chalk.cyan('\nTo edit configuration:\n'));
-  console.log(chalk.white('  Open: ') + chalk.green('.proagents/proagents.config.yaml'));
+  console.log(chalk.white('  Open: ') + chalk.green('proagents.config.yaml'));
   console.log(chalk.white('  Docs: ') + chalk.green('.proagents/config/README.md\n'));
 }
 
@@ -261,7 +261,7 @@ function parseValue(value) {
  */
 export function configSetCommand(key, value) {
   const targetDir = process.cwd();
-  const configPath = join(targetDir, '.proagents', 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
 
   console.log('');
 
@@ -297,7 +297,7 @@ export function configSetCommand(key, value) {
  */
 export function configGetCommand(key) {
   const targetDir = process.cwd();
-  const configPath = join(targetDir, '.proagents', 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
 
   console.log('');
 
@@ -324,13 +324,25 @@ export function configGetCommand(key) {
   }
 }
 
+/**
+ * Save config setup progress (for resume after interrupt)
+ */
+function saveSetupProgress(configPath, config, step) {
+  config._config_setup = {
+    last_step: step,
+    timestamp: new Date().toISOString()
+  };
+  const yamlContent = yaml.dump(config, { indent: 2, lineWidth: 120 });
+  writeFileSync(configPath, yamlContent);
+}
+
 /**
  * Command: proagents config setup
  * Interactive wizard for main configuration
  */
 export async function configSetupCommand() {
   const targetDir = process.cwd();
-  const configPath = join(targetDir, '.proagents', 'proagents.config.yaml');
+  const configPath = join(targetDir, 'proagents.config.yaml');
 
   console.log('\n' + chalk.bold.blue('ProAgents Configuration Wizard'));
   console.log(chalk.blue('===============================\n'));
@@ -366,15 +378,22 @@ export async function configSetupCommand() {
       config = yaml.load(readFileSync(configPath, 'utf-8')) || {};
     }
 
+    // Check for interrupted setup
+    if (config._config_setup) {
+      console.log(chalk.cyan('📋 Resuming with your previous choices...\n'));
+    }
+
     console.log(chalk.cyan('Project Settings\n'));
 
     // Project settings
     config.project = config.project || {};
     config.project.name = await question('Project name', config.project.name || 'My Project');
+    saveSetupProgress(configPath, config, 'project_name');
 
     const projectTypes = ['web-frontend', 'fullstack', 'mobile', 'backend'];
     console.log(chalk.gray('  Types: ' + projectTypes.join(', ')));
     config.project.type = await question('Project type', config.project.type || 'fullstack');
+    saveSetupProgress(configPath, config, 'project_type');
 
     console.log('\n' + chalk.cyan('Checkpoints (pause for approval)\n'));
 
@@ -386,12 +405,14 @@ export async function configSetupCommand() {
     config.checkpoints.after_implementation = await yesNo('Pause after implementation?', config.checkpoints.after_implementation ?? false);
     config.checkpoints.after_testing = await yesNo('Pause after testing?', config.checkpoints.after_testing ?? false);
     config.checkpoints.before_deployment = await yesNo('Pause before deployment?', config.checkpoints.before_deployment ?? true);
+    saveSetupProgress(configPath, config, 'checkpoints');
 
     console.log('\n' + chalk.cyan('Git Settings\n'));
 
     // Git settings
     config.git = config.git || {};
     config.git.enabled = await yesNo('Enable git integration?', config.git.enabled ?? true);
+    saveSetupProgress(configPath, config, 'git_enabled');
 
     if (config.git.enabled) {
       config.git.branch_prefix = await question('Branch prefix', config.git.branch_prefix || 'feature/');
@@ -400,6 +421,7 @@ export async function configSetupCommand() {
       console.log(chalk.gray('  Conventions: ' + conventions.join(', ')));
       config.git.commit_convention = await question('Commit convention', config.git.commit_convention || 'conventional');
       config.git.require_pr = await yesNo('Require pull requests?', config.git.require_pr ?? true);
+      saveSetupProgress(configPath, config, 'git');
     }
 
     console.log('\n' + chalk.cyan('Parallel Features\n'));
@@ -407,20 +429,25 @@ export async function configSetupCommand() {
     // Parallel features
     config.parallel_features = config.parallel_features || {};
     config.parallel_features.enabled = await yesNo('Enable parallel features?', config.parallel_features.enabled ?? true);
+    saveSetupProgress(configPath, config, 'parallel_enabled');
 
     if (config.parallel_features.enabled) {
       const maxStr = await question('Max concurrent features', String(config.parallel_features.max_concurrent || 3));
       config.parallel_features.max_concurrent = parseInt(maxStr) || 3;
+      saveSetupProgress(configPath, config, 'parallel');
     }
 
     rl.close();
 
-    // Save config
+    // Remove setup progress marker (setup complete)
+    delete config._config_setup;
+
+    // Save final config
     const header = `# ProAgents Configuration\n# Generated by setup wizard\n# Last updated: ${new Date().toISOString().split('T')[0]}\n\n`;
     const yamlContent = yaml.dump(config, { indent: 2, lineWidth: 120 });
     writeFileSync(configPath, header + yamlContent);
 
-    console.log(chalk.green('\n✓ Configuration saved to proagents/proagents.config.yaml\n'));
+    console.log(chalk.green('\n✓ Configuration saved to proagents.config.yaml\n'));
 
   } catch (error) {
     rl.close();

package/lib/commands/init.js

@@ -595,6 +595,77 @@ function detectProjectType(targetDir) {
   return detectedTypes;
 }
 
+/**
+ * Check if setup was interrupted (incomplete)
+ * Returns true if .proagents exists but setup wasn't completed
+ */
+function checkIncompleteSetup(targetDir) {
+  const configPath = join(targetDir, 'proagents.config.yaml');
+  const readmePath = join(targetDir, 'README.md');
+  const gitignorePath = join(targetDir, '.gitignore');
+
+  // Check 1: No config file in root = incomplete
+  if (!existsSync(configPath)) {
+    return true;
+  }
+
+  // Check 2: No AI instruction files at all = incomplete
+  const aiFiles = ['CLAUDE.md', '.cursorrules', '.windsurfrules', 'CHATGPT.md', 'GEMINI.md'];
+  const hasAnyAiFile = aiFiles.some(f => existsSync(join(targetDir, f)));
+  if (!hasAnyAiFile) {
+    return true;
+  }
+
+  // Check 3: README exists but no ProAgents section = incomplete
+  if (existsSync(readmePath)) {
+    const readmeContent = readFileSync(readmePath, 'utf-8');
+    if (!readmeContent.includes('PROAGENTS:START')) {
+      return true;
+    }
+  }
+
+  // Check 4: .gitignore exists but no proagents entry = incomplete
+  if (existsSync(gitignorePath)) {
+    const gitignoreContent = readFileSync(gitignorePath, 'utf-8');
+    if (!gitignoreContent.includes('.proagents')) {
+      return true;
+    }
+  }
+
+  return false;
+}
+
+/**
+ * Prompt user for what to do with incomplete setup
+ */
+async function promptIncompleteSetupChoice() {
+  const rl = createInterface({
+    input: process.stdin,
+    output: process.stdout
+  });
+
+  const question = (prompt) => new Promise(resolve => rl.question(prompt, resolve));
+
+  console.log(chalk.cyan('What would you like to do?'));
+  console.log(chalk.white('  1. Continue setup') + chalk.green(' (recommended)'));
+  console.log(chalk.gray('     Complete the remaining setup steps'));
+  console.log('');
+  console.log(chalk.white('  2. Restart fresh'));
+  console.log(chalk.gray('     Remove everything and start over'));
+  console.log('');
+  console.log(chalk.white('  3. Update only'));
+  console.log(chalk.gray('     Just update framework files, skip setup'));
+  console.log('');
+
+  const choice = await question(chalk.yellow('  Choose (1, 2, or 3, default=1): '));
+  rl.close();
+
+  const trimmed = choice.trim();
+  if (trimmed === '2') return 'restart';
+  if (trimmed === '3') return 'update';
+  return 'continue';
+}
+
 /**
  * Prompt user for .gitignore preference
  */
@@ -626,8 +697,10 @@ async function promptGitignoreChoice() {
 
 /**
  * Interactive prompt for project configuration
+ * @param {string} targetDir - The target directory
+ * @param {object} existingConfig - Existing partial config from interrupted setup
  */
-async function promptProjectConfig(targetDir) {
+async function promptProjectConfig(targetDir, existingConfig = {}) {
   const rl = createInterface({
     input: process.stdin,
     output: process.stdout
@@ -635,12 +708,19 @@ async function promptProjectConfig(targetDir) {
 
   const question = (prompt) => new Promise(resolve => rl.question(prompt, resolve));
 
+  // Get saved values from interrupted setup
+  const savedProject = existingConfig.project || {};
+  const savedName = savedProject.name;
+  const savedType = savedProject.type;
+
   // Detect project name
-  const detectedName = detectProjectName(targetDir);
+  const detectedName = savedName || detectProjectName(targetDir);
 
   // Detect project types
   const detectedTypes = detectProjectType(targetDir);
-  const topDetectedType = detectedTypes.length > 0 ? detectedTypes[0] : null;
+  const topDetectedType = savedType
+    ? PROJECT_TYPES.find(t => t.id === savedType)
+    : (detectedTypes.length > 0 ? detectedTypes[0] : null);
 
   // Detect tech stack
   const detectedTechStack = detectTechStack(targetDir);
@@ -648,9 +728,16 @@ async function promptProjectConfig(targetDir) {
   console.log(chalk.bold('\nProject Configuration'));
   console.log(chalk.gray('─'.repeat(40) + '\n'));
 
+  // Show resume notice if we have saved values
+  if (savedName || savedType) {
+    console.log(chalk.cyan('📋 Resuming with your previous choices...\n'));
+  }
+
   // Project Name
   console.log(chalk.cyan('Project Name'));
-  if (detectedName) {
+  if (savedName) {
+    console.log(chalk.green(`  Previously saved: ${savedName}`));
+  } else if (detectedName) {
     console.log(chalk.gray(`  Detected: ${detectedName}`));
   }
   const nameInput = await question(chalk.yellow(`  Enter name (press Enter for "${detectedName}"): `));
@@ -765,6 +852,44 @@ function applyTemplate(templateId, targetDir) {
   };
 }
 
+/**
+ * Load existing partial config (for resume after interrupted setup)
+ */
+function loadPartialConfig(configPath) {
+  if (!existsSync(configPath)) return {};
+
+  try {
+    const content = readFileSync(configPath, 'utf-8');
+    return yaml.load(content) || {};
+  } catch {
+    return {};
+  }
+}
+
+/**
+ * Save partial config progress (called after each setup step)
+ */
+function savePartialConfig(configPath, updates) {
+  let config = loadPartialConfig(configPath);
+
+  // Deep merge updates into config
+  for (const [key, value] of Object.entries(updates)) {
+    if (typeof value === 'object' && value !== null && !Array.isArray(value)) {
+      config[key] = { ...(config[key] || {}), ...value };
+    } else {
+      config[key] = value;
+    }
+  }
+
+  // Add setup progress marker
+  config._setup = config._setup || {};
+  config._setup.last_step = updates._step || config._setup.last_step;
+  config._setup.timestamp = new Date().toISOString();
+
+  const yamlContent = yaml.dump(config, { indent: 2, lineWidth: 120 });
+  writeFileSync(configPath, yamlContent);
+}
+
 /**
  * Save project config to proagents.config.yaml
  */
@@ -829,6 +954,10 @@ export async function initCommand(options = {}) {
   const targetDir = process.cwd();
   const proagentsDir = join(targetDir, '.proagents');
   const sourceDir = join(__dirname, '..', '..', '.proagents');
+  const configPath = join(targetDir, 'proagents.config.yaml');
+
+  // Load any existing partial config (from interrupted setup)
+  const existingConfig = loadPartialConfig(configPath);
 
   console.log('\n' + chalk.bold.blue('ProAgents Initialization'));
   console.log(chalk.blue('========================\n'));
@@ -836,24 +965,56 @@ export async function initCommand(options = {}) {
   // Check if already initialized
   const alreadyInitialized = existsSync(proagentsDir);
 
+  // Check for incomplete setup (user killed terminal mid-setup)
+  const isIncompleteSetup = alreadyInitialized && checkIncompleteSetup(targetDir);
+
   if (alreadyInitialized && !options.force) {
-    // Smart update mode - preserve user files, update framework
-    console.log(chalk.cyan('ℹ️  ProAgents detected. Running smart update...'));
-    console.log(chalk.gray('   (Preserving your customizations)\n'));
+    if (isIncompleteSetup) {
+      // Incomplete setup detected - ask user what to do
+      console.log(chalk.yellow('⚠️  Incomplete setup detected!'));
+      console.log(chalk.gray('   Previous setup was interrupted before completion.\n'));
+
+      const choice = await promptIncompleteSetupChoice();
+
+      if (choice === 'continue') {
+        console.log(chalk.cyan('\nContinuing setup...\n'));
+        // Fall through to fresh install (but keep .proagents folder)
+      } else if (choice === 'restart') {
+        console.log(chalk.cyan('\nRestarting fresh setup...\n'));
+        rmSync(proagentsDir, { recursive: true, force: true });
+        // Fall through to fresh install
+      } else {
+        // Update only
+        console.log(chalk.cyan('\nRunning smart update...\n'));
+        try {
+          await smartUpdate(sourceDir, proagentsDir);
+          console.log(chalk.green('\n✓ ProAgents updated successfully!\n'));
+          return;
+        } catch (error) {
+          console.error(chalk.red('\n✗ Error updating ProAgents:'));
+          console.error(chalk.red(error.message));
+          process.exit(1);
+        }
+      }
+    } else {
+      // Complete setup exists - run smart update
+      console.log(chalk.cyan('ℹ️  ProAgents detected. Running smart update...'));
+      console.log(chalk.gray('   (Preserving your customizations)\n'));
 
-    try {
-      await smartUpdate(sourceDir, proagentsDir);
-      console.log(chalk.green('\n✓ ProAgents updated successfully!\n'));
-      console.log(chalk.gray('Preserved:'));
-      console.log(chalk.gray('  • active-features/ (your work in progress)'));
-      console.log(chalk.gray('  • proagents.config.yaml (your values + new options merged)'));
-      console.log(chalk.gray('  • .learning/ (learned patterns)'));
-      console.log(chalk.gray('  • cache/ (analysis cache)\n'));
-      return;
-    } catch (error) {
-      console.error(chalk.red('\n✗ Error updating ProAgents:'));
-      console.error(chalk.red(error.message));
-      process.exit(1);
+      try {
+        await smartUpdate(sourceDir, proagentsDir);
+        console.log(chalk.green('\n✓ ProAgents updated successfully!\n'));
+        console.log(chalk.gray('Preserved:'));
+        console.log(chalk.gray('  • active-features/ (your work in progress)'));
+        console.log(chalk.gray('  • proagents.config.yaml (your values + new options merged)'));
+        console.log(chalk.gray('  • .learning/ (learned patterns)'));
+        console.log(chalk.gray('  • cache/ (analysis cache)\n'));
+        return;
+      } catch (error) {
+        console.error(chalk.red('\n✗ Error updating ProAgents:'));
+        console.error(chalk.red(error.message));
+        process.exit(1);
+      }
     }
   }
 
@@ -949,6 +1110,12 @@ Generated by [ProAgents](https://github.com/prakashpro3/proAgents)
       } else {
         console.log(chalk.green('✓ Added .proagents/ local data to .gitignore'));
       }
+
+      // Save progress after gitignore choice
+      savePartialConfig(configPath, {
+        gitignore_mode: gitignoreChoice,
+        _step: 'gitignore'
+      });
     }
 
     // Create placeholder CHANGELOG.md if not exists
@@ -1016,10 +1183,19 @@ No releases yet. Use \`pa:release\` to generate release notes.
       }
       console.log(chalk.green(`\n✓ Using template: ${PROJECT_TEMPLATES[options.template].name}`));
     } else {
-      // Interactive prompts
-      projectConfig = await promptProjectConfig(targetDir);
+      // Interactive prompts - pass existing config for pre-filling
+      projectConfig = await promptProjectConfig(targetDir, existingConfig);
     }
 
+    // Save progress after project config
+    savePartialConfig(configPath, {
+      project: {
+        name: projectConfig.name,
+        type: projectConfig.type
+      },
+      _step: 'project_config'
+    });
+
     // Add ProAgents section to README.md (AI tools auto-read this)
     const readmePath = join(targetDir, 'README.md');
     const proagentsSection = `
@@ -1058,9 +1234,16 @@ For detailed commands, see \`./.proagents/PROAGENTS.md\`
       selectedPlatforms = projectConfig.platforms;
       console.log(chalk.gray(`  Using template platforms: ${selectedPlatforms.join(', ')}`));
     } else {
-      selectedPlatforms = await selectPlatforms();
+      // Pass existing config for pre-selection
+      selectedPlatforms = await selectPlatforms(existingConfig.ai_platforms);
     }
 
+    // Save progress after platform selection
+    savePartialConfig(configPath, {
+      ai_platforms: selectedPlatforms,
+      _step: 'platforms'
+    });
+
     // Copy AI instruction files for selected platforms (merges with existing files)
     const aiResults = copyPlatformFiles(selectedPlatforms, sourceDir, targetDir);
 
@@ -1074,11 +1257,16 @@ For detailed commands, see \`./.proagents/PROAGENTS.md\`
       console.log(chalk.green(`✓ Merged with existing: ${aiResults.merged.join(', ')}`));
     }
 
-    // Save project and platform config to ROOT config (not proagents/ folder)
-    const configPath = join(targetDir, 'proagents.config.yaml');
+    // Save final project and platform config (removes _setup marker)
     saveProjectConfig(projectConfig, configPath);
     savePlatformConfig(selectedPlatforms, configPath);
 
+    // Clean up setup progress marker
+    const finalConfig = loadPartialConfig(configPath);
+    delete finalConfig._setup;
+    const yamlContent = yaml.dump(finalConfig, { indent: 2, lineWidth: 120 });
+    writeFileSync(configPath, yamlContent);
+
     // Success message
     console.log(chalk.green('\n✓ ProAgents initialized successfully!\n'));
 

package/lib/commands/uninstall.js

@@ -19,6 +19,50 @@ const AI_FILES = [
   'AI_INSTRUCTIONS.md',
 ];
 
+// ProAgents markers used in merged files
+const PROAGENTS_START = '<!-- PROAGENTS:START -->';
+const PROAGENTS_END = '<!-- PROAGENTS:END -->';
+
+/**
+ * Remove only ProAgents section from a file, keep user's original content
+ * Returns: 'deleted' (file removed), 'cleaned' (section removed), 'skipped' (no ProAgents section)
+ */
+function removeProagentsSectionFromFile(filePath) {
+  try {
+    const content = readFileSync(filePath, 'utf-8');
+
+    const startIndex = content.indexOf(PROAGENTS_START);
+    const endIndex = content.indexOf(PROAGENTS_END);
+
+    if (startIndex !== -1 && endIndex !== -1) {
+      // Has ProAgents section - remove it, keep the rest
+      const before = content.substring(0, startIndex).trim();
+      const after = content.substring(endIndex + PROAGENTS_END.length).trim();
+      const remaining = (before + '\n\n' + after).trim();
+
+      if (remaining.length === 0) {
+        // File only had ProAgents content - delete it
+        rmSync(filePath, { force: true });
+        return 'deleted';
+      } else {
+        // File has other content - keep it, remove only ProAgents section
+        writeFileSync(filePath, remaining + '\n');
+        return 'cleaned';
+      }
+    } else {
+      // No ProAgents markers - file was created by ProAgents (not merged)
+      // Check if it's a ProAgents-generated file by looking for ProAgents reference
+      if (content.includes('proagents') || content.includes('ProAgents') || content.includes('.proagents/')) {
+        rmSync(filePath, { force: true });
+        return 'deleted';
+      }
+      return 'skipped';
+    }
+  } catch (error) {
+    return 'skipped';
+  }
+}
+
 /**
  * Command: proagents uninstall
  */
@@ -46,7 +90,7 @@ export async function uninstallCommand(options = {}) {
 
     console.log(chalk.yellow('This will remove:'));
     console.log(chalk.gray('  • ./.proagents/ folder'));
-    console.log(chalk.gray('  • AI instruction files (CLAUDE.md, .cursorrules, etc.)'));
+    console.log(chalk.gray('  • ProAgents sections from AI files (keeps your original config)'));
     console.log(chalk.gray('  • ProAgents section from README.md\n'));
 
     const answer = await question(chalk.yellow('Are you sure? (yes/no): '));
@@ -66,26 +110,39 @@ export async function uninstallCommand(options = {}) {
     console.log(chalk.green('✓ Removed ./.proagents/ folder'));
   }
 
-  // 2. Remove AI instruction files from project root
+  // 2. Remove AI instruction files from project root (smart removal)
   let aiFilesRemoved = 0;
+  let aiFilesCleaned = 0;
+
   for (const file of AI_FILES) {
     const filePath = join(targetDir, file);
     if (existsSync(filePath)) {
-      rmSync(filePath, { force: true });
-      aiFilesRemoved++;
+      const result = removeProagentsSectionFromFile(filePath);
+      if (result === 'deleted') {
+        aiFilesRemoved++;
+      } else if (result === 'cleaned') {
+        aiFilesCleaned++;
+      }
     }
   }
 
   // Remove .github/copilot-instructions.md
   const copilotPath = join(targetDir, '.github', 'copilot-instructions.md');
   if (existsSync(copilotPath)) {
-    rmSync(copilotPath, { force: true });
-    aiFilesRemoved++;
+    const result = removeProagentsSectionFromFile(copilotPath);
+    if (result === 'deleted') {
+      aiFilesRemoved++;
+    } else if (result === 'cleaned') {
+      aiFilesCleaned++;
+    }
   }
 
   if (aiFilesRemoved > 0) {
     console.log(chalk.green(`✓ Removed ${aiFilesRemoved} AI instruction file(s)`));
   }
+  if (aiFilesCleaned > 0) {
+    console.log(chalk.green(`✓ Cleaned ProAgents section from ${aiFilesCleaned} AI file(s) (kept original config)`));
+  }
 
   // 3. Remove ProAgents section from README.md
   const readmePath = join(targetDir, 'README.md');

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "proagents",
-  "version": "1.6.7",
+  "version": "1.6.9",
   "description": "AI-agnostic development workflow framework that automates the full software development lifecycle",
   "type": "module",
   "main": "lib/index.js",