agileflow 3.3.0 → 3.4.1

package/src/core/templates/agileflow-metadata.json

@@ -71,7 +71,8 @@
           "wip": true,
           "context": true,
           "cost": true,
-          "git": true
+          "git": true,
+          "ultradeep": true
         }
       },
       "mcp": {
@@ -127,5 +128,23 @@
   "security": {
     "mcpJsonGitignored": false,
     "envGitignored": false
+  },
+  "models": {
+    "default_audit_model": null,
+    "description": "Override via MODEL=haiku|sonnet|opus in audit command arguments. null = use agent defaults."
+  },
+  "ci_feedback_loops": {
+    "enabled": true,
+    "max_rounds": 3,
+    "description": "Auto-retry agent work when CI/tests fail, up to max_rounds before escalating to human"
+  },
+  "ultradeep": {
+    "tab_naming": "prefix:name",
+    "custom_colors": null,
+    "auto_attach": true,
+    "completion_timeout_minutes": 30,
+    "max_sessions_per_audit": 20,
+    "stagger_seconds": 3,
+    "max_concurrent": 0
   }
 }

package/tools/cli/commands/setup.js

@@ -89,7 +89,14 @@ module.exports = {
         config = await promptInstall();
       }
 
-      displaySection('Setting Up AgileFlow', `Target: ${config.directory}`);
+      const totalSteps = 5;
+      let currentStep = 0;
+      const step = label => {
+        currentStep++;
+        return `[${currentStep}/${totalSteps}] ${label}`;
+      };
+
+      displaySection(step('Installing Core Content'), `Target: ${config.directory}`);
 
       // Run core installation
       const coreResult = await installer.install(config);
@@ -104,17 +111,81 @@ module.exports = {
       success(`Installed ${coreResult.counts.skills} skills`);
 
       // Setup IDE configurations
-      displaySection('Configuring IDEs');
+      displaySection(step('Configuring IDEs'));
 
       ideManager.setAgileflowFolder(config.agileflowFolder);
       ideManager.setDocsFolder(config.docsFolder);
 
+      // Check for existing IDE configs before overwriting
+      if (!options.yes) {
+        const existingConfigs = [];
+        const ideConfigDirs = {
+          'claude-code': '.claude',
+          cursor: '.cursor',
+          windsurf: '.windsurf',
+        };
+
+        for (const ide of config.ides) {
+          const configDir = ideConfigDirs[ide];
+          if (configDir) {
+            const fullPath = path.join(config.directory, configDir);
+            if (fs.existsSync(fullPath)) {
+              existingConfigs.push({ ide, dir: configDir });
+            }
+          }
+        }
+
+        if (existingConfigs.length > 0) {
+          const { confirmOverwrite } = require('inquirer');
+          const configList = existingConfigs.map(c => `  ${c.dir}/`).join('\n');
+          console.log(chalk.yellow(`\n  Existing IDE configs detected:\n${configList}\n`));
+          console.log(
+            chalk.dim(
+              '  AgileFlow will add commands and hooks to these directories.\n' +
+                '  Existing settings will be merged (not replaced).\n'
+            )
+          );
+
+          let proceed = true;
+          try {
+            const inquirer = require('inquirer');
+            const answer = await inquirer.prompt([
+              {
+                type: 'confirm',
+                name: 'proceed',
+                message: 'Continue with IDE configuration?',
+                default: true,
+              },
+            ]);
+            proceed = answer.proceed;
+          } catch {
+            // If inquirer not available or stdin not interactive, proceed
+            proceed = true;
+          }
+
+          if (!proceed) {
+            info('Skipping IDE configuration. Core installation is complete.');
+            console.log(chalk.dim('  Run setup again to configure IDEs later.\n'));
+            // Skip to docs structure
+            displaySection('Creating Documentation Structure', `Folder: ${config.docsFolder}/`);
+            const docsResult = await createDocsStructure(config.directory, config.docsFolder, {
+              updateGitignore: config.updateGitignore,
+            });
+            if (!docsResult.success) {
+              error('Failed to create docs structure');
+            }
+            console.log(chalk.green('\n✨ Setup complete (without IDE configs)!\n'));
+            return;
+          }
+        }
+      }
+
       for (const ide of config.ides) {
         await ideManager.setup(ide, config.directory, coreResult.path);
       }
 
       // Create docs structure
-      displaySection('Creating Documentation Structure', `Folder: ${config.docsFolder}/`);
+      displaySection(step('Creating Documentation Structure'), `Folder: ${config.docsFolder}/`);
       const docsResult = await createDocsStructure(config.directory, config.docsFolder, {
         updateGitignore: config.updateGitignore,
       });
@@ -127,6 +198,7 @@ module.exports = {
       }
 
       // Update metadata with config tracking
+      displaySection(step('Updating Configuration'));
       try {
         const metadataPath = path.join(
           config.directory,
@@ -149,6 +221,16 @@ module.exports = {
       }
 
       // Final summary
+      displaySection(step('Verifying Installation'));
+      const { counts } = coreResult;
+      const totalItems = (counts.commands || 0) + (counts.agents || 0) + (counts.skills || 0);
+      console.log(
+        chalk.green(
+          `  Setup complete: ${counts.commands} commands, ${counts.agents} agents, ${counts.skills} skills installed`
+        )
+      );
+      console.log(chalk.dim(`  IDEs configured: ${config.ides.join(', ')}`));
+
       console.log(chalk.green('\n✨ Setup complete!\n'));
 
       console.log(chalk.bold('Get started:'));

package/tools/cli/commands/update.js

@@ -230,6 +230,48 @@ module.exports = {
 
       console.log(chalk.green(`\n✨ Update complete! (${status.version} → ${latestVersion})\n`));
 
+      // Show changelog diff between old and new version
+      try {
+        const fs = require('node:fs');
+        const changelogPath = path.join(status.path, 'CHANGELOG.md');
+        if (fs.existsSync(changelogPath)) {
+          const changelog = fs.readFileSync(changelogPath, 'utf8');
+          const oldVer = status.version.replace(/^v/, '');
+          const newVer = latestVersion.replace(/^v/, '');
+
+          // Extract sections between old and new version headers
+          const versionPattern = /^##\s+\[?\d+\.\d+\.\d+\]?/m;
+          const lines = changelog.split('\n');
+          const relevantLines = [];
+          let capturing = false;
+
+          for (const line of lines) {
+            if (versionPattern.test(line)) {
+              if (line.includes(oldVer)) {
+                break; // Stop at old version
+              }
+              capturing = true;
+            }
+            if (capturing) {
+              relevantLines.push(line);
+            }
+          }
+
+          if (relevantLines.length > 0) {
+            const maxLines = 20;
+            const display = relevantLines.slice(0, maxLines);
+            console.log(chalk.hex('#e8683a').bold(`  What's New in v${newVer}:\n`));
+            display.forEach(l => console.log(chalk.dim(`  ${l}`)));
+            if (relevantLines.length > maxLines) {
+              console.log(chalk.dim(`  ... and ${relevantLines.length - maxLines} more lines`));
+            }
+            console.log(chalk.dim(`\n  Run /agileflow:whats-new for full changelog\n`));
+          }
+        }
+      } catch {
+        // Changelog display is non-critical
+      }
+
       // If running from outdated global installation, remind user to update it
       if (
         npmLatestVersion &&

package/tools/cli/installers/ide/_base-ide.js

@@ -82,15 +82,18 @@ class BaseIdeSetup {
    * Uses content-transformer module for consistent injection
    * @param {string} content - Template file content
    * @param {string} agileflowDir - AgileFlow installation directory
+   * @param {Object} [options] - Additional injection options
+   * @param {boolean} [options.minimal] - When true, skip full list injection (use discovery pointers)
    * @returns {string} Content with placeholders replaced
    */
-  injectDynamicContent(content, agileflowDir) {
+  injectDynamicContent(content, agileflowDir, options = {}) {
     // agileflowDir is the user's .agileflow installation directory
     // which has agents/, commands/, skills/ at the root level
     return injectDynamicContentHelper(content, {
       coreDir: agileflowDir,
       agileflowFolder: this.agileflowFolder,
       version: this.getVersion(),
+      minimal: options.minimal || false,
     });
   }
 
@@ -107,6 +110,30 @@ class BaseIdeSetup {
     }
   }
 
+  /**
+   * Detect minimal context mode from project metadata.
+   * Reads the contextVerbosity setting from /configure.
+   * @param {string} projectDir - Project directory
+   * @returns {boolean} True if minimal mode should be used
+   */
+  _detectMinimalMode(projectDir) {
+    try {
+      const metadataPath = path.join(
+        projectDir,
+        this.docsFolder,
+        '00-meta',
+        'agileflow-metadata.json'
+      );
+      if (!fs.existsSync(metadataPath)) return false;
+      const metadata = JSON.parse(fs.readFileSync(metadataPath, 'utf8'));
+      const mode = metadata?.features?.contextVerbosity?.mode;
+      if (mode === 'minimal') return true;
+      return false;
+    } catch {
+      return false;
+    }
+  }
+
   /**
    * Main setup method - must be implemented by subclasses
    * @param {string} projectDir - Project directory
@@ -128,6 +155,7 @@ class BaseIdeSetup {
    * @param {string} config.agileflowFolder - AgileFlow folder name (e.g., 'agileflow', 'AgileFlow')
    * @param {string} [config.commandLabel='commands'] - Label for commands in output (e.g., 'workflows')
    * @param {string} [config.agentLabel='agents'] - Label for agents in output
+   * @param {boolean} [config.minimal=false] - When true, skip full agent/command list injection. Auto-detected from metadata if not set.
    * @returns {Promise<{success: boolean, commands: number, agents: number}>}
    */
   async setupStandard(projectDir, agileflowDir, config) {
@@ -136,8 +164,12 @@ class BaseIdeSetup {
       agileflowFolder,
       commandLabel = 'commands',
       agentLabel = 'agents',
+      minimal: explicitMinimal,
     } = config;
 
+    // Auto-detect minimal mode from /configure context verbosity setting
+    const minimal = explicitMinimal ?? this._detectMinimalMode(projectDir);
+
     console.log(chalk.hex('#e8683a')(`  Setting up ${this.displayName}...`));
 
     // Clean up old installation first
@@ -154,7 +186,9 @@ class BaseIdeSetup {
       commandsSource,
       agileflowTargetDir,
       agileflowDir,
-      true // Inject dynamic content
+      true, // Inject dynamic content
+      null, // No IDE transform
+      { minimal } // Pass minimal flag for content injection
     );
 
     // Install agents as subdirectory
@@ -379,6 +413,7 @@ class BaseIdeSetup {
    * @param {string} agileflowDir - AgileFlow installation directory (for dynamic content)
    * @param {boolean} injectDynamic - Whether to inject dynamic content (only for top-level commands)
    * @param {Function} [ideTransform] - Optional IDE transformation function: (content, filename) => string
+   * @param {Object} [injectionOptions] - Options passed to injectDynamicContent (e.g., { minimal: true })
    * @returns {Promise<{commands: number, subdirs: number}>} Count of installed items
    * @throws {CommandInstallationError} If command installation fails
    * @throws {FilePermissionError} If permission denied
@@ -402,7 +437,8 @@ class BaseIdeSetup {
     targetDir,
     agileflowDir,
     injectDynamic = false,
-    ideTransform = null
+    ideTransform = null,
+    injectionOptions = {}
   ) {
     let commandCount = 0;
     let subdirCount = 0;
@@ -434,7 +470,7 @@ class BaseIdeSetup {
           // Inject dynamic content if enabled (for top-level commands)
           if (injectDynamic) {
             try {
-              content = this.injectDynamicContent(content, agileflowDir);
+              content = this.injectDynamicContent(content, agileflowDir, injectionOptions);
             } catch (injectionError) {
               throw new ContentInjectionError(this.displayName, sourcePath, injectionError.message);
             }
@@ -467,7 +503,8 @@ class BaseIdeSetup {
           targetPath,
           agileflowDir,
           false, // Don't inject dynamic content in subdirectories
-          ideTransform // Pass ideTransform to recursive calls
+          ideTransform, // Pass ideTransform to recursive calls
+          injectionOptions // Pass injection options to recursive calls
         );
         commandCount += subResult.commands;
         subdirCount += 1 + subResult.subdirs;

package/tools/cli/installers/ide/claude-code.js

@@ -52,11 +52,11 @@ class ClaudeCodeSetup extends BaseIdeSetup {
     await this.installCommandsRecursive(agentsSource, spawnableAgentsDir, agileflowDir, false);
     console.log(chalk.dim(`    - Spawnable agents: .claude/agents/agileflow/`));
 
-    // Claude Code specific: Create skills directory for user-generated skills
-    // AgileFlow no longer ships static skills - users generate them via /agileflow:skill:create
+    // Claude Code specific: Create skills directory for marketplace skills
+    // Users browse and install skills via /agileflow:skill:recommend or npx skills add
     const skillsTargetDir = path.join(ideDir, 'skills');
     await this.ensureDir(skillsTargetDir);
-    console.log(chalk.dim(`    - Skills directory: .claude/skills/ (for user-generated skills)`));
+    console.log(chalk.dim(`    - Skills directory: .claude/skills/ (for marketplace skills)`));
 
     // Claude Code specific: Setup damage control hooks
     await this.setupDamageControl(projectDir, agileflowDir, ideDir, options);
@@ -64,6 +64,9 @@ class ClaudeCodeSetup extends BaseIdeSetup {
     // Claude Code specific: Setup SessionStart hooks (welcome, archive, context-loader)
     await this.setupSessionStartHooks(projectDir, agileflowDir, ideDir, options);
 
+    // Claude Code specific: Setup PostToolUse hooks (native team observer)
+    await this.setupPostToolUseHooks(projectDir, agileflowDir, ideDir, options);
+
     return result;
   }
 
@@ -297,6 +300,71 @@ class ClaudeCodeSetup extends BaseIdeSetup {
     );
   }
 
+  /**
+   * Setup PostToolUse hooks for native Agent Teams observability.
+   * Registers native-team-observer.js for TeamCreate, SendMessage, ListTeams.
+   * @param {string} projectDir - Project directory
+   * @param {string} agileflowDir - AgileFlow installation directory
+   * @param {string} claudeDir - .claude directory path
+   * @param {Object} options - Setup options
+   */
+  async setupPostToolUseHooks(projectDir, agileflowDir, claudeDir, options = {}) {
+    const settingsPath = path.join(claudeDir, 'settings.json');
+    let settings = {};
+
+    if (fs.existsSync(settingsPath)) {
+      try {
+        settings = JSON.parse(fs.readFileSync(settingsPath, 'utf8'));
+      } catch (e) {
+        settings = {};
+      }
+    }
+
+    if (!settings.hooks) settings.hooks = {};
+    if (!settings.hooks.PostToolUse) settings.hooks.PostToolUse = [];
+
+    const observerCommand = 'node $CLAUDE_PROJECT_DIR/.agileflow/scripts/native-team-observer.js';
+
+    const postToolUseHooks = [
+      {
+        matcher: 'TeamCreate',
+        hooks: [{ type: 'command', command: observerCommand, timeout: 5000 }],
+      },
+      {
+        matcher: 'SendMessage',
+        hooks: [{ type: 'command', command: observerCommand, timeout: 5000 }],
+      },
+      {
+        matcher: 'ListTeams',
+        hooks: [{ type: 'command', command: observerCommand, timeout: 5000 }],
+      },
+    ];
+
+    // Merge with existing hooks (don't duplicate)
+    for (const newHook of postToolUseHooks) {
+      const existingIdx = settings.hooks.PostToolUse.findIndex(h => h.matcher === newHook.matcher);
+      if (existingIdx === -1) {
+        settings.hooks.PostToolUse.push(newHook);
+      } else {
+        const existing = settings.hooks.PostToolUse[existingIdx];
+        if (!existing.hooks) existing.hooks = [];
+        const hasObserver = existing.hooks.some(
+          h => h.type === 'command' && h.command && h.command.includes('native-team-observer')
+        );
+        if (!hasObserver) {
+          existing.hooks.push(newHook.hooks[0]);
+        }
+      }
+    }
+
+    await fs.writeFile(settingsPath, JSON.stringify(settings, null, 2));
+    console.log(
+      chalk.dim(
+        `    - PostToolUse hooks: native team observer (TeamCreate, SendMessage, ListTeams)`
+      )
+    );
+  }
+
   /**
    * Remove AgileFlow command duplicates from user-level ~/.claude/commands/
    * When the same command exists in both ~/.claude/commands/ and

package/tools/cli/lib/content-injector.js

@@ -70,9 +70,46 @@ function isPathSafe(filePath, baseDir) {
 }
 
 /**
- * Scan agents directory and generate formatted agent list
+ * Derive agent category from name for compact grouping.
+ * @param {string} name - Agent name
+ * @returns {string} Category name
+ */
+function categorizeAgent(name) {
+  // Audit analyzer families
+  const analyzerMatch = name.match(/^(logic|security|perf|test|completeness|legal)-analyzer-/);
+  if (analyzerMatch) {
+    const familyNames = {
+      logic: 'Logic',
+      security: 'Security',
+      perf: 'Performance',
+      test: 'Tests',
+      completeness: 'Completeness',
+      legal: 'Legal',
+    };
+    return `Audit - ${familyNames[analyzerMatch[1]] || analyzerMatch[1]}`;
+  }
+  // Consensus coordinators for audit families
+  const consensusMatch = name.match(/^(logic|security|perf|test|completeness|legal)-consensus$/);
+  if (consensusMatch) {
+    const familyNames = {
+      logic: 'Logic',
+      security: 'Security',
+      perf: 'Performance',
+      test: 'Tests',
+      completeness: 'Completeness',
+      legal: 'Legal',
+    };
+    return `Audit - ${familyNames[consensusMatch[1]] || consensusMatch[1]}`;
+  }
+  if (name.startsWith('council-')) return 'Council';
+  if (name.endsWith('-validator')) return 'Validation';
+  return 'Domain';
+}
+
+/**
+ * Scan agents directory and generate compact category-grouped agent list
  * @param {string} agentsDir - Path to agents directory
- * @returns {string} Formatted agent list
+ * @returns {string} Formatted agent list grouped by category
  */
 function generateAgentList(agentsDir) {
   if (!fs.existsSync(agentsDir)) return '';
@@ -117,16 +154,20 @@ function generateAgentList(agentsDir) {
 
   // Sanitize the count value
   const safeCount = sanitize.count(agents.length);
+
+  // Group by category for compact output
+  const categories = {};
+  for (const agent of agents) {
+    const cat = categorizeAgent(agent.name);
+    if (!categories[cat]) categories[cat] = [];
+    categories[cat].push(agent.name);
+  }
+
   let output = `**AVAILABLE AGENTS (${safeCount} total)**:\n\n`;
 
-  agents.forEach((agent, index) => {
-    // All values are already sanitized by sanitizeAgentData
-    output += `${index + 1}. **${agent.name}** (model: ${agent.model})\n`;
-    output += `   - **Purpose**: ${agent.description}\n`;
-    output += `   - **Tools**: ${agent.tools.join(', ')}\n`;
-    output += `   - **Usage**: \`subagent_type: "agileflow-${agent.name}"\`\n`;
-    output += `\n`;
-  });
+  for (const [category, names] of Object.entries(categories)) {
+    output += `**${category}**: ${names.join(', ')}\n`;
+  }
 
   return output;
 }
@@ -235,6 +276,94 @@ function generateCommandList(commandsDir) {
   return output;
 }
 
+/**
+ * Generate a compact category summary for agents (no individual names).
+ * Used by minimal mode and generators that want a discovery-oriented summary.
+ * @param {string} agentsDir - Path to agents directory
+ * @returns {string} Compact category summary with counts
+ */
+function generateAgentSummary(agentsDir) {
+  if (!fs.existsSync(agentsDir)) return '';
+
+  const files = fs.readdirSync(agentsDir).filter(f => f.endsWith('.md'));
+  const agents = [];
+
+  for (const file of files) {
+    const filePath = path.join(agentsDir, file);
+    if (!isPathSafe(filePath, agentsDir)) continue;
+
+    const content = fs.readFileSync(filePath, 'utf8');
+    const frontmatter = parseFrontmatter(content);
+    if (!frontmatter || Object.keys(frontmatter).length === 0) continue;
+
+    const name = frontmatter.name || path.basename(file, '.md');
+    agents.push(name);
+  }
+
+  // Group by category, count per category
+  const categories = {};
+  for (const name of agents) {
+    const cat = categorizeAgent(name);
+    if (!categories[cat]) categories[cat] = 0;
+    categories[cat]++;
+  }
+
+  const safeCount = sanitize.count(agents.length);
+  let output = `**${safeCount} agents** across ${Object.keys(categories).length} categories:\n`;
+  for (const [category, count] of Object.entries(categories)) {
+    output += `- **${category}**: ${count} agents\n`;
+  }
+  output += `\nRun \`/agileflow:help agents\` or browse \`.agileflow/agents/\` for the full list.`;
+  return output;
+}
+
+/**
+ * Generate a compact category summary for commands (no individual names).
+ * Used by minimal mode and generators that want a discovery-oriented summary.
+ * @param {string} commandsDir - Path to commands directory
+ * @returns {string} Compact category summary with counts
+ */
+function generateCommandSummary(commandsDir) {
+  if (!fs.existsSync(commandsDir)) return '';
+
+  const commands = [];
+
+  // Count main command files
+  const mainFiles = fs.readdirSync(commandsDir).filter(f => f.endsWith('.md'));
+  for (const file of mainFiles) {
+    const filePath = path.join(commandsDir, file);
+    if (!isPathSafe(filePath, commandsDir)) continue;
+
+    const content = fs.readFileSync(filePath, 'utf8');
+    const frontmatter = parseFrontmatter(content);
+    if (!frontmatter || Object.keys(frontmatter).length === 0) continue;
+    commands.push(path.basename(file, '.md'));
+  }
+
+  // Count subdirectory command files
+  const entries = fs.readdirSync(commandsDir, { withFileTypes: true });
+  for (const entry of entries) {
+    if (entry.isDirectory()) {
+      const subDir = path.join(commandsDir, entry.name);
+      if (!isPathSafe(subDir, commandsDir)) continue;
+
+      const subFiles = fs.readdirSync(subDir).filter(f => f.endsWith('.md'));
+      for (const file of subFiles) {
+        const filePath = path.join(subDir, file);
+        if (!isPathSafe(filePath, commandsDir)) continue;
+
+        const content = fs.readFileSync(filePath, 'utf8');
+        const frontmatter = parseFrontmatter(content);
+        if (!frontmatter || Object.keys(frontmatter).length === 0) continue;
+        commands.push(`${entry.name}:${path.basename(file, '.md')}`);
+      }
+    }
+  }
+
+  const safeCount = sanitize.count(commands.length);
+  return `**${safeCount} commands** available. Run \`/agileflow:help\` for the full list with descriptions.`;
+}
+
 // =============================================================================
 // Template Generation Functions
 // =============================================================================
@@ -480,6 +609,8 @@ function clearPreserveRulesCache() {
  * @param {string} context.agileflowFolder - AgileFlow folder name
  * @param {string} context.docsFolder - Docs folder name (default: 'docs')
  * @param {string} context.version - AgileFlow version
+ * @param {boolean} context.minimal - When true, skip AGENT_LIST and COMMAND_LIST injection
+ *   (replaces with discovery pointers). Keeps session harness, quality gates, preserve_rules.
  * @returns {string} Content with all placeholders replaced
  */
 function injectContent(content, context = {}) {
@@ -488,6 +619,7 @@ function injectContent(content, context = {}) {
     agileflowFolder = '.agileflow',
     docsFolder = 'docs',
     version = 'unknown',
+    minimal = false,
   } = context;
 
   let result = content;
@@ -541,7 +673,13 @@ function injectContent(content, context = {}) {
   // List generation already includes sanitization via sanitizeAgentData/sanitizeCommandData
   if (coreDir && fs.existsSync(coreDir)) {
     if (result.includes('{{AGENT_LIST}}')) {
-      const agentList = generateAgentList(path.join(coreDir, 'agents'));
+      let agentList;
+      if (minimal) {
+        // Minimal mode: replace with compact discovery pointer
+        agentList = `**Agents**: ${safeAgentCount} available. Run \`/agileflow:help agents\` or \`ls .agileflow/agents/\` to browse.`;
+      } else {
+        agentList = generateAgentList(path.join(coreDir, 'agents'));
+      }
       result = replaceInBodyOnly(result, body => {
         let updated = body.replace(/<!-- \{\{AGENT_LIST\}\} -->/g, agentList);
         updated = updated.replace(/\{\{AGENT_LIST\}\}/g, agentList);
@@ -550,7 +688,13 @@ function injectContent(content, context = {}) {
     }
 
     if (result.includes('{{COMMAND_LIST}}')) {
-      const commandList = generateCommandList(path.join(coreDir, 'commands'));
+      let commandList;
+      if (minimal) {
+        // Minimal mode: replace with compact discovery pointer
+        commandList = `**Commands**: ${safeCommandCount} available. Run \`/agileflow:help\` or \`ls .agileflow/commands/\` to browse.`;
+      } else {
+        commandList = generateCommandList(path.join(coreDir, 'commands'));
+      }
       result = replaceInBodyOnly(result, body => {
         let updated = body.replace(/<!-- \{\{COMMAND_LIST\}\} -->/g, commandList);
         updated = updated.replace(/\{\{COMMAND_LIST\}\}/g, commandList);
@@ -798,6 +942,10 @@ module.exports = {
   generateAgentList,
   generateCommandList,
 
+  // Summary generation (compact, for minimal mode)
+  generateAgentSummary,
+  generateCommandSummary,
+
   // Template generation
   generateSessionHarnessContent,
   clearSessionHarnessCache,

package/tools/cli/lib/docs-setup.js

@@ -190,7 +190,7 @@ Project-level planning and tracking.
 - **milestones.md**: Release milestones
 - **risks.md**: Project risks and mitigation strategies
 - **ideation/**: Ideation reports from \`/agileflow:ideate:new\`
-- **logic-audits/**: Logic audit reports from \`/agileflow:audit:logic\`
+- **code-audits/**: Code audit reports from \`/agileflow:code:logic\`
 `,
 
     [`${docsFolder}/09-agents/README.md`]: `# Agent Status Tracking