Move test scripts to scripts/ directory and fix simulation completion

- Moved test-protocols.sh, test-quick.sh, test-verbose.sh to scripts/
- Updated references in README.md and docs/testing-guide.md
- Fixed HeadlessSimulationRunner to properly run simulations to completion
- Fixed message delivery timing (now respects 500-2000ms delays)
- Added proper process time synchronization
- Fixed HeadlessProtocolRunner to exit cleanly

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

9 files changed, 177 insertions, 58 deletions

diff --git a/README.md b/README.md
index 9c1ac63..e7a7573 100644
--- a/README.md
+++ b/README.md
@@ -125,7 +125,7 @@ mvn clean package -DskipTests
 DS-Sim includes a framework for testing protocol simulations:
 ```bash
 # Interactive test runner (Note: produces GUI errors in headless mode)
-./test-protocols.sh
+./scripts/test-protocols.sh
 ```
 
 For detailed testing information, see [docs/testing-guide.md](docs/testing-guide.md).
diff --git a/docs/testing-guide.md b/docs/testing-guide.md
index b7f3182..b40c1bb 100644
--- a/docs/testing-guide.md
+++ b/docs/testing-guide.md
@@ -28,7 +28,7 @@ With the GUI decoupling implementation complete, protocol simulations now run cl
 
 ```bash
 # Use the interactive test script
-./test-protocols.sh
+./scripts/test-protocols.sh
 
 # Run all protocol tests directly
 java -cp target/classes:target/test-classes -Djava.awt.headless=true \
@@ -181,7 +181,7 @@ All tests now work in CI/CD environments:
 - name: Run all tests
   run: |
     mvn test
-    ./test-protocols.sh
+    ./scripts/test-protocols.sh
 ```
 
 ## Troubleshooting
diff --git a/test-protocols.sh b/scripts/test-protocols.sh
index 2edbef9..2edbef9 100755
--- a/test-protocols.sh
+++ b/scripts/test-protocols.sh
diff --git a/scripts/test-quick.sh b/scripts/test-quick.sh
new file mode 100755
index 0000000..a37c399
--- /dev/null
+++ b/scripts/test-quick.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+#
+# Quick test to verify simulation runs correctly
+#
+
+echo "Quick DS-Sim Protocol Test"
+echo "========================="
+echo
+
+# Test ping-pong with shorter timeout
+echo "Testing ping-pong protocol..."
+timeout 5 java -cp target/classes:target/test-classes \
+    -Djava.awt.headless=true \
+    -Dds.sim.headless=true \
+    testing.HeadlessProtocolRunner saved-simulations/ping-pong.dat
+
+if [ $? -eq 124 ]; then
+    echo "✗ Test timed out after 5 seconds"
+else
+    echo "✓ Test completed successfully"
+fi
\ No newline at end of file
diff --git a/test-verbose.sh b/scripts/test-verbose.sh
index b8fbbe3..e3362b3 100755
--- a/test-verbose.sh
+++ b/scripts/test-verbose.sh
@@ -51,4 +51,7 @@ javac -cp target/classes /tmp/TestVerbose.java -d /tmp
 java -cp /tmp:target/classes:target/test-classes -Djava.awt.headless=true TestVerbose "$@"
 
 # Clean up
-rm -f /tmp/TestVerbose.java /tmp/TestVerbose.class
\ No newline at end of file
+rm -f /tmp/TestVerbose.java /tmp/TestVerbose.class
+
+# Exit cleanly
+exit 0
\ No newline at end of file
diff --git a/src/main/java/simulator/engine/AbstractSimulationEngine.java b/src/main/java/simulator/engine/AbstractSimulationEngine.java
index 21be5c7..45b2522 100644
--- a/src/main/java/simulator/engine/AbstractSimulationEngine.java
+++ b/src/main/java/simulator/engine/AbstractSimulationEngine.java
@@ -16,7 +16,7 @@ public abstract class AbstractSimulationEngine implements SimulationEngine {
     protected final VSPrefs prefs;
     protected final List<VSInternalProcess> processes;
     protected final List<SimulationVisualizer> visualizers;
-    protected final VSTaskManager taskManager;
+    protected VSTaskManager taskManager;
     protected VSLogging loging;
     
     protected long time;
@@ -38,19 +38,16 @@ public abstract class AbstractSimulationEngine implements SimulationEngine {
     
     @Override
     public void sendMessage(VSMessage message) {
+        // Calculate proper delivery time
+        long deliveryTime = calculateDeliveryTime(message);
+        
         // Schedule message delivery to all processes (broadcast model)
-        scheduleMessageDelivery(message, time);
+        scheduleMessageDelivery(message, deliveryTime);
         
         // Notify visualizers
         for (SimulationVisualizer visualizer : visualizers) {
             visualizer.onMessageSent(message);
         }
-        
-        // Log the message
-        if (loging != null) {
-            loging.log("Message sent; ID: " + message.getMessageID() + 
-                      "; Protocol: " + message.getName());
-        }
     }
     
     protected abstract long calculateDeliveryTime(VSMessage message);
@@ -100,6 +97,14 @@ public abstract class AbstractSimulationEngine implements SimulationEngine {
         return taskManager;
     }
     
+    /**
+     * Set the task manager for this engine.
+     * Used when integrating with existing simulation infrastructure.
+     */
+    public void setTaskManager(VSTaskManager taskManager) {
+        this.taskManager = taskManager;
+    }
+    
     @Override
     public long getTime() {
         return time;
diff --git a/src/main/java/simulator/engine/HeadlessSimulationEngine.java b/src/main/java/simulator/engine/HeadlessSimulationEngine.java
index 36a64a7..fa6dde8 100644
--- a/src/main/java/simulator/engine/HeadlessSimulationEngine.java
+++ b/src/main/java/simulator/engine/HeadlessSimulationEngine.java
@@ -24,23 +24,12 @@ public class HeadlessSimulationEngine extends AbstractSimulationEngine {
             return time; // Deliver immediately if process not found
         }
         
-        // Calculate network delay
-        long networkDelay = prefs.getLong("sim.network.delay");
-        long variability = prefs.getLong("sim.network.variability");
+        // Use the process's getDurationTime method to get the message duration
+        // This respects the message.sendingtime.min and message.sendingtime.max preferences
+        long durationTime = source.getDurationTime();
         
-        // Add random variability
-        if (variability > 0) {
-            long variance = (long)(Math.random() * variability * 2) - variability;
-            networkDelay += variance;
-        }
-        
-        // Ensure minimum delay
-        if (networkDelay < 0) {
-            networkDelay = 0;
-        }
-        
-        // Calculate delivery time based on source process time
-        return source.getTime() + networkDelay;
+        // Calculate delivery time based on source process's global time + duration
+        return source.getGlobalTime() + durationTime;
     }
     
     @Override
@@ -49,6 +38,13 @@ public class HeadlessSimulationEngine extends AbstractSimulationEngine {
         VSInternalProcess sendingProcess = (VSInternalProcess) message.getSendingProcess();
         boolean recvOwn = prefs.getBoolean("sim.message.own.recv");
         
+        // Debug logging
+        if (loging != null) {
+            loging.log("Message " + message.getMessageID() + " scheduled for delivery at time " + 
+                      deliveryTime + " (sent at globalTime=" + sendingProcess.getGlobalTime() + 
+                      ", duration=" + (deliveryTime - sendingProcess.getGlobalTime()) + "ms)");
+        }
+        
         // Schedule delivery to all processes
         for (VSInternalProcess receiverProcess : processes) {
             if (receiverProcess.equals(sendingProcess)) {
@@ -62,12 +58,6 @@ public class HeadlessSimulationEngine extends AbstractSimulationEngine {
             VSMessageReceiveEvent receiveEvent = new VSMessageReceiveEvent(message);
             VSTask task = new VSTask(deliveryTime, receiverProcess, receiveEvent, VSTask.GLOBAL);
             taskManager.addTask(task);
-            
-            if (loging != null) {
-                loging.log("Message scheduled for delivery to process " + 
-                          receiverProcess.getProcessNum() + "; ID: " + 
-                          message.getMessageID() + "; Time: " + deliveryTime);
-            }
         }
     }
     
diff --git a/src/main/java/testing/HeadlessProtocolRunner.java b/src/main/java/testing/HeadlessProtocolRunner.java
index d68d743..daf96aa 100644
--- a/src/main/java/testing/HeadlessProtocolRunner.java
+++ b/src/main/java/testing/HeadlessProtocolRunner.java
@@ -38,7 +38,7 @@ public class HeadlessProtocolRunner {
         
         try {
             long startTime = System.currentTimeMillis();
-            SimulationResult result = runner.runSimulation(simFile, 5000); // 5 second timeout
+            SimulationResult result = runner.runSimulation(simFile, 10000); // 10 second timeout
             long duration = System.currentTimeMillis() - startTime;
             
             if (verbose) {
@@ -59,6 +59,9 @@ public class HeadlessProtocolRunner {
         } finally {
             runner.shutdown();
         }
+        
+        // Exit explicitly when running single simulation
+        System.exit(0);
     }
     
     private static void runAllSimulations(boolean verbose) throws Exception {
@@ -87,7 +90,7 @@ public class HeadlessProtocolRunner {
             
             try {
                 long startTime = System.currentTimeMillis();
-                SimulationResult result = runner.runSimulation(simFile.getPath(), 3000); // 3 second timeout
+                SimulationResult result = runner.runSimulation(simFile.getPath(), 10000); // 10 second timeout
                 long duration = System.currentTimeMillis() - startTime;
                 
                 System.out.println("✓ PASSED in " + duration + "ms");
diff --git a/src/main/java/testing/HeadlessSimulationRunner.java b/src/main/java/testing/HeadlessSimulationRunner.java
index ef50995..9d2274c 100644
--- a/src/main/java/testing/HeadlessSimulationRunner.java
+++ b/src/main/java/testing/HeadlessSimulationRunner.java
@@ -70,12 +70,16 @@ public class HeadlessSimulationRunner {
             }
             installLogCapture();
             
-            System.out.println("Running simulation for " + maxTime + "ms...");
+            // Get the simulation's configured end time
+            long untilTime = viz.getUntilTime();
+            long actualMaxTime = Math.min(maxTime, untilTime);
+            
+            System.out.println("Running simulation for up to " + actualMaxTime + "ms (until time: " + untilTime + "ms)...");
             
             // Run simulation
             Future<Void> runFuture = executor.submit(() -> {
                 try {
-                    runSimulationSteps(maxTime);
+                    runSimulationSteps(actualMaxTime);
                 } catch (Exception e) {
                     System.err.println("Error during simulation: " + e.getMessage());
                     e.printStackTrace();
@@ -85,7 +89,7 @@ public class HeadlessSimulationRunner {
             
             // Wait for completion or timeout
             try {
-                runFuture.get(maxTime * 2, TimeUnit.MILLISECONDS);
+                runFuture.get(actualMaxTime * 2, TimeUnit.MILLISECONDS);
             } catch (TimeoutException e) {
                 System.out.println("Simulation timeout - stopping...");
                 runFuture.cancel(true);
@@ -113,31 +117,126 @@ public class HeadlessSimulationRunner {
             .getDeclaredField("time");
         timeField.setAccessible(true);
         
-        // Find runTasks method with correct signature
-        Method runTasksMethod = VSTaskManager.class
-            .getDeclaredMethod("runTasks", long.class, long.class, long.class);
-        runTasksMethod.setAccessible(true);
+        // Get simulatorTime field for accurate time tracking
+        Field simulatorTimeField = VSSimulatorVisualization.class
+            .getDeclaredField("simulatorTime");
+        simulatorTimeField.setAccessible(true);
+        
+        // Get isPaused and hasFinished fields
+        Field isPausedField = VSSimulatorVisualization.class
+            .getDeclaredField("isPaused");
+        isPausedField.setAccessible(true);
+        Field hasFinishedField = VSSimulatorVisualization.class
+            .getDeclaredField("hasFinished");
+        hasFinishedField.setAccessible(true);
+        
+        // Get clockSpeed field and ensure it's set
+        Field clockSpeedField = VSSimulatorVisualization.class
+            .getDeclaredField("clockSpeed");
+        clockSpeedField.setAccessible(true);
+        double clockSpeed = clockSpeedField.getDouble(viz);
+        if (clockSpeed == 0) {
+            // Set default clock speed if not initialized
+            clockSpeed = 1.0;
+            clockSpeedField.setDouble(viz, clockSpeed);
+        }
+        
+        // Get task queue fields for checking if tasks remain
+        Field globalTasksField = VSTaskManager.class.getDeclaredField("globalTasks");
+        globalTasksField.setAccessible(true);
+        
+        // Set isPaused to false to allow simulation to run
+        isPausedField.setBoolean(viz, false);
+        hasFinishedField.setBoolean(viz, false);
         
         long startTime = timeField.getLong(viz);
         long currentTime = startTime;
+        long endTime = startTime + maxTime;
+        int noActivityCount = 0;
+        int lastLogCount = 0;
+        long lastActiveTime = 0;
         
-        while (currentTime - startTime < maxTime) {
-            // Update time
-            timeField.setLong(viz, currentTime);
-            
-            // Sync process times
+        // Call updateSimulator method to advance simulation
+        Method updateSimulatorMethod = VSSimulatorVisualization.class
+            .getDeclaredMethod("updateSimulator", long.class, long.class);
+        updateSimulatorMethod.setAccessible(true);
+        
+        System.out.println("Starting simulation at time " + startTime + ", running until " + endTime);
+        
+        while (currentTime < endTime) {
+            // Sync all process times BEFORE running tasks
             for (int i = 0; i < viz.getNumProcesses(); i++) {
-                viz.getProcess(i).syncTime(currentTime);
+                VSInternalProcess process = viz.getProcess(i);
+                if (process != null) {
+                    process.syncTime(currentTime);
+                }
             }
             
-            // Run tasks (step, offset, lastGlobalTime)
-            runTasksMethod.invoke(taskManager, currentTime, 0L, currentTime - 1);
+            // Update simulation time - this also runs tasks internally
+            updateSimulatorMethod.invoke(viz, currentTime, currentTime - 1);
+            long simulatorTime = simulatorTimeField.getLong(viz);
+            
+            // Check if there's been any activity
+            int currentLogCount = logCapture.getTotalLogCount();
+            boolean hasActivity = currentLogCount > lastLogCount || 
+                                 hasPendingActivity(taskManager, globalTasksField, simulatorTime);
+            
+            if (hasActivity) {
+                noActivityCount = 0;
+                lastLogCount = currentLogCount;
+                lastActiveTime = currentTime;
+            } else {
+                noActivityCount++;
+                // If no activity for 3000ms (3 seconds) of simulation time, stop
+                // This accounts for message delivery times of 500-2000ms plus some buffer
+                if (noActivityCount > 3000 && (currentTime - lastActiveTime) > 3000) {
+                    System.out.println("No activity detected for 3 seconds - simulation complete at time " + simulatorTime);
+                    break;
+                }
+            }
             
             // Advance time by 1ms
             currentTime++;
+            timeField.setLong(viz, currentTime);
             
-            // Small delay to prevent CPU spinning
-            Thread.sleep(1);
+            // No delay needed - let simulation run at full speed
+        }
+        
+        // Set isPaused back to true when done
+        isPausedField.setBoolean(viz, true);
+    }
+    
+    private boolean hasPendingActivity(VSTaskManager taskManager, Field globalTasksField, long currentTime) {
+        try {
+            // Check global tasks
+            Queue<?> globalTasks = (Queue<?>) globalTasksField.get(taskManager);
+            if (globalTasks != null && !globalTasks.isEmpty()) {
+                return true; // If any global tasks exist, keep running
+            }
+            
+            // Check process-specific tasks
+            for (int i = 0; i < viz.getNumProcesses(); i++) {
+                VSInternalProcess process = viz.getProcess(i);
+                if (process != null) {
+                    Queue<VSTask> tasks = process.getTasks();
+                    if (tasks != null && !tasks.isEmpty()) {
+                        return true; // If any process tasks exist, keep running
+                    }
+                }
+            }
+            
+            // Check for messages in transit
+            Field messageLinesField = VSSimulatorVisualization.class.getDeclaredField("messageLines");
+            messageLinesField.setAccessible(true);
+            LinkedList<?> messageLines = (LinkedList<?>) messageLinesField.get(viz);
+            if (messageLines != null && !messageLines.isEmpty()) {
+                return true; // Messages are still being delivered
+            }
+            
+            return false;
+        } catch (Exception e) {
+            // If we can't check, assume there might be activity
+            return true;
         }
     }
     
@@ -202,6 +301,9 @@ public class HeadlessSimulationRunner {
         // Create a headless simulation engine
         HeadlessSimulationEngine engine = new HeadlessSimulationEngine(prefs, logCapture);
         
+        // Set the task manager from the visualization
+        engine.setTaskManager(viz.getTaskManager());
+        
         // Copy processes to engine
         for (int i = 0; i < viz.getNumProcesses(); i++) {
             VSInternalProcess process = viz.getProcess(i);
@@ -213,10 +315,5 @@ public class HeadlessSimulationRunner {
                 process.setMessageHandler(handler);
             }
         }
-        
-        // Note: Task manager state is not copied because:
-        // - Global tasks are in VSTaskManager.globalTasks
-        // - Local tasks are stored in each VSInternalProcess.tasks
-        // - The engine already has references to the processes which contain their tasks
     }
 }
\ No newline at end of file