agileflow 2.89.0 → 2.89.1

package/CHANGELOG.md

@@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [2.89.1] - 2026-01-14
+
+### Fixed
+- Fix active_commands preservation after conversation compact
+
 ## [2.89.0] - 2026-01-14
 
 ### Added

package/lib/file-cache.js

@@ -130,9 +130,10 @@ class LRUCache {
       ...this.stats,
       size: this.cache.size,
       maxSize: this.maxSize,
-      hitRate: this.stats.hits + this.stats.misses > 0
-        ? (this.stats.hits / (this.stats.hits + this.stats.misses) * 100).toFixed(1) + '%'
-        : '0%',
+      hitRate:
+        this.stats.hits + this.stats.misses > 0
+          ? ((this.stats.hits / (this.stats.hits + this.stats.misses)) * 100).toFixed(1) + '%'
+          : '0%',
     };
   }
 

package/lib/progress.js

@@ -168,7 +168,8 @@ class Spinner {
     }
 
     const elapsed = this.startTime ? Date.now() - this.startTime : 0;
-    const suffix = elapsed > DOHERTY_THRESHOLD_MS ? ` ${c.dim}(${formatDuration(elapsed)})${c.reset}` : '';
+    const suffix =
+      elapsed > DOHERTY_THRESHOLD_MS ? ` ${c.dim}(${formatDuration(elapsed)})${c.reset}` : '';
 
     console.log(`${color}${symbol}${c.reset} ${message}${suffix}`);
     return this;
@@ -179,7 +180,7 @@ class Spinner {
    * @returns {boolean}
    */
   wasFast() {
-    return this.startTime && (Date.now() - this.startTime) < DOHERTY_THRESHOLD_MS;
+    return this.startTime && Date.now() - this.startTime < DOHERTY_THRESHOLD_MS;
   }
 }
 
@@ -263,7 +264,7 @@ class ProgressBar {
       return this;
     }
 
-    const percent = this.total > 0 ? (current / this.total) : 0;
+    const percent = this.total > 0 ? current / this.total : 0;
     const filled = Math.round(this.width * percent);
     const empty = this.width - filled;
 
@@ -300,7 +301,8 @@ class ProgressBar {
     }
 
     const elapsed = Date.now() - this.startTime;
-    const suffix = elapsed > DOHERTY_THRESHOLD_MS ? ` ${c.dim}(${formatDuration(elapsed)})${c.reset}` : '';
+    const suffix =
+      elapsed > DOHERTY_THRESHOLD_MS ? ` ${c.dim}(${formatDuration(elapsed)})${c.reset}` : '';
     const msg = message || `${this.label} complete`;
 
     console.log(`${c.green}✓${c.reset} ${msg} (${this.total} items)${suffix}`);

package/lib/validate.js

@@ -427,8 +427,7 @@ function validatePath(inputPath, baseDir, options = {}) {
     ? normalizedBase
     : normalizedBase + path.sep;
 
-  const isWithinBase =
-    resolvedPath === normalizedBase || resolvedPath.startsWith(baseWithSep);
+  const isWithinBase = resolvedPath === normalizedBase || resolvedPath.startsWith(baseWithSep);
 
   if (!isWithinBase) {
     return {

package/lib/yaml-utils.js

@@ -53,11 +53,7 @@ function safeLoadAll(content, options = {}) {
   }
 
   const documents = [];
-  yaml.loadAll(
-    content,
-    (doc) => documents.push(doc),
-    { schema: yaml.DEFAULT_SCHEMA, ...options }
-  );
+  yaml.loadAll(content, doc => documents.push(doc), { schema: yaml.DEFAULT_SCHEMA, ...options });
   return documents;
 }
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agileflow",
-  "version": "2.89.0",
+  "version": "2.89.1",
   "description": "AI-driven agile development system for Claude Code, Cursor, Windsurf, and more",
   "keywords": [
     "agile",

package/scripts/agileflow-welcome.js

@@ -274,7 +274,7 @@ function runArchival(rootDir, cache = null) {
 }
 
 function clearActiveCommands(rootDir, cache = null) {
-  const result = { ran: false, cleared: 0, commandNames: [] };
+  const result = { ran: false, cleared: 0, commandNames: [], preserved: false };
 
   try {
     const sessionStatePath = path.join(rootDir, 'docs/09-agents/session-state.json');
@@ -291,6 +291,31 @@ function clearActiveCommands(rootDir, cache = null) {
       result.ran = true;
     }
 
+    // Check if PreCompact just ran (within last 30 seconds)
+    // If so, preserve active_commands instead of clearing them (post-compact session start)
+    if (state.last_precompact_at) {
+      const precompactTime = new Date(state.last_precompact_at).getTime();
+      const now = Date.now();
+      const secondsSincePrecompact = (now - precompactTime) / 1000;
+
+      if (secondsSincePrecompact < 30) {
+        // This is a post-compact session start - preserve active commands
+        result.preserved = true;
+        // Capture command names for display (but don't clear)
+        if (state.active_commands && state.active_commands.length > 0) {
+          for (const cmd of state.active_commands) {
+            if (cmd.name) result.commandNames.push(cmd.name);
+          }
+        }
+        // Clear the precompact timestamp so next true session start will clear
+        delete state.last_precompact_at;
+        fs.writeFileSync(sessionStatePath, JSON.stringify(state, null, 2) + '\n');
+        return result;
+      }
+      // Precompact was too long ago - clear as normal
+      delete state.last_precompact_at;
+    }
+
     // Handle new array format (active_commands)
     if (state.active_commands && state.active_commands.length > 0) {
       result.cleared = state.active_commands.length;
@@ -1061,10 +1086,18 @@ function formatTable(
   }
 
   // Session cleanup
-  const sessionStatus = session.cleared > 0 ? `cleared ${session.cleared} command(s)` : `clean`;
-  lines.push(
-    row('Session state', sessionStatus, c.lavender, session.cleared > 0 ? c.mintGreen : c.dim)
-  );
+  let sessionStatus, sessionColor;
+  if (session.preserved) {
+    sessionStatus = `preserved ${session.commandNames.length} command(s)`;
+    sessionColor = c.mintGreen;
+  } else if (session.cleared > 0) {
+    sessionStatus = `cleared ${session.cleared} command(s)`;
+    sessionColor = c.mintGreen;
+  } else {
+    sessionStatus = `clean`;
+    sessionColor = c.dim;
+  }
+  lines.push(row('Session state', sessionStatus, c.lavender, sessionColor));
 
   // PreCompact status with version check
   if (precompact.configured && precompact.scriptExists) {
@@ -1269,12 +1302,14 @@ async function main() {
   if (parallelSessions.cleaned > 0 && parallelSessions.cleanedSessions) {
     console.log('');
     console.log(`${c.amber}📋 Cleaned ${parallelSessions.cleaned} inactive session(s):${c.reset}`);
-    parallelSessions.cleanedSessions.forEach((sess) => {
+    parallelSessions.cleanedSessions.forEach(sess => {
       const name = sess.nickname ? `${sess.id} "${sess.nickname}"` : `Session ${sess.id}`;
       const reason = sess.reason === 'pid_dead' ? 'process ended' : sess.reason;
       console.log(`   ${c.dim}└─ ${name} (${reason}, PID ${sess.pid})${c.reset}`);
     });
-    console.log(`   ${c.slate}Sessions are cleaned when their Claude Code process is no longer running.${c.reset}`);
+    console.log(
+      `   ${c.slate}Sessions are cleaned when their Claude Code process is no longer running.${c.reset}`
+    );
   }
 
   // Story claiming: cleanup stale claims and show warnings

package/scripts/batch-pmap-loop.js

@@ -46,11 +46,14 @@ function saveSessionState(rootDir, state) {
 async function resolveGlob(pattern, rootDir) {
   // Use bash globbing for pattern expansion
   try {
-    const result = execSync(`bash -c 'shopt -s nullglob; for f in ${pattern}; do echo "$f"; done'`, {
-      cwd: rootDir,
-      encoding: 'utf8',
-      timeout: 10000,
-    });
+    const result = execSync(
+      `bash -c 'shopt -s nullglob; for f in ${pattern}; do echo "$f"; done'`,
+      {
+        cwd: rootDir,
+        encoding: 'utf8',
+        timeout: 10000,
+      }
+    );
     const files = result
       .split('\n')
       .filter(f => f.trim())
@@ -218,7 +221,9 @@ function handleBatchLoop(rootDir) {
       );
       console.log('');
       console.log(`${c.green}Pattern: ${loop.pattern}${c.reset}`);
-      console.log(`${c.dim}${summary.completed} items completed in ${iteration - 1} iterations${c.reset}`);
+      console.log(
+        `${c.dim}${summary.completed} items completed in ${iteration - 1} iterations${c.reset}`
+      );
       return;
     }
 
@@ -287,7 +292,9 @@ function handleBatchLoop(rootDir) {
       console.log(`${c.cyan}━━━ Next Item ━━━${c.reset}`);
       console.log(`${c.bold}${nextItem}${c.reset}`);
       console.log('');
-      console.log(`${c.dim}Progress: ${summary.completed}/${summary.total} items complete${c.reset}`);
+      console.log(
+        `${c.dim}Progress: ${summary.completed}/${summary.total} items complete${c.reset}`
+      );
       console.log('');
       console.log(`${c.brand}▶ Implement "${loop.action}" for this file${c.reset}`);
       console.log(`${c.dim}  Run tests when ready. Loop will validate and continue.${c.reset}`);
@@ -310,7 +317,9 @@ function handleBatchLoop(rootDir) {
       console.log('');
       console.log(`${c.green}Pattern: ${loop.pattern}${c.reset}`);
       console.log(`${c.green}Action: ${loop.action}${c.reset}`);
-      console.log(`${c.dim}${summary.completed} items completed in ${iteration} iterations${c.reset}`);
+      console.log(
+        `${c.dim}${summary.completed} items completed in ${iteration} iterations${c.reset}`
+      );
     }
   } else {
     // Tests failed - continue iterating
@@ -353,9 +362,7 @@ async function handleInit(args, rootDir) {
   }
 
   const pattern = patternArg.split('=').slice(1).join('=').replace(/"/g, '');
-  const action = actionArg
-    ? actionArg.split('=').slice(1).join('=').replace(/"/g, '')
-    : 'process';
+  const action = actionArg ? actionArg.split('=').slice(1).join('=').replace(/"/g, '') : 'process';
   const maxIterations = parseIntBounded(maxArg ? maxArg.split('=')[1] : null, 50, 1, 200);
 
   // Resolve glob pattern
@@ -432,7 +439,9 @@ function handleStatus(rootDir) {
   console.log(`  Pattern: ${loop.pattern}`);
   console.log(`  Action: ${loop.action}`);
   console.log(`  Current Item: ${loop.current_item || 'none'}`);
-  console.log(`  Progress: ${summary.completed}/${summary.total} (${summary.in_progress} in progress)`);
+  console.log(
+    `  Progress: ${summary.completed}/${summary.total} (${summary.in_progress} in progress)`
+  );
   console.log(`  Iteration: ${loop.iteration || 0}/${loop.max_iterations || 50}`);
 }
 

package/scripts/obtain-context.js

@@ -461,10 +461,10 @@ function generateFullContent() {
       'loop-mode': 'Autonomous epic execution (MODE=loop)',
       'multi-session': 'Multi-session coordination detected',
       'visual-e2e': 'Visual screenshot verification (VISUAL=true)',
-      'delegation': 'Expert spawning patterns (load when spawning)',
-      'stuck': 'Research prompt guidance (load after 2 failures)',
+      delegation: 'Expert spawning patterns (load when spawning)',
+      stuck: 'Research prompt guidance (load after 2 failures)',
       'plan-mode': 'Planning workflow details (load when entering plan mode)',
-      'tools': 'Tool usage guidance (load when needed)',
+      tools: 'Tool usage guidance (load when needed)',
     };
 
     content += `\n${C.dim}Section meanings:${C.reset}\n`;

package/scripts/precompact-context.sh

@@ -121,3 +121,17 @@ cat << EOF
 3. Review docs/02-practices/ for implementation patterns
 4. Check git log for recent changes
 EOF
+
+# Mark that PreCompact just ran - tells SessionStart to preserve active_commands
+# This prevents the welcome script from clearing commands right after compact
+if [ -f "docs/09-agents/session-state.json" ]; then
+  node -e "
+    const fs = require('fs');
+    const path = 'docs/09-agents/session-state.json';
+    try {
+      const state = JSON.parse(fs.readFileSync(path, 'utf8'));
+      state.last_precompact_at = new Date().toISOString();
+      fs.writeFileSync(path, JSON.stringify(state, null, 2) + '\n');
+    } catch (e) {}
+  " 2>/dev/null
+fi

package/scripts/session-manager.js

@@ -228,9 +228,8 @@ function registerSession(nickname = null, threadType = null) {
   registry.next_id++;
 
   const isMain = cwd === ROOT;
-  const detectedType = threadType && THREAD_TYPES.includes(threadType)
-    ? threadType
-    : detectThreadType(null, !isMain);
+  const detectedType =
+    threadType && THREAD_TYPES.includes(threadType) ? threadType : detectThreadType(null, !isMain);
 
   registry.sessions[sessionId] = {
     path: cwd,
@@ -750,10 +749,10 @@ function getSessionPhase(session) {
 
     // Count commits since branch diverged from main
     const mainBranch = getMainBranch();
-    const commitCount = execSync(
-      `git rev-list --count ${mainBranch}..HEAD 2>/dev/null || echo 0`,
-      { cwd: sessionPath, encoding: 'utf8' }
-    ).trim();
+    const commitCount = execSync(`git rev-list --count ${mainBranch}..HEAD 2>/dev/null || echo 0`, {
+      cwd: sessionPath,
+      encoding: 'utf8',
+    }).trim();
 
     const commits = parseInt(commitCount, 10);
 
@@ -1037,7 +1036,9 @@ function main() {
         if (nickname) registry.sessions[sessionId].nickname = nickname;
         // Ensure thread_type exists (migration for old sessions)
         if (!registry.sessions[sessionId].thread_type) {
-          registry.sessions[sessionId].thread_type = registry.sessions[sessionId].is_main ? 'base' : 'parallel';
+          registry.sessions[sessionId].thread_type = registry.sessions[sessionId].is_main
+            ? 'base'
+            : 'parallel';
         }
         writeLock(sessionId, pid);
       } else {
@@ -1218,7 +1219,9 @@ function main() {
         const sessionId = args[2];
         const threadType = args[3];
         if (!sessionId || !threadType) {
-          console.log(JSON.stringify({ success: false, error: 'Usage: thread-type set <sessionId> <type>' }));
+          console.log(
+            JSON.stringify({ success: false, error: 'Usage: thread-type set <sessionId> <type>' })
+          );
           return;
         }
         const result = setSessionThreadType(sessionId, threadType);
@@ -1910,7 +1913,10 @@ function getSessionThreadType(sessionId = null) {
  */
 function setSessionThreadType(sessionId, threadType) {
   if (!THREAD_TYPES.includes(threadType)) {
-    return { success: false, error: `Invalid thread type: ${threadType}. Valid: ${THREAD_TYPES.join(', ')}` };
+    return {
+      success: false,
+      error: `Invalid thread type: ${threadType}. Valid: ${THREAD_TYPES.join(', ')}`,
+    };
   }
 
   const registry = loadRegistry();

package/scripts/test-session-boundary.js

@@ -63,8 +63,8 @@ console.log(`File Being Edited:   ${normalizedFile}`);
 console.log('');
 
 // Check if file is within active session path
-const isInsideSession = normalizedFile.startsWith(normalizedActive + path.sep) ||
-                        normalizedFile === normalizedActive;
+const isInsideSession =
+  normalizedFile.startsWith(normalizedActive + path.sep) || normalizedFile === normalizedActive;
 
 if (isInsideSession) {
   console.log('✅ ALLOWED - File is inside the active session directory');

package/tools/cli/commands/config.js

@@ -130,11 +130,7 @@ async function handleGet(status, key) {
   const handler = new ErrorHandler('config');
 
   if (!key) {
-    handler.warning(
-      'Missing key',
-      'Provide a config key to get',
-      'npx agileflow config get <key>'
-    );
+    handler.warning('Missing key', 'Provide a config key to get', 'npx agileflow config get <key>');
   }
 
   const validKeys = ['userName', 'ides', 'agileflowFolder', 'docsFolder', 'version'];

package/tools/cli/commands/setup.js

@@ -103,11 +103,7 @@ module.exports = {
 
       if (!coreResult.success) {
         const handler = new ErrorHandler('setup');
-        handler.warning(
-          'Core setup failed',
-          'Check directory permissions',
-          'npx agileflow doctor'
-        );
+        handler.warning('Core setup failed', 'Check directory permissions', 'npx agileflow doctor');
       }
 
       success(`Installed ${coreResult.counts.agents} agents`);

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

@@ -195,11 +195,7 @@ class BaseIdeSetup {
                 `Permission denied: ${error.message}`
               );
             }
-            throw new CleanupError(
-              this.displayName,
-              agileflowPath,
-              error.message
-            );
+            throw new CleanupError(this.displayName, agileflowPath, error.message);
           }
         }
       }
@@ -332,11 +328,7 @@ class BaseIdeSetup {
             try {
               content = this.injectDynamicContent(content, agileflowDir);
             } catch (injectionError) {
-              throw new ContentInjectionError(
-                this.displayName,
-                sourcePath,
-                injectionError.message
-              );
+              throw new ContentInjectionError(this.displayName, sourcePath, injectionError.message);
             }
           }
 
@@ -350,12 +342,10 @@ class BaseIdeSetup {
           if (error.name && error.name.includes('Error') && error.ideName) {
             throw error;
           }
-          throw new CommandInstallationError(
-            this.displayName,
-            entry.name,
-            error.message,
-            { sourcePath, targetPath }
-          );
+          throw new CommandInstallationError(this.displayName, entry.name, error.message, {
+            sourcePath,
+            targetPath,
+          });
         }
       } else if (entry.isDirectory()) {
         // Recursively process subdirectory

package/tools/cli/installers/ide/cursor.js

@@ -7,6 +7,7 @@
 
 const path = require('node:path');
 const fs = require('fs-extra');
+const chalk = require('chalk');
 const { BaseIdeSetup } = require('./_base-ide');
 
 /**

package/tools/cli/installers/ide/windsurf.js

@@ -7,6 +7,7 @@
 
 const path = require('node:path');
 const fs = require('fs-extra');
+const chalk = require('chalk');
 const { BaseIdeSetup } = require('./_base-ide');
 
 /**