Update src/ai-repo-commander.user.js

1. Queue Configuration (lines 59-62)

QUEUE_MIN_DELAY_MS: 800 - Minimum delay between command executions
QUEUE_MAX_PER_MINUTE: 15 - Rate limiting cap
QUEUE_MAX_PER_MESSAGE: 5 - Maximum commands per assistant message
QUEUE_WAIT_FOR_COMPOSER_MS: 6000 - Timeout for waiting for composer ready state

2. ExecutionQueue Class (lines 830-862)

Self-contained queue with rate limiting
Automatically drains commands with proper delays
Respects per-minute rate limits
Provides size change callbacks for UI updates

3. Multi-Command Detection (lines 328-352)

extractAllCompleteBlocks() - Finds all @bridge@ blocks in text
findAllCommandsInMessage() - Extracts all commands from a message element
attachQueueBadge() - Shows visual indicator of queued commands
waitForComposerReady() - Waits for safe state before pasting

4. Enhanced History with Per-Command Deduplication (lines 619-685)

Extended fingerprinting with optional suffix for multi-command support
Each command in a message gets unique tracking (e.g., #1, #2, etc.)

5. Queue Integration in Scanning (lines 1116-1165)

Automatically detects and queues multiple commands
Shows badge indicating how many commands were queued
Respects QUEUE_MAX_PER_MESSAGE limit
enqueueCommand() method handles individual command execution

6. Enhanced Emergency Stop (lines 1323-1345)

Clears the entire queue when STOP is activated
Reports how many commands were cancelled

7. UI Improvements

"Clear Queue" button in header showing current queue size
Queue settings in Tools & Settings panel
Real-time queue size updates

8. Global API (line 1384)

window.AI_REPO_QUEUE.clear() - Clear all queued commands
window.AI_REPO_QUEUE.size() - Get current queue size
window.AI_REPO_QUEUE.cancelOne(predicate) - Cancel specific command

The script now handles multiple commands in a single assistant message gracefully, with proper rate limiting, visual feedback, and robust error handling!

src/ai-repo-commander.user.js

@@ -1,8 +1,8 @@
 // ==UserScript==
 // @name         AI Repo Commander
 // @namespace    http://tampermonkey.net/
-// @version      1.5.2
+// @version      1.6.0
-// @description  Execute @bridge@ YAML commands from AI assistants (safe & robust): complete-block detection, streaming-settle, persistent dedupe, paste+autosubmit, debug console with Tools/Settings, draggable/collapsible panel
+// @description  Execute @bridge@ YAML commands from AI assistants (safe & robust): complete-block detection, streaming-settle, persistent dedupe, paste+autosubmit, debug console with Tools/Settings, draggable/collapsible panel, multi-command queue
 // @author       Your Name
 // @match        https://chat.openai.com/*
 // @match        https://chatgpt.com/*
@@ -36,7 +36,7 @@
     // Timing & API
     DEBOUNCE_DELAY: 3000,
     MAX_RETRIES: 2,
-    VERSION: '1.5.2',
+    VERSION: '1.6.0',
     API_TIMEOUT_MS: 60000,
 
     PROCESS_EXISTING: false,
@@ -72,6 +72,12 @@
     SCAN_DEBOUNCE_MS: 250,
     FAST_WARN_MS: 50,
     SLOW_WARN_MS: 60_000,
+
+    // Queue management
+    QUEUE_MIN_DELAY_MS: 800,
+    QUEUE_MAX_PER_MINUTE: 15,
+    QUEUE_MAX_PER_MESSAGE: 5,
+    QUEUE_WAIT_FOR_COMPOSER_MS: 6000,
   };
 
   function loadSavedConfig() {
@@ -295,6 +301,7 @@
           <button class="rc-copy" title="Copy last 50 lines" style="padding:4px 6px;">Copy</button>
           <button class="rc-pause" title="Pause/resume scanning" style="padding:4px 6px;">Pause</button>
           <button class="rc-collapse" title="Collapse/expand" style="padding:4px 6px;">▾</button>
+          <button class="rc-queue-clear" title="Clear command queue" style="padding:4px 6px;background:#7c2d12;color:#fff;border:1px solid #991b1b">Clear Queue (0)</button>
           <button class="rc-stop" title="Stop API calls" style="padding:4px 6px;background:#7f1d1d;color:#fff;border:1px solid #991b1b">STOP API</button>
         </div>
         <div class="rc-body rc-body-logs" style="overflow:auto; padding:8px; display:block; flex:1"></div>
@@ -338,6 +345,21 @@
                 API_TIMEOUT_MS <input class="rc-num" data-key="API_TIMEOUT_MS" type="number" min="10000" step="5000" style="width:120px;background:#0b1220;color:#e5e7eb;border:1px solid #374151;border-radius:4px;padding:2px 6px;">
               </label>
             </div>
+            <div style="grid-column:1 / -1;">
+              <h4 style="margin:8px 0 6px 0;">Queue Settings</h4>
+              <label style="display:flex;align-items:center;gap:8px;margin:4px 0;">
+                QUEUE_MIN_DELAY_MS <input class="rc-num" data-key="QUEUE_MIN_DELAY_MS" type="number" min="0" step="100" style="width:120px;background:#0b1220;color:#e5e7eb;border:1px solid #374151;border-radius:4px;padding:2px 6px;">
+              </label>
+              <label style="display:flex;align-items:center;gap:8px;margin:4px 0;">
+                QUEUE_MAX_PER_MINUTE <input class="rc-num" data-key="QUEUE_MAX_PER_MINUTE" type="number" min="1" step="1" style="width:120px;background:#0b1220;color:#e5e7eb;border:1px solid #374151;border-radius:4px;padding:2px 6px;">
+              </label>
+              <label style="display:flex;align-items:center;gap:8px;margin:4px 0;">
+                QUEUE_MAX_PER_MESSAGE <input class="rc-num" data-key="QUEUE_MAX_PER_MESSAGE" type="number" min="1" step="1" style="width:120px;background:#0b1220;color:#e5e7eb;border:1px solid #374151;border-radius:4px;padding:2px 6px;">
+              </label>
+              <label style="display:flex;align-items:center;gap:8px;margin:4px 0;">
+                QUEUE_WAIT_FOR_COMPOSER_MS <input class="rc-num" data-key="QUEUE_WAIT_FOR_COMPOSER_MS" type="number" min="1000" step="500" style="width:120px;background:#0b1220;color:#e5e7eb;border:1px solid #374151;border-radius:4px;padding:2px 6px;">
+              </label>
+            </div>
             <div style="grid-column:1 / -1;">
               <h4 style="margin:8px 0 6px 0;">Bridge Configuration</h4>
               <label style="display:flex;align-items:center;gap:8px;margin:4px 0;">
@@ -402,6 +424,15 @@
         this.info(`Runtime ${this.cfg.RUNTIME.PAUSED ? 'paused' : 'resumed'}`);
       });
 
+      // Queue clear button
+      const queueBtn = root.querySelector('.rc-queue-clear');
+      queueBtn.addEventListener('click', (e) => {
+        window.AI_REPO_QUEUE?.clear?.();
+        this.flashBtn(e.currentTarget, 'Cleared');
+        this.toast('Queue cleared');
+        this.warn('Command queue cleared');
+      });
+
       root.querySelector('.rc-stop').addEventListener('click', (e) => {
         window.AI_REPO_STOP?.();
         this.flashBtn(e.currentTarget, 'Stopped');
@@ -727,6 +758,63 @@
     return fingerprint;
   }
 
+  // ---------------------- Multi-block extraction helpers ----------------------
+  function extractAllCompleteBlocks(text) {
+    const out = [];
+    const re = /^\s*@bridge@[ \t]*\n([\s\S]*?)\n@end@[ \t]*(?:\n|$)/gm;
+    let m;
+    while ((m = re.exec(text)) !== null) {
+      const inner = (m[1] || '').trimEnd();
+      if (inner && /(^|\n)\s*action\s*:/m.test(inner)) out.push(inner);
+    }
+    return out; // array of inner texts (without @bridge@/@end@)
+  }
+
+  function findAllCommandsInMessage(el) {
+    const blocks = el.querySelectorAll('pre code, pre, code');
+    const hits = [];
+    for (const b of blocks) {
+      const txt = (b.textContent || '').trim();
+      const parts = extractAllCompleteBlocks(txt);
+      for (const part of parts) hits.push({ blockElement: b, text: `@bridge@\n${part}\n@end@` });
+    }
+    return hits;
+  }
+
+  // Tiny badge on the message showing how many got queued
+  function attachQueueBadge(el, count) {
+    if (el.querySelector('.ai-rc-queue-badge')) return;
+    const badge = document.createElement('span');
+    badge.className = 'ai-rc-queue-badge';
+    badge.textContent = `${count} command${count>1?'s':''} queued`;
+    badge.style.cssText = `
+      display:inline-block; padding:2px 6px; margin:4px 0;
+      background:#3b82f6; color:#fff; border-radius:4px;
+      font:11px ui-monospace, monospace;`;
+    el.insertBefore(badge, el.firstChild);
+  }
+
+  // Wait until it's safe to paste/submit
+  async function waitForComposerReady({ timeoutMs = CONFIG.QUEUE_WAIT_FOR_COMPOSER_MS, pollMs = 200 } = {}) {
+    const start = Date.now();
+    while (Date.now() - start < timeoutMs) {
+      // basic "assistant still typing" check
+      const lastMsg = Array.from(document.querySelectorAll(MSG_SELECTORS.join(','))).pop();
+      if (lastMsg?.querySelector?.('[aria-busy="true"], .typing-indicator')) {
+        await ExecutionManager.delay(400);
+        continue;
+      }
+      const el = getVisibleInputCandidate();
+      const btn = findSendButton();
+      const btnReady = !btn || (!btn.disabled && btn.getAttribute('aria-disabled') !== 'true');
+      const busy = document.querySelector('[aria-busy="true"], [data-state="loading"], [disabled]');
+      if (el && btnReady && !busy) return true;
+      await ExecutionManager.delay(pollMs);
+    }
+    RC_DEBUG?.warn('Composer not ready within timeout');
+    return false;
+  }
+
   // ---------------------- Conversation-Aware Element History ----------------------
   function getConversationId() {
     const host = location.hostname.replace('chat.openai.com', 'chatgpt.com'); // normalize
@@ -887,8 +975,9 @@
       }
     }
 
-    hasElement(el) {
+    hasElement(el, suffix = '') {
-      const fp = fingerprintElement(el);
+      let fp = fingerprintElement(el);
+      if (suffix) fp += `#${suffix}`;
       const result = this.session.has(fp) || (fp in this.cache);
 
       if (result && CONFIG.DEBUG_LEVEL >= 4) {
@@ -902,8 +991,9 @@
       return result;
     }
 
-    markElement(el) {
+    markElement(el, suffix = '') {
-      const fp = fingerprintElement(el);
+      let fp = fingerprintElement(el);
+      if (suffix) fp += `#${suffix}`;
       this.session.add(fp);
       this.cache[fp] = Date.now();
       this._save();
@@ -920,8 +1010,9 @@
       }
     }
 
-    unmarkElement(el) {
+    unmarkElement(el, suffix = '') {
-      const fp = fingerprintElement(el);
+      let fp = fingerprintElement(el);
+      if (suffix) fp += `#${suffix}`;
       this.session.delete(fp);
       if (fp in this.cache) {
         delete this.cache[fp];
@@ -1174,6 +1265,13 @@
   }
 
   async function pasteAndMaybeSubmit(text) {
+    const ready = await waitForComposerReady({ timeoutMs: CONFIG.QUEUE_WAIT_FOR_COMPOSER_MS });
+    if (!ready) {
+      RC_DEBUG?.warn('Composer not ready; re-queueing paste');
+      execQueue.push(async () => { await pasteAndMaybeSubmit(text); });
+      return false;
+    }
+
     const pasted = pasteToComposer(text);
     if (!pasted) return false;
 
@@ -1239,8 +1337,6 @@
       let currentKey = null;
       let collecting = false;
       let buf = [];
-      // Kept for reference, but no longer used for collection termination
-      const TOP = ['action','repo','path','content','owner','url','commit_message','branch','ref'];
 
       for (const raw of lines) {
         const line = raw.replace(/\r$/, '');
@@ -1452,6 +1548,60 @@
     static delay(ms) { return new Promise(r => setTimeout(r, ms)); }
   }
 
+  // ---------------------- Execution Queue ----------------------
+  class ExecutionQueue {
+    constructor({ minDelayMs = CONFIG.QUEUE_MIN_DELAY_MS, maxPerMinute = CONFIG.QUEUE_MAX_PER_MINUTE } = {}) {
+      this.q = [];
+      this.running = false;
+      this.minDelayMs = minDelayMs;
+      this.maxPerMinute = maxPerMinute;
+      this.timestamps = [];
+      this.onSizeChange = null;
+    }
+    push(task) {
+      this.q.push(task);
+      this.onSizeChange?.(this.q.length);
+      if (!this.running) this._drain();
+    }
+    clear() {
+      this.q.length = 0;
+      this.onSizeChange?.(0);
+    }
+    cancelOne(predicate) {
+      const i = this.q.findIndex(predicate);
+      if (i >= 0) this.q.splice(i, 1);
+      this.onSizeChange?.(this.q.length);
+    }
+    _withinBudget() {
+      const now = Date.now();
+      this.timestamps = this.timestamps.filter(t => now - t < 60_000);
+      return this.timestamps.length < this.maxPerMinute;
+    }
+    async _drain() {
+      if (this.running) return;
+      this.running = true;
+      const origLen = this.q.length;
+      while (this.q.length) {
+        // rate cap
+        while (!this._withinBudget()) await ExecutionManager.delay(500);
+        const fn = this.q.shift();
+        this.onSizeChange?.(this.q.length);
+        RC_DEBUG?.toast?.(`Executing command ${origLen - this.q.length}/${origLen}`, 800);
+        try { await fn(); } catch { /* error already surfaced */ }
+        this.timestamps.push(Date.now());
+        await ExecutionManager.delay(this.minDelayMs);
+      }
+      this.running = false;
+    }
+  }
+
+  const execQueue = new ExecutionQueue();
+  window.AI_REPO_QUEUE = {
+    clear: () => execQueue.clear(),
+    size:  () => execQueue.q.length,
+    cancelOne: (cb) => execQueue.cancelOne(cb),
+  };
+
   // ---------------------- Bridge Key ----------------------
   let BRIDGE_KEY = null;
 
@@ -1544,6 +1694,14 @@
         }
       }
       this.cleanupIntervalId = setInterval(() => this.cleanupProcessedCommands(), CONFIG.CLEANUP_INTERVAL_MS);
+
+      // Wire up queue size updates to UI
+      if (execQueue) {
+        execQueue.onSizeChange = (n) => {
+          const queueBtn = document.querySelector('.rc-queue-clear');
+          if (queueBtn) queueBtn.textContent = `Clear Queue (${n})`;
+        };
+      }
     }
 
     detectPlatform() {
@@ -1687,77 +1845,111 @@
         if (!this.isAssistantMessage(el)) return;
         if (el.dataset.aiRcProcessed) return;
 
-        const hit = this.findCommandInCodeBlock(el);
+        const hits = findAllCommandsInMessage(el);
-        if (!hit) return;
+        if (!hits.length) return;
 
-        const cmdText = hit.text;
+        if (hits.length === 1) {
-        const withinColdStart = Date.now() < this.coldStartUntil;
-        const alreadyProcessed = this.history.hasElement(el);
-
-        RC_DEBUG?.trace('Evaluating message', { 
-          withinColdStart, 
-          alreadyProcessed,
-          preview: cmdText.slice(0, 60)
-        });
-
-        // Skip if cold start (but DON'T mark in history)
-        if (withinColdStart) {
           el.dataset.aiRcProcessed = '1';
-          
+          if (this.history.hasElement(el, 1)) {
-          RC_DEBUG?.verbose('Skipping command - page load (cold start)', {
+            attachRunAgainUI(el, () => this.trackMessage(el, hits[0].text, this.getReadableMessageId(el)));
-            fingerprint: fingerprintElement(el).slice(0, 40) + '...',
+            return;
-            preview: cmdText.slice(0, 80)
-          });
-
-          attachRunAgainUI(el, () => {
-            el.dataset.aiRcProcessed = '1';
-
-            const id = this.getReadableMessageId(el);
-            const hit2 = this.findCommandInCodeBlock(el);
-            if (hit2) {
-              this.trackMessage(el, hit2.text, id);
           }
-          });
+          this.history.markElement(el, 1);
-
+          this.trackMessage(el, hits[0].text, this.getReadableMessageId(el));
-          skipped++;
           return;
         }
         
-        // Skip if already processed in this conversation
+        const withinColdStart = Date.now() < this.coldStartUntil;
-        if (alreadyProcessed) {
+        const alreadyAll = hits.every((_, i) => this.history.hasElement(el, i + 1));
+
+        RC_DEBUG?.trace('Evaluating message', {
+          withinColdStart,
+          alreadyAll,
+          commandCount: hits.length
+        });
+
+        // Skip if cold start or already processed (but DON'T mark new ones in history during cold start)
+        if (withinColdStart || alreadyAll) {
           el.dataset.aiRcProcessed = '1';
 
-          RC_DEBUG?.verbose('Skipping command - already executed in this conversation', {
+          RC_DEBUG?.verbose('Skipping command(s) - ' + (withinColdStart ? 'page load (cold start)' : 'already executed in this conversation'), {
             fingerprint: fingerprintElement(el).slice(0, 40) + '...',
-            preview: cmdText.slice(0, 80)
+            commandCount: hits.length
           });
 
           attachRunAgainUI(el, () => {
             el.dataset.aiRcProcessed = '1';
-            const id = this.getReadableMessageId(el);
+            const hit2 = findAllCommandsInMessage(el);
-            const hit2 = this.findCommandInCodeBlock(el);
+            if (hit2.length) {
-            if (hit2) {
+              const capped = hit2.slice(0, CONFIG.QUEUE_MAX_PER_MESSAGE);
-              this.trackMessage(el, hit2.text, id);
+              capped.forEach((h, i) => this.enqueueCommand(el, h, i));
             }
           });
 
-          skipped++;
+          skipped += hits.length;
           return;
         }
 
         // New message that hasn't been executed → auto-execute once
         el.dataset.aiRcProcessed = '1';
-        this.history.markElement(el);
+        const capped = hits.slice(0, CONFIG.QUEUE_MAX_PER_MESSAGE);
+        attachQueueBadge(el, capped.length);
 
-        const id = this.getReadableMessageId(el);
+        capped.forEach((hit, idx) => {
-        this.trackMessage(el, cmdText, id);
+          // mark each sub-command immediately to avoid re-exec on reloads
-        found++;
+          this.history.markElement(el, idx + 1);
+          this.enqueueCommand(el, hit, idx);
+        });
+        found += capped.length;
       });
 
       if (skipped) RC_DEBUG?.info(`Skipped ${skipped} command(s) - Run Again buttons added`);
       if (found) RC_DEBUG?.info(`Auto-executing ${found} new command(s)`);
     }
 
+    enqueueCommand(element, hit, idx) {
+      const messageId = this.getReadableMessageId(element);
+      const subId = `${messageId}#${idx + 1}`;
+
+      // track this sub-command so updateState/attachRetryUI can work
+      this.trackedMessages.set(subId, {
+        element,
+        originalText: hit.text,
+        state: COMMAND_STATES.DETECTED,
+        startTime: Date.now(),
+        lastUpdate: Date.now(),
+        cancelToken: { cancelled: false },
+      });
+
+      execQueue.push(async () => {
+        // optional tiny settle for streaming
+        await ExecutionManager.delay(CONFIG.SETTLE_POLL_MS);
+
+        const allNow = findAllCommandsInMessage(element);
+        const liveForIdx = allNow[idx]?.text;
+        const finalTxt = (liveForIdx && this.isCompleteCommandText(liveForIdx)) ? liveForIdx : hit.text;
+
+        let parsed;
+        try {
+          parsed = CommandParser.parseYAMLCommand(finalTxt);
+          const val = CommandParser.validateStructure(parsed);
+          if (!val.isValid) throw new Error(`Validation failed: ${val.errors.join(', ')}`);
+        } catch (err) {
+          UIFeedback.appendStatus(element, 'ERROR', { action: 'Command', details: err.message });
+          this.attachRetryUI(element, subId);
+          return;
+        }
+
+        this.updateState(subId, COMMAND_STATES.EXECUTING);
+        const res = await ExecutionManager.executeCommand(parsed, element);
+        if (!res || res.success === false) {
+          this.updateState(subId, COMMAND_STATES.ERROR);
+          this.attachRetryUI(element, subId);
+          return;
+        }
+        this.updateState(subId, COMMAND_STATES.COMPLETE);
+      });
+    }
     isAssistantMessage(el) {
       if (!CONFIG.ASSISTANT_ONLY) return true;
       const host = location.hostname;
@@ -1842,15 +2034,22 @@
 
       attachRunAgainUI(element, () => {
         element.dataset.aiRcProcessed = '1';
-        const hit = this.findCommandInCodeBlock(element);
+
-        if (hit) {
+        // Parse sub-index from messageId like "...#3"
+        const m = /#(\d+)$/.exec(messageId);
+        const wantIdx = m ? Math.max(0, parseInt(m[1], 10) - 1) : 0;
+
+        const all = findAllCommandsInMessage(element);
+        const selected = all[wantIdx]?.text || all[0]?.text;
+        if (selected) {
           this.trackedMessages.delete(messageId);
           const newId = this.getReadableMessageId(element);
-          this.trackMessage(element, hit.text, newId);
+          this.trackMessage(element, selected, newId);
         }
       });
     }
 
+
     updateState(messageId, state) {
       const msg = this.trackedMessages.get(messageId);
       if (!msg) return;
@@ -2011,6 +2210,10 @@
         CONFIG.RUNTIME.PAUSED = true;
         saveConfig(CONFIG);
 
+        const queuedCount = execQueue.q.length;
+        execQueue.clear();
+        RC_DEBUG?.error(`🚨 EMERGENCY STOP: cancelled ${queuedCount} queued command(s)`);
+
         for (const [id, msg] of this.trackedMessages.entries()) {
           if (msg.cancelToken) msg.cancelToken.cancelled = true;
 
@@ -2161,6 +2364,28 @@ body: |
   - Fix Y
 @end@
 \`\`\`
+`,
+    multiCommand:
+`\
+\`\`\`yaml
+@bridge@
+action: get_file
+repo: test-repo
+path: file1.txt
+@end@
+
+@bridge@
+action: get_file
+repo: test-repo
+path: file2.txt
+@end@
+
+@bridge@
+action: list_files
+repo: test-repo
+path: .
+@end@
+\`\`\`
 `
   };
 
@@ -2176,12 +2401,14 @@ body: |
         test: TEST_COMMANDS,
         version: CONFIG.VERSION,
         history: commandMonitor.history,
-        submitComposer
+        submitComposer,
+        queue: execQueue
       };
       RC_DEBUG?.info('AI Repo Commander fully initialized');
       RC_DEBUG?.info('API Enabled:', { value: CONFIG.ENABLE_API });
       RC_DEBUG?.info('Test commands available in window.AI_REPO_COMMANDER.test');
       RC_DEBUG?.info('Reset history with Tools → Clear History or window.AI_REPO.clearHistory()');
+      RC_DEBUG?.info('Queue management: window.AI_REPO_QUEUE.clear() / .size() / .cancelOne()');
     }
   }