Merge lp:~danilovesky/workcraft/trunk-ui-tools-output into lp:workcraft

[Danil Sokolov]

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/stg/CircuitStgUtils.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/stg/CircuitStgUtils.java	2016-01-02 22:46:33 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/stg/CircuitStgUtils.java	2016-01-15 17:12:28 +0000
@@ -114,7 +114,7 @@
 	}
 
 	public static Result<? extends Object> exportStg(STG stg, File stgFile, File directory, 
-			ProgressMonitor<? super MpsatChainResult> monitor) throws IOException {
+			ProgressMonitor<? super MpsatChainResult> monitor) {
 		
 		Framework framework = Framework.getInstance();
 		PluginManager pluginManager = framework.getPluginManager();
@@ -123,7 +123,7 @@
 			throw new RuntimeException("Exporter not available: model class " + stg.getClass().getName() + " to .g format.");
 		}
 		
-		ExportTask exportTask = new ExportTask(stgExporter, stg, stgFile.getCanonicalPath());
+		ExportTask exportTask = new ExportTask(stgExporter, stg, stgFile.getAbsolutePath());
 		String description = "Exporting " + stgFile.getAbsolutePath();
 		SubtaskMonitor<Object> subtaskMonitor = null;
 		if (monitor != null) {
 
=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/tasks/CheckCircuitTask.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/tasks/CheckCircuitTask.java	2016-01-09 22:12:07 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/tasks/CheckCircuitTask.java	2016-01-15 17:12:28 +0000
@@ -176,7 +176,7 @@
 			Result<? extends ExternalProcessResult> punfResult = null;
 			if (checkDeadlock || checkHazard) {
 				unfoldingFile = new File(directory, StgUtils.SYSTEM_FILE_NAME + PunfUtilitySettings.getUnfoldingExtension(true));
-				punfTask = new PunfTask(sysStgFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+				punfTask = new PunfTask(sysStgFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 				SubtaskMonitor<Object> punfMonitor = new SubtaskMonitor<Object>(monitor);
 				punfResult = framework.getTaskManager().execute(punfTask, "Unfolding .g", punfMonitor);
 				
@@ -195,7 +195,7 @@
 			if (hasEnvironment && checkConformation) {
 				if ((sysStgFile != sysModStgFile) || (unfoldingModFile == null)) {
 					unfoldingModFile = new File(directory, StgUtils.SYSTEM_FILE_NAME + StgUtils.MODIFIED_FILE_SUFFIX + PunfUtilitySettings.getUnfoldingExtension(true));
-					punfModTask = new PunfTask(sysModStgFile.getCanonicalPath(), unfoldingModFile.getCanonicalPath());
+					punfModTask = new PunfTask(sysModStgFile.getAbsolutePath(), unfoldingModFile.getAbsolutePath());
 					SubtaskMonitor<Object> punfModMonitor = new SubtaskMonitor<Object>(monitor);
 					punfModResult = framework.getTaskManager().execute(punfModTask, "Unfolding .g", punfModMonitor);
 					
@@ -214,7 +214,7 @@
 			// Check for deadlock (if requested)
 			if (checkDeadlock) {
 				MpsatTask mpsatDeadlockTask = new MpsatTask(deadlockSettings.getMpsatArguments(directory),
-						unfoldingFile.getCanonicalPath(), directory, true);
+						unfoldingFile.getAbsolutePath(), directory, true);
 				SubtaskMonitor<Object> mpsatMonitor = new SubtaskMonitor<Object>(monitor);
 				Result<? extends ExternalProcessResult> mpsatDeadlockResult = framework.getTaskManager().execute(
 						mpsatDeadlockTask, "Running deadlock check [MPSat]", mpsatMonitor);
@@ -240,7 +240,7 @@
 			// Check for hazards (if requested)
 			if (checkHazard) {
 				MpsatTask mpsatHazardTask = new MpsatTask(hazardSettings.getMpsatArguments(directory),
-						unfoldingFile.getCanonicalPath(), directory, true);
+						unfoldingFile.getAbsolutePath(), directory, true);
 				if (MpsatUtilitySettings.getDebugReach()) {
 					System.out.println("\nReach expression for the hazard property:");
 					System.out.println(hazardSettings.getReach());
@@ -281,7 +281,7 @@
 						MpsatUtilitySettings.getSolutionCount(), reachConformation, true);
 				
 				MpsatTask mpsatConformationTask = new MpsatTask(conformationSettings.getMpsatArguments(directory),
-						unfoldingModFile.getCanonicalPath(), directory, true);
+						unfoldingModFile.getAbsolutePath(), directory, true);
 				SubtaskMonitor<Object> mpsatMonitor = new SubtaskMonitor<Object>(monitor);
 				Result<? extends ExternalProcessResult>  mpsatConformationResult = framework.getTaskManager().execute(
 						mpsatConformationTask, "Running conformation check [MPSat]", mpsatMonitor);
 
=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/ProcessIO.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/ProcessIO.java	2010-11-29 15:02:36 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/ProcessIO.java	2016-01-15 17:12:28 +0000
@@ -65,7 +65,7 @@
 			
 			writeFile(input, inputFile);
 			
-			Process minisat = Runtime.getRuntime().exec(new String[]{minisatPath, inputFile.getCanonicalPath(), outputFile.getCanonicalPath()});
+			Process minisat = Runtime.getRuntime().exec(new String[]{minisatPath, inputFile.getAbsolutePath(), outputFile.getAbsolutePath()});
 			minisat.getOutputStream().close();
 			while(true) {
 				int r = minisat.getInputStream().read();
@@ -80,7 +80,6 @@
 			}
 			
 			result = readFile(outputFile);
-			
 		} catch (IOException e) {
 			throw new RuntimeException(e);
 		}
 
=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/PGMinerTask.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/PGMinerTask.java	2015-12-26 23:27:09 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/PGMinerTask.java	2016-01-15 17:12:28 +0000
@@ -42,7 +42,7 @@
 			command.add(inputFile.getAbsolutePath());
 			
 			//Call PGMiner
-			ExternalProcessTask task = new ExternalProcessTask(command, new File("."));
+			ExternalProcessTask task = new ExternalProcessTask(command, new File("."), false, false);
 			SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor);
 			
 			Result<? extends ExternalProcessResult> result = task.run(mon);
 
=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ScencoExternalToolTask.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ScencoExternalToolTask.java	2015-11-02 13:37:58 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ScencoExternalToolTask.java	2016-01-15 17:12:28 +0000
@@ -2,8 +2,6 @@
 
 import java.util.ArrayList;
 
-import javax.swing.JOptionPane;
-
 import org.workcraft.interop.ExternalProcessListener;
 import org.workcraft.plugins.shared.tasks.ExternalProcessResult;
 import org.workcraft.plugins.shared.tasks.ExternalProcessTask;
@@ -37,9 +35,9 @@
 		}
 		
 		// Running the tool through external process interface
-		ExternalProcessTask externalProcessTask = new ExternalProcessTask(args);
+		ExternalProcessTask task = new ExternalProcessTask(args, null, false, false);
 		SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor); 
-		Result<? extends ExternalProcessResult> result = externalProcessTask.run(mon);
+		Result<? extends ExternalProcessResult> result = task.run(mon);
 		
 		// Handling the result
 		if (result.getOutcome() == Outcome.CANCELLED) {
 
=== modified file 'DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowDeadlockTask.java'
--- DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowDeadlockTask.java	2016-01-09 22:12:07 +0000
+++ DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowDeadlockTask.java	2016-01-15 17:12:28 +0000
@@ -58,7 +58,7 @@
 			monitor.progressUpdate(0.10);
 			
 			File netFile = new File(directory, "net" + exporter.getExtenstion());
-			ExportTask exportTask = new ExportTask(exporter, model, netFile.getCanonicalPath());
+			ExportTask exportTask = new ExportTask(exporter, model, netFile.getAbsolutePath());
 			SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor);
 			Result<? extends Object> exportResult = framework.getTaskManager().execute(
 					exportTask, "Exporting .g", mon);
@@ -73,7 +73,7 @@
 			monitor.progressUpdate(0.20);
 			
 			File unfoldingFile = new File(directory, "unfolding" + PunfUtilitySettings.getUnfoldingExtension(true));
-			PunfTask punfTask = new PunfTask(netFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+			PunfTask punfTask = new PunfTask(netFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(
 					punfTask, "Unfolding .g", mon);
 			
@@ -87,7 +87,7 @@
 			monitor.progressUpdate(0.70);
 
 			MpsatTask mpsatTask = new MpsatTask(settings.getMpsatArguments(directory),
-					unfoldingFile.getCanonicalPath(), directory, true);
+					unfoldingFile.getAbsolutePath(), directory, true);
 			Result<? extends ExternalProcessResult> mpsatResult = framework.getTaskManager().execute(
 					mpsatTask, "Running deadlock checking [MPSat]", mon);
 			
 
=== modified file 'DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowHazardTask.java'
--- DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowHazardTask.java	2016-01-09 22:12:07 +0000
+++ DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowHazardTask.java	2016-01-15 17:12:28 +0000
@@ -58,7 +58,7 @@
 			monitor.progressUpdate(0.10);
 			
 			File netFile = new File(directory, "net" + exporter.getExtenstion());
-			ExportTask exportTask = new ExportTask(exporter, model, netFile.getCanonicalPath());
+			ExportTask exportTask = new ExportTask(exporter, model, netFile.getAbsolutePath());
 			SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor);
 			Result<? extends Object> exportResult = framework.getTaskManager().execute(
 					exportTask, "Exporting .g", mon);
@@ -73,7 +73,7 @@
 			monitor.progressUpdate(0.20);
 			
 			File unfoldingFile = new File(directory, "unfolding" + PunfUtilitySettings.getUnfoldingExtension(true));
-			PunfTask punfTask = new PunfTask(netFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+			PunfTask punfTask = new PunfTask(netFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(
 					punfTask, "Unfolding .g", mon);
 			
@@ -87,7 +87,7 @@
 			monitor.progressUpdate(0.40);
 
 			MpsatTask mpsatTask = new MpsatTask(settings.getMpsatArguments(directory),
-					unfoldingFile.getCanonicalPath(), directory, true);
+					unfoldingFile.getAbsolutePath(), directory, true);
 			Result<? extends ExternalProcessResult> mpsatResult = framework.getTaskManager().execute(
 					mpsatTask, "Running semimodularity checking [MPSat]", mon);
 			
 
=== modified file 'DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowTask.java'
--- DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowTask.java	2016-01-09 22:12:07 +0000
+++ DfsPlugin/src/org/workcraft/plugins/dfs/tasks/CheckDataflowTask.java	2016-01-15 17:12:28 +0000
@@ -63,7 +63,7 @@
 			monitor.progressUpdate(0.10);
 			
 			File netFile = new File(directory, "net" + exporter.getExtenstion());
-			ExportTask exportTask = new ExportTask(exporter, model, netFile.getCanonicalPath());
+			ExportTask exportTask = new ExportTask(exporter, model, netFile.getAbsolutePath());
 			SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor);
 			Result<? extends Object> exportResult = framework.getTaskManager().execute(
 					exportTask, "Exporting .g", mon);
@@ -78,7 +78,7 @@
 			monitor.progressUpdate(0.20);
 			
 			File unfoldingFile = new File(directory, "unfolding" + PunfUtilitySettings.getUnfoldingExtension(true));
-			PunfTask punfTask = new PunfTask(netFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+			PunfTask punfTask = new PunfTask(netFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(
 					punfTask, "Unfolding .g", mon);
 			
@@ -92,7 +92,7 @@
 			monitor.progressUpdate(0.40);
 
 			MpsatTask mpsatTask = new MpsatTask(deadlockSettings.getMpsatArguments(directory),
-					unfoldingFile.getCanonicalPath(), directory, true);
+					unfoldingFile.getAbsolutePath(), directory, true);
 			Result<? extends ExternalProcessResult> mpsatResult = framework.getTaskManager().execute(
 					mpsatTask, "Running deadlock checking [MPSat]", mon);
 			
@@ -113,7 +113,7 @@
 			monitor.progressUpdate(0.70);
 
 			mpsatTask = new MpsatTask(hazardSettings.getMpsatArguments(directory), 
-					unfoldingFile.getCanonicalPath(), directory, true);
+					unfoldingFile.getAbsolutePath(), directory, true);
 			mpsatResult = framework.getTaskManager().execute(mpsatTask, "Running semimodularity checking [MPSat]", mon);
 			if (mpsatResult.getOutcome() != Outcome.FINISHED) {
 				if (mpsatResult.getOutcome() == Outcome.CANCELLED) {
 
=== modified file 'FstPlugin/src/org/workcraft/plugins/fst/task/WriteSgConversionTask.java'
--- FstPlugin/src/org/workcraft/plugins/fst/task/WriteSgConversionTask.java	2015-10-13 17:22:00 +0000
+++ FstPlugin/src/org/workcraft/plugins/fst/task/WriteSgConversionTask.java	2016-01-15 17:12:28 +0000
@@ -88,7 +88,7 @@
 
 			// Generating .g file for Petri Net
 			pnFile = File.createTempFile("stg_", ".g");
-			ExportTask pnExportTask = new ExportTask(pnExporter, pn, pnFile.getCanonicalPath());
+			ExportTask pnExportTask = new ExportTask(pnExporter, pn, pnFile.getAbsolutePath());
 			Result<? extends Object> pnExportResult = framework.getTaskManager().execute(
 					pnExportTask, "Exporting .g", subtaskMonitor);
 			
@@ -107,7 +107,7 @@
 			}
 
 			while (true) {
-				WriteSgTask writeSgTask = new WriteSgTask(pnFile.getCanonicalPath(), null, writeSgOptions);
+				WriteSgTask writeSgTask = new WriteSgTask(pnFile.getAbsolutePath(), null, writeSgOptions);
 				Result<? extends ExternalProcessResult> writeSgResult = framework.getTaskManager().execute(
 						writeSgTask, "Building state graph", subtaskMonitor);
 				
 
=== modified file 'MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/MpsatSynthesisUtilitySettings.java'
--- MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/MpsatSynthesisUtilitySettings.java	2015-12-30 23:43:20 +0000
+++ MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/MpsatSynthesisUtilitySettings.java	2016-01-15 17:12:28 +0000
@@ -35,12 +35,18 @@
 	
 	private static final String keyCommand = prefix + ".command";
 	private static final String keyExtraArgs = prefix + ".args";
+	private static final String keyPrintStdout= prefix + ".printStdout";
+	private static final String keyPrintStderr= prefix + ".printStderr";
 	
 	private static final String defaultCommand = (DesktopApi.getOs().isWindows() ? "tools\\UnfoldingTools\\mpsat.exe" : "tools/UnfoldingTools/mpsat");
 	private static final String defaultExtraArgs = "";
+	private static final Boolean defaultPrintStdout = true;
+	private static final Boolean defaultPrintStderr = true;
 
 	private static String command = defaultCommand;
 	private static String extraArgs = defaultExtraArgs;
+	private static Boolean printStdout = defaultPrintStdout;
+	private static Boolean printStderr = defaultPrintStderr;
 
 	public MpsatSynthesisUtilitySettings() {
 		properties.add(new PropertyDeclaration<MpsatSynthesisUtilitySettings, String>(
@@ -57,11 +63,32 @@
 				this, "Additional parameters", String.class, true, false, false) {
 			protected void setter(MpsatSynthesisUtilitySettings object, String value) {
 				setExtraArgs(value);
+				
 			}
 			protected String getter(MpsatSynthesisUtilitySettings object) {
 				return getExtraArgs();
 			}
 		});
+
+		properties.add(new PropertyDeclaration<MpsatSynthesisUtilitySettings, Boolean>(
+				this, "Output stdout", Boolean.class, true, false, false) {
+			protected void setter(MpsatSynthesisUtilitySettings object, Boolean value) {
+				setPrintStdout(value);
+			}
+			protected Boolean getter(MpsatSynthesisUtilitySettings object) {
+				return getPrintStdout();
+			}
+		});
+
+		properties.add(new PropertyDeclaration<MpsatSynthesisUtilitySettings, Boolean>(
+				this, "Output stderr", Boolean.class, true, false, false) {
+			protected void setter(MpsatSynthesisUtilitySettings object, Boolean value) {
+				setPrintStderr(value);
+			}
+			protected Boolean getter(MpsatSynthesisUtilitySettings object) {
+				return getPrintStderr();
+			}
+		});
 	}
 	
 	@Override
@@ -73,12 +100,16 @@
 	public void load(Config config) {
 		setCommand(config.getString(keyCommand, defaultCommand));
 		setExtraArgs(config.getString(keyExtraArgs, defaultExtraArgs));
+		setPrintStdout(config.getBoolean(keyPrintStdout, defaultPrintStdout));
+		setPrintStderr(config.getBoolean(keyPrintStderr, defaultPrintStderr));
 	}
 
 	@Override
 	public void save(Config config) {
 		config.set(keyCommand, getCommand());
 		config.set(keyExtraArgs, getExtraArgs());
+		config.setBoolean(keyPrintStdout, getPrintStdout());
+		config.setBoolean(keyPrintStderr, getPrintStderr());
 	}
 	
 	@Override
@@ -107,4 +138,20 @@
 		extraArgs = value;
 	}
 
+	public static Boolean getPrintStdout() {
+		return printStdout;
+	}
+
+	public static void setPrintStdout(Boolean value) {
+		printStdout = value;
+	}
+
+	public static Boolean getPrintStderr() {
+		return printStderr;
+	}
+
+	public static void setPrintStderr(Boolean value) {
+		printStderr = value;
+	}
+
 }
 
=== modified file 'MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatSynthesisChainTask.java'
--- MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatSynthesisChainTask.java	2016-01-09 22:12:07 +0000
+++ MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatSynthesisChainTask.java	2016-01-15 17:12:28 +0000
@@ -49,7 +49,7 @@
 
 			// Generate .g for the model
 			File netFile = new File(directory, "net" + exporter.getExtenstion());
-			ExportTask exportTask = new ExportTask(exporter, model, netFile.getCanonicalPath());
+			ExportTask exportTask = new ExportTask(exporter, model, netFile.getAbsolutePath());
 			Result<? extends Object> exportResult = framework.getTaskManager().execute(
 					exportTask, "Exporting .g", subtaskMonitor);
 
@@ -65,7 +65,7 @@
 			// Generate unfolding
 			boolean tryPnml = settings.getMode().canPnml();
 			File unfoldingFile = new File(directory, "unfolding" + PunfUtilitySettings.getUnfoldingExtension(tryPnml));
-			PunfTask punfTask = new PunfTask(netFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+			PunfTask punfTask = new PunfTask(netFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(punfTask, "Unfolding .g", subtaskMonitor);
 			
 			if (punfResult.getOutcome() != Outcome.FINISHED) {
@@ -80,7 +80,7 @@
 			// Run MPSat on the generated unfolding
 			boolean needLib = settings.getMode().needLib();
 			MpsatSynthesisTask mpsatTask = new MpsatSynthesisTask(settings.getMpsatArguments(directory), 
-					unfoldingFile.getCanonicalPath(), directory, tryPnml, needLib);
+					unfoldingFile.getAbsolutePath(), directory, tryPnml, needLib);
 			Result<? extends ExternalProcessResult> mpsatResult = framework.getTaskManager().execute(
 					mpsatTask, "Running synthesis [MPSat]", subtaskMonitor);
 			
 
=== modified file 'MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatSynthesisTask.java'
--- MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatSynthesisTask.java	2016-01-03 21:57:29 +0000
+++ MpsatSynthesisPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatSynthesisTask.java	2016-01-15 17:12:28 +0000
@@ -87,8 +87,10 @@
 		File outputFile = new File(directory, outputFileName);
 		command.add(outputFile.getAbsolutePath());
 		
-		ExternalProcessTask externalProcessTask = new ExternalProcessTask(command, directory);
-		Result<? extends ExternalProcessResult> res = externalProcessTask.run(monitor);
+		boolean printStdout = MpsatSynthesisUtilitySettings.getPrintStdout();
+		boolean printStderr = MpsatSynthesisUtilitySettings.getPrintStderr();
+		ExternalProcessTask task = new ExternalProcessTask(command, directory, printStdout, printStderr);
+		Result<? extends ExternalProcessResult> res = task.run(monitor);
 		if(res.getOutcome() == Outcome.CANCELLED) {
 			return res;
 		}
 
=== modified file 'MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/MpsatSettings.java'
--- MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/MpsatSettings.java	2016-01-06 16:36:03 +0000
+++ MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/MpsatSettings.java	2016-01-15 17:12:28 +0000
@@ -199,7 +199,7 @@
 				}
 				FileUtils.dumpString(reachFile, getReach());
 				args.add("-d");
-				args.add("@" + reachFile.getCanonicalPath());
+				args.add("@" + reachFile.getAbsolutePath());
 			} catch (IOException e) {
 				throw new RuntimeException(e);
 			}
 
=== modified file 'MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/MpsatUtilitySettings.java'
--- MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/MpsatUtilitySettings.java	2015-12-30 23:43:20 +0000
+++ MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/MpsatUtilitySettings.java	2016-01-15 17:12:28 +0000
@@ -38,16 +38,22 @@
 	private static final String keyCommand = prefix + ".command";
 	private static final String keySolutionMode = prefix + ".solutionMode";
 	private static final String keyExtraArgs = prefix + ".args";
+	private static final String keyPrintStdout= prefix + ".printStdout";
+	private static final String keyPrintStderr= prefix + ".printStderr";
 	private static final String keyDebugReach = prefix + ".debugReach";
 	
 	private static final String defaultCommand = (DesktopApi.getOs().isWindows() ? "tools\\UnfoldingTools\\mpsat.exe" : "tools/UnfoldingTools/mpsat");
 	private static final SolutionMode defaultSolutionMode = SolutionMode.MINIMUM_COST;
 	private static final String defaultExtraArgs = "";
+	private static final Boolean defaultPrintStdout = true;
+	private static final Boolean defaultPrintStderr = true;
 	private static final Boolean defaultDebugReach = false;
 
 	private static String command = defaultCommand;
 	private static SolutionMode solutionMode = defaultSolutionMode;
 	private static String extraArgs = defaultExtraArgs;
+	private static Boolean printStdout = defaultPrintStdout;
+	private static Boolean printStderr = defaultPrintStderr;
 	private static Boolean debugReach = defaultDebugReach;
 
 	public MpsatUtilitySettings() {
@@ -82,7 +88,27 @@
 		});
 
 		properties.add(new PropertyDeclaration<MpsatUtilitySettings, Boolean>(
-				this, "Print out Reach expressions (debug)", Boolean.class, true, false, false) {
+				this, "Output stdout", Boolean.class, true, false, false) {
+			protected void setter(MpsatUtilitySettings object, Boolean value) {
+				setPrintStdout(value);
+			}
+			protected Boolean getter(MpsatUtilitySettings object) {
+				return getPrintStdout();
+			}
+		});
+
+		properties.add(new PropertyDeclaration<MpsatUtilitySettings, Boolean>(
+				this, "Output stderr", Boolean.class, true, false, false) {
+			protected void setter(MpsatUtilitySettings object, Boolean value) {
+				setPrintStderr(value);
+			}
+			protected Boolean getter(MpsatUtilitySettings object) {
+				return getPrintStderr();
+			}
+		});
+
+		properties.add(new PropertyDeclaration<MpsatUtilitySettings, Boolean>(
+				this, "Output Reach expressions", Boolean.class, true, false, false) {
 			protected void setter(MpsatUtilitySettings object, Boolean value) {
 				setDebugReach(value);
 			}
@@ -102,6 +128,8 @@
 		setCommand(config.getString(keyCommand, defaultCommand));
 		setSolutionMode(config.getEnum(keySolutionMode, SolutionMode.class, defaultSolutionMode));
 		setExtraArgs(config.getString(keyExtraArgs, defaultExtraArgs));
+		setPrintStdout(config.getBoolean(keyPrintStdout, defaultPrintStdout));
+		setPrintStderr(config.getBoolean(keyPrintStderr, defaultPrintStderr));
 		setDebugReach(config.getBoolean(keyDebugReach, defaultDebugReach));
 	}
 
@@ -110,6 +138,8 @@
 		config.set(keyCommand, getCommand());
 		config.setEnum(keySolutionMode, SolutionMode.class, getSolutionMode());
 		config.set(keyExtraArgs, getExtraArgs());
+		config.setBoolean(keyPrintStdout, getPrintStdout());
+		config.setBoolean(keyPrintStderr, getPrintStderr());
 		config.setBoolean(keyDebugReach, getDebugReach());
 	}
 	
@@ -151,6 +181,22 @@
 		return (solutionMode == SolutionMode.ALL) ? 10 : 1;
 	}
 
+	public static Boolean getPrintStdout() {
+		return printStdout;
+	}
+
+	public static void setPrintStdout(Boolean value) {
+		printStdout = value;
+	}
+
+	public static Boolean getPrintStderr() {
+		return printStderr;
+	}
+
+	public static void setPrintStderr(Boolean value) {
+		printStderr = value;
+	}
+
 	public static Boolean getDebugReach() {
 		return debugReach;
 	}
 
=== modified file 'MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatChainTask.java'
--- MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatChainTask.java	2016-01-09 22:12:07 +0000
+++ MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatChainTask.java	2016-01-15 17:12:28 +0000
@@ -49,7 +49,7 @@
 
 			// Generate .g for the model
 			File netFile = new File(directory, "net" + exporter.getExtenstion());
-			ExportTask exportTask = new ExportTask(exporter, model, netFile.getCanonicalPath());
+			ExportTask exportTask = new ExportTask(exporter, model, netFile.getAbsolutePath());
 			Result<? extends Object> exportResult = framework.getTaskManager().execute(
 					exportTask, "Exporting .g", subtaskMonitor);
 
@@ -65,7 +65,7 @@
 			// Generate unfolding
 			boolean tryPnml = settings.getMode().canPnml();
 			File unfoldingFile = new File(directory, "unfolding" + PunfUtilitySettings.getUnfoldingExtension(tryPnml));
-			PunfTask punfTask = new PunfTask(netFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+			PunfTask punfTask = new PunfTask(netFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(punfTask, "Unfolding .g", subtaskMonitor);
 			
 			if (punfResult.getOutcome() != Outcome.FINISHED) {
@@ -79,7 +79,7 @@
 
 			// Run MPSat on the generated unfolding
 			MpsatTask mpsatTask = new MpsatTask(settings.getMpsatArguments(directory), 
-					unfoldingFile.getCanonicalPath(), directory, tryPnml);
+					unfoldingFile.getAbsolutePath(), directory, tryPnml);
 			Result<? extends ExternalProcessResult> mpsatResult = framework.getTaskManager().execute(
 					mpsatTask, "Running verification [MPSat]", subtaskMonitor);
 			
 
=== modified file 'MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatCombinedChainTask.java'
--- MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatCombinedChainTask.java	2016-01-09 22:12:07 +0000
+++ MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatCombinedChainTask.java	2016-01-15 17:12:28 +0000
@@ -51,7 +51,7 @@
 
 			// Generate .g for the model
 			File netFile = new File(directory, "net" + exporter.getExtenstion());
-			ExportTask exportTask = new ExportTask(exporter, model, netFile.getCanonicalPath());
+			ExportTask exportTask = new ExportTask(exporter, model, netFile.getAbsolutePath());
 			Result<? extends Object> exportResult = framework.getTaskManager().execute(
 					exportTask, "Exporting .g", subtaskMonitor);
 
@@ -70,7 +70,7 @@
 				tryPnml &= settings.getMode().canPnml();
 			}
 			File unfoldingFile = new File(directory, "unfolding" + PunfUtilitySettings.getUnfoldingExtension(tryPnml));
-			PunfTask punfTask = new PunfTask(netFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+			PunfTask punfTask = new PunfTask(netFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(punfTask, "Unfolding .g", subtaskMonitor);
 			
 			if (punfResult.getOutcome() != Outcome.FINISHED) {
@@ -86,7 +86,7 @@
 			ArrayList<Result<? extends ExternalProcessResult>> mpsatResultList = new ArrayList<>(settingsList.size());
 			for (MpsatSettings settings: settingsList) {
 				MpsatTask mpsatTask = new MpsatTask(settings.getMpsatArguments(directory), 
-						unfoldingFile.getCanonicalPath(), directory, tryPnml);
+						unfoldingFile.getAbsolutePath(), directory, tryPnml);
 				Result<? extends ExternalProcessResult> mpsatResult = framework.getTaskManager().execute(
 						mpsatTask, "Running verification [MPSat]", subtaskMonitor);
 				mpsatResultList.add(mpsatResult);
 
=== modified file 'MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatConformationTask.java'
--- MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatConformationTask.java	2016-01-09 22:12:07 +0000
+++ MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatConformationTask.java	2016-01-15 17:12:28 +0000
@@ -70,7 +70,7 @@
 
 			// Generating .g for the model
 			File devStgFile =  new File(directory, "dev.g");
-			ExportTask devExportTask = new ExportTask(devStgExporter, devStg, devStgFile.getCanonicalPath());
+			ExportTask devExportTask = new ExportTask(devStgExporter, devStg, devStgFile.getAbsolutePath());
 			Result<? extends Object> devExportResult = framework.getTaskManager().execute(
 					devExportTask, "Exporting circuit .g", subtaskMonitor);
 			
@@ -92,7 +92,7 @@
 				STG envStg = (STG)framework.loadFile(envFile).getMathModel();
 				Exporter envStgExporter = Export.chooseBestExporter(framework.getPluginManager(), envStg, Format.STG);
 				envStgFile = new File(directory, "env.g");
-				ExportTask envExportTask = new ExportTask(envStgExporter, envStg, envStgFile.getCanonicalPath());
+				ExportTask envExportTask = new ExportTask(envStgExporter, envStg, envStgFile.getAbsolutePath());
 				Result<? extends Object> envExportResult = framework.getTaskManager().execute(
 						envExportTask, "Exporting environment .g", subtaskMonitor);
 				
@@ -127,7 +127,7 @@
 			
 			// Generate unfolding
 			File unfoldingFile = new File(directory, "system" + PunfUtilitySettings.getUnfoldingExtension(true));
-			PunfTask punfTask = new PunfTask(stgFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+			PunfTask punfTask = new PunfTask(stgFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(
 					punfTask, "Unfolding .g", subtaskMonitor);
 			
@@ -153,7 +153,7 @@
 					MpsatUtilitySettings.getSolutionCount(), reachConformation, true);
 			
 			MpsatTask mpsatConformationTask = new MpsatTask(conformationSettings.getMpsatArguments(directory), 
-					unfoldingFile.getCanonicalPath(), directory, true);
+					unfoldingFile.getAbsolutePath(), directory, true);
 			Result<? extends ExternalProcessResult>  mpsatConformationResult = framework.getTaskManager().execute(
 					mpsatConformationTask, "Running conformation check [MPSat]", subtaskMonitor);
 
 
=== modified file 'MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatTask.java'
--- MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatTask.java	2016-01-03 21:57:29 +0000
+++ MpsatVerificationPlugin/src/org/workcraft/plugins/mpsat/tasks/MpsatTask.java	2016-01-15 17:12:28 +0000
@@ -59,8 +59,10 @@
 		// Input file
 		command.add(inputFileName);
 
-		ExternalProcessTask externalProcessTask = new ExternalProcessTask(command, directory);
-		Result<? extends ExternalProcessResult> res = externalProcessTask.run(monitor);
+		boolean printStdout = MpsatUtilitySettings.getPrintStdout();
+		boolean printStderr = MpsatUtilitySettings.getPrintStderr();
+		ExternalProcessTask task = new ExternalProcessTask(command, directory, printStdout, printStderr);
+		Result<? extends ExternalProcessResult> res = task.run(monitor);
 		if(res.getOutcome() == Outcome.CANCELLED) {
 			return res;
 		}
 
=== modified file 'PcompPlugin/src/org/workcraft/plugins/pcomp/tasks/PcompTask.java'
--- PcompPlugin/src/org/workcraft/plugins/pcomp/tasks/PcompTask.java	2016-01-03 21:57:29 +0000
+++ PcompPlugin/src/org/workcraft/plugins/pcomp/tasks/PcompTask.java	2016-01-15 17:12:28 +0000
@@ -88,7 +88,8 @@
 			command.add(inputFile.getAbsolutePath());
 		}
 		
-		Result<? extends ExternalProcessResult> res = new ExternalProcessTask(command).run(monitor);
+		ExternalProcessTask task = new ExternalProcessTask(command, directory, false, true);
+		Result<? extends ExternalProcessResult> res = task.run(monitor);
 		if (res.getOutcome() != Outcome.FINISHED) {
 			return res;
 		}
 
=== modified file 'PetrifyExtraPlugin/src/org/workcraft/plugins/petrify/tasks/DrawAstgTask.java'
--- PetrifyExtraPlugin/src/org/workcraft/plugins/petrify/tasks/DrawAstgTask.java	2016-01-03 21:57:29 +0000
+++ PetrifyExtraPlugin/src/org/workcraft/plugins/petrify/tasks/DrawAstgTask.java	2016-01-15 17:12:28 +0000
@@ -49,8 +49,8 @@
 		command.add("-o");
 		command.add(outputPath);
 		
-
-		Result<? extends ExternalProcessResult> res = new ExternalProcessTask(command).run(monitor);
+		ExternalProcessTask task = new ExternalProcessTask(command, null, false, false);
+		Result<? extends ExternalProcessResult> res = task.run(monitor);
 		
 		if (res.getOutcome() != Outcome.FINISHED)
 			return res;
 
=== modified file 'PetrifyExtraPlugin/src/org/workcraft/plugins/petrify/tasks/WriteSgTask.java'
--- PetrifyExtraPlugin/src/org/workcraft/plugins/petrify/tasks/WriteSgTask.java	2016-01-03 21:57:29 +0000
+++ PetrifyExtraPlugin/src/org/workcraft/plugins/petrify/tasks/WriteSgTask.java	2016-01-15 17:12:28 +0000
@@ -69,7 +69,8 @@
 			command.add(outputPath);
 		}
 		
-		Result<? extends ExternalProcessResult> res = new ExternalProcessTask(command).run(monitor);
+		ExternalProcessTask task = new ExternalProcessTask(command, null, false, false);
+		Result<? extends ExternalProcessResult> res = task.run(monitor);
 		if (res.getOutcome() != Outcome.FINISHED) {
 			return res;
 		}
 
=== modified file 'PetrifyPlugin/src/org/workcraft/plugins/petrify/PetrifyUtilitySettings.java'
--- PetrifyPlugin/src/org/workcraft/plugins/petrify/PetrifyUtilitySettings.java	2015-12-30 23:43:20 +0000
+++ PetrifyPlugin/src/org/workcraft/plugins/petrify/PetrifyUtilitySettings.java	2016-01-15 17:12:28 +0000
@@ -36,13 +36,19 @@
 	
 	private static final String keyPetrifyCkeyPmmand = prefix + ".petrify.command";
 	private static final String keyPetrifyArgs = prefix + ".petrify.args";
+	private static final String keyPrintStdout= prefix + ".printStdout";
+	private static final String keyPrintStderr= prefix + ".printStderr";
 	
 	private static final String defaultPetrifyCommand = (DesktopApi.getOs().isWindows() ? "tools\\PetrifyTools\\petrify.exe" : "tools/PetrifyTools/petrify");
 	private static final String defaultPetrifyArgs = "";
+	private static final Boolean defaultPrintStdout = true;
+	private static final Boolean defaultPrintStderr = true;
 
 	private static String petrifyCommand = defaultPetrifyCommand;
 	private static String petrifyArgs = defaultPetrifyArgs;
-	
+	private static Boolean printStdout = defaultPrintStdout;
+	private static Boolean printStderr = defaultPrintStderr;
+
 	public PetrifyUtilitySettings() {
 		properties.add(new PropertyDeclaration<PetrifyUtilitySettings, String>(
 				this, "Petrify command", String.class, true, false, false) {
@@ -63,6 +69,26 @@
 				return getPetrifyArgs();
 			}
 		});
+
+		properties.add(new PropertyDeclaration<PetrifyUtilitySettings, Boolean>(
+				this, "Output stdout", Boolean.class, true, false, false) {
+			protected void setter(PetrifyUtilitySettings object, Boolean value) {
+				setPrintStdout(value);
+			}
+			protected Boolean getter(PetrifyUtilitySettings object) {
+				return getPrintStdout();
+			}
+		});
+
+		properties.add(new PropertyDeclaration<PetrifyUtilitySettings, Boolean>(
+				this, "Output stderr", Boolean.class, true, false, false) {
+			protected void setter(PetrifyUtilitySettings object, Boolean value) {
+				setPrintStderr(value);
+			}
+			protected Boolean getter(PetrifyUtilitySettings object) {
+				return getPrintStderr();
+			}
+		});
 	}
 	
 	@Override
@@ -74,12 +100,16 @@
 	public void load(Config config) {
 		setPetrifyCommand(config.getString(keyPetrifyCkeyPmmand, defaultPetrifyCommand));
 		setPetrifyArgs(config.getString(keyPetrifyArgs, defaultPetrifyArgs));
+		setPrintStdout(config.getBoolean(keyPrintStdout, defaultPrintStdout));
+		setPrintStderr(config.getBoolean(keyPrintStderr, defaultPrintStderr));
 	}
 
 	@Override
 	public void save(Config config) {
 		config.set(keyPetrifyCkeyPmmand, getPetrifyCommand());
 		config.set(keyPetrifyArgs, getPetrifyArgs());
+		config.setBoolean(keyPrintStdout, getPrintStdout());
+		config.setBoolean(keyPrintStderr, getPrintStderr());
 	}
 
 	@Override
@@ -108,4 +138,20 @@
 		petrifyArgs = value;
 	}
 
+	public static Boolean getPrintStdout() {
+		return printStdout;
+	}
+
+	public static void setPrintStdout(Boolean value) {
+		printStdout = value;
+	}
+
+	public static Boolean getPrintStderr() {
+		return printStderr;
+	}
+
+	public static void setPrintStderr(Boolean value) {
+		printStderr = value;
+	}
+
 }
 
=== removed file 'PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/PetrifyTask.java'
--- PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/PetrifyTask.java	2016-01-03 21:57:29 +0000
+++ PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/PetrifyTask.java	1970-01-01 00:00:00 +0000
@@ -1,135 +0,0 @@
-package org.workcraft.plugins.petrify.tasks;
-
-import java.io.IOException;
-import java.util.ArrayList;
-
-import org.workcraft.interop.ExternalProcess;
-import org.workcraft.interop.ExternalProcessListener;
-import org.workcraft.plugins.petrify.PetrifyUtilitySettings;
-import org.workcraft.plugins.shared.tasks.ExternalProcessResult;
-import org.workcraft.tasks.ProgressMonitor;
-import org.workcraft.tasks.Result;
-import org.workcraft.tasks.Result.Outcome;
-import org.workcraft.tasks.Task;
-import org.workcraft.util.DataAccumulator;
-
-public class PetrifyTask implements Task<ExternalProcessResult>, ExternalProcessListener {
-		private String[] args;
-		private String inputFileName;
-		
-		private volatile boolean finished;
-		private volatile int returnCode;
-		private boolean userCancelled = false;
-		private ProgressMonitor<? super ExternalProcessResult> monitor;
-		
-		private DataAccumulator stdoutAccum = new DataAccumulator();
-		private DataAccumulator stderrAccum = new DataAccumulator();
-				
-		public PetrifyTask(String[] args, String inputFileName) {
-			this.args = args;
-			this.inputFileName = inputFileName;
-		}
-		
-		@Override
-		public Result<? extends ExternalProcessResult> run(ProgressMonitor<? super ExternalProcessResult> monitor) {
-			this.monitor = monitor;
-			ArrayList<String> command = new ArrayList<String>();
-
-			// Name of the executable
-			String toolName = PetrifyUtilitySettings.getPetrifyCommand();
-			command.add(toolName);
-			
-			// Built-in arguments
-			for (String arg : args) {
-				command.add(arg);
-			}
-			
-			// Extra arguments (should go before the file parameters)
-			for (String arg : PetrifyUtilitySettings.getPetrifyArgs().split(" ")) {
-				if (!arg.isEmpty()) {
-					command.add(arg);
-				}
-			}
-
-			// Input file
-			command.add(inputFileName);
-			
-			ExternalProcess petrifyProcess = new ExternalProcess(command.toArray(new String[command.size()]), ".");
-			petrifyProcess.addListener(this);
-			
-			try {
-				System.out.println("Running external command: " + getCommandLine(command));
-				petrifyProcess.start();
-			} catch (IOException e) {
-				return new Result<ExternalProcessResult>(e);
-			}
-			
-			while (true) {
-				if (monitor.isCancelRequested() && petrifyProcess.isRunning()) {
-					petrifyProcess.cancel();
-					userCancelled = true;
-				}
-				if (finished) {
-					break;
-				}
-				try {
-					Thread.sleep(20);
-				} catch (InterruptedException e) {
-					petrifyProcess.cancel();
-					userCancelled = true;
-					break;
-				}
-			}
-			
-			if (userCancelled) {
-				return new Result<ExternalProcessResult>(Outcome.CANCELLED);
-			}
-			
-			ExternalProcessResult result = new ExternalProcessResult(returnCode, stdoutAccum.getData(), stderrAccum.getData());
-			
-			if (returnCode == 0) {
-				return new Result<ExternalProcessResult>(Outcome.FINISHED, result);
-			}
-			
-			return new Result<ExternalProcessResult>(Outcome.FAILED, result);
-		}
-
-		private String getCommandLine(ArrayList<String> command) {
-			String commandLine = "";
-			for (String arg: command) {
-				if (commandLine.isEmpty()) {
-					commandLine = "";
-				} else {
-					commandLine += " ";
-				}
-				commandLine += arg;
-			}
-			return commandLine;
-		}
-
-		@Override
-		public void errorData(byte[] data) {
-			try {
-				stderrAccum.write(data);
-			} catch (IOException e) {
-				throw new RuntimeException(e);
-			}
-			monitor.stderr(data);
-		}
-
-		@Override
-		public void outputData(byte[] data) {
-			try {
-				stdoutAccum.write(data);
-			} catch (IOException e) {
-				throw new RuntimeException(e);
-			}
-			monitor.stdout(data);
-		}
-
-		@Override
-		public void processFinished(int returnCode) {
-			this.returnCode = returnCode;
-			this.finished = true;
-		}
-	}
 \ No newline at end of file
 
=== modified file 'PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/SynthesisTask.java'
--- PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/SynthesisTask.java	2016-01-03 21:57:29 +0000
+++ PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/SynthesisTask.java	2016-01-15 17:12:28 +0000
@@ -66,32 +66,38 @@
 		// As there may be non-alpha-numerical symbols in the model title, it is better not to include it to the directory name.				
 		String prefix = FileUtils.getTempPrefix(null/* we.getTitle() */);
 		File directory = FileUtils.createTempDirectory(prefix);
+
+		File outFile = new File(directory, "result.g");
+		command.add("-o");
+		command.add(outFile.getAbsolutePath());
+
+		File equationsFile = new File(directory, "petrify.eqn");
+		command.add("-eqn");
+		command.add(equationsFile.getAbsolutePath());
+
+		File verilogFile = new File(directory, "petrify.v");
+		command.add("-vl");
+		command.add(verilogFile.getAbsolutePath());
+
+		File blifFile = new File(directory, "petrify.blif");
+		command.add("-blif");
+		command.add(blifFile.getAbsolutePath());
+
+		File logFile = new File(directory, "petrify.log");
+		command.add("-log");
+		command.add(logFile.getAbsolutePath());
+
+		// Input file
+		STGModel stg = WorkspaceUtils.getAs(we, STGModel.class);
+		File stgFile = getInputFile(stg, directory);
+		command.add(stgFile.getAbsolutePath());
+
+		boolean printStdout = PetrifyUtilitySettings.getPrintStdout();
+		boolean printStderr = PetrifyUtilitySettings.getPrintStderr();
+		ExternalProcessTask task = new ExternalProcessTask(command, null, printStdout, printStderr);
+		SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor); 
+		Result<? extends ExternalProcessResult> res = task.run(mon);
 		try {
-			File equationsFile = new File(directory, "petrify.eqn");
-			command.add("-eqn");
-			command.add(equationsFile.getCanonicalPath());
-
-			File verilogFile = new File(directory, "petrify.v");
-			command.add("-vl");
-			command.add(verilogFile.getCanonicalPath());
-
-			File blifFile = new File(directory, "petrify.blif");
-			command.add("-blif");
-			command.add(blifFile.getCanonicalPath());
-
-			File logFile = new File(directory, "petrify.log");
-			command.add("-log");
-			command.add(logFile.getCanonicalPath());
-			
-			// Input file
-			STGModel stg = WorkspaceUtils.getAs(we, STGModel.class);
-			File stgFile = getInputStg(stg, directory);
-			command.add(stgFile.getCanonicalPath());
-		
-			ExternalProcessTask externalProcessTask = new ExternalProcessTask(command, null);
-			SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor); 
-			Result<? extends ExternalProcessResult> res = externalProcessTask.run(mon);
-
 			if (res.getOutcome() == Outcome.CANCELLED) {
 				return new Result<SynthesisResult>(Outcome.CANCELLED);
 			} else {
@@ -110,24 +116,24 @@
 				SynthesisResult result = new SynthesisResult(equations, verilog, log, stdout, stderr);
 				return new Result<SynthesisResult>(outcome, result);
 			}
-		} catch (IOException e1) {
-			throw new RuntimeException(e1);
+		} catch (IOException e) {
+			throw new RuntimeException(e);
 		} finally {
 			FileUtils.deleteFile(directory, CommonDebugSettings.getKeepTemporaryFiles());
 		}
 	}
 
-	private File getInputStg(Model model, File directory) throws IOException {
+	private File getInputFile(Model model, File directory) {
 		final Framework framework = Framework.getInstance();
 		Exporter stgExporter = Export.chooseBestExporter(framework.getPluginManager(), model, Format.STG);
 		if (stgExporter == null) {
-			throw new RuntimeException ("Exporter not available: model class " + model.getClass().getName() + " to format STG.");
+			throw new RuntimeException("Exporter not available: model class " + model.getClass().getName() + " to format STG.");
 		}
 		
 		File stgFile = new File(directory, "petrify" + stgExporter.getExtenstion());
-		ExportTask exportTask = new ExportTask(stgExporter, model, stgFile.getCanonicalPath());
-		Result<? extends Object> res = framework.getTaskManager().execute(exportTask, "Exporting .g");
-		if (res.getOutcome() != Outcome.FINISHED) {
+		ExportTask exportTask = new ExportTask(stgExporter, model, stgFile.getAbsolutePath());
+		Result<? extends Object> exportResult = framework.getTaskManager().execute(exportTask, "Exporting .g");
+		if (exportResult.getOutcome() != Outcome.FINISHED) {
 			stgFile = null;
 		}
 		return stgFile;
 
=== modified file 'PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/TransformationTask.java'
--- PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/TransformationTask.java	2015-10-12 14:02:20 +0000
+++ PetrifyPlugin/src/org/workcraft/plugins/petrify/tasks/TransformationTask.java	2016-01-15 17:12:28 +0000
@@ -2,98 +2,157 @@
 
 import java.io.ByteArrayInputStream;
 import java.io.File;
+import java.util.ArrayList;
 import java.util.UUID;
 
 import org.workcraft.Framework;
 import org.workcraft.dom.Model;
 import org.workcraft.exceptions.DeserialisationException;
+import org.workcraft.exceptions.SerialisationException;
+import org.workcraft.interop.ExternalProcessListener;
 import org.workcraft.plugins.fsm.Fsm;
 import org.workcraft.plugins.petri.PetriNetModel;
+import org.workcraft.plugins.petrify.PetrifyUtilitySettings;
 import org.workcraft.plugins.shared.CommonDebugSettings;
 import org.workcraft.plugins.shared.tasks.ExternalProcessResult;
+import org.workcraft.plugins.shared.tasks.ExternalProcessTask;
 import org.workcraft.plugins.stg.STGModel;
 import org.workcraft.plugins.stg.interop.DotGImporter;
 import org.workcraft.serialisation.Format;
 import org.workcraft.tasks.ProgressMonitor;
 import org.workcraft.tasks.Result;
 import org.workcraft.tasks.Result.Outcome;
+import org.workcraft.tasks.SubtaskMonitor;
 import org.workcraft.tasks.Task;
 import org.workcraft.util.Export;
 import org.workcraft.util.Export.ExportTask;
 import org.workcraft.util.FileUtils;
+import org.workcraft.util.ToolUtils;
 import org.workcraft.workspace.WorkspaceEntry;
 
-public class TransformationTask implements Task<TransformationResult>{
-	private WorkspaceEntry workspaceEntry;
-	String description;
-	String[] parameters;
+public class TransformationTask implements Task<TransformationResult>, ExternalProcessListener {
+	private WorkspaceEntry we;
+	String[] args;
 
-	public TransformationTask(WorkspaceEntry workspaceEntry, String description, String[] parameters) {
-		this.workspaceEntry = workspaceEntry;
-		this.description = description;
-		this.parameters = parameters;
+	public TransformationTask(WorkspaceEntry we, String description, String[] args) {
+		this.we = we;
+		this.args = args;
 	}
 
 	public WorkspaceEntry getWorkspaceEntry() {
-		return workspaceEntry;
+		return we;
 	}
 
 	@Override
 	public Result<? extends TransformationResult> run(ProgressMonitor<? super TransformationResult> monitor) {
-		File modelFile = null;
+		ArrayList<String> command = new ArrayList<String>();
+
+		// Name of the executable
+		String toolName = ToolUtils.getAbsoluteCommandPath(PetrifyUtilitySettings.getPetrifyCommand());
+		command.add(toolName);
+
+		// Built-in arguments
+		for (String arg : args) {
+			command.add(arg);
+		}
+
+		// Extra arguments (should go before the file parameters)
+		for (String arg : PetrifyUtilitySettings.getPetrifyArgs().split(" ")) {
+			if (!arg.isEmpty()) {
+				command.add(arg);
+			}
+		}
+
+		String prefix = FileUtils.getTempPrefix(we.getTitle());
+		File directory = FileUtils.createTempDirectory(prefix);
 		try {
-			final Framework framework = Framework.getInstance();
-			modelFile = File.createTempFile("stg_", ".g");
+			File logFile = new File(directory, "petrify.log");
+			command.add("-log");
+			command.add(logFile.getAbsolutePath());
+
+			File outFile = new File(directory, "result.g");
+			command.add("-o");
+			command.add(outFile.getAbsolutePath());
+
+			// Input file
+			Model model = we.getModelEntry().getMathModel();
+			File modelFile = getInputFile(model, directory);
+			command.add(modelFile.getAbsolutePath());
 			
-			Model model = workspaceEntry.getModelEntry().getMathModel();
-			UUID format = null;
-			if (model instanceof PetriNetModel) {
-				format = Format.STG;
-			} else if (model instanceof Fsm) {
-				format = Format.SG;
-			}
-			if (format == null) {
-				return Result.exception(new Throwable("This tool is not applicable to " + model.getDisplayName() + " model."));
-			}
-
-			ExportTask exportTask = Export.createExportTask(model, modelFile, format, framework.getPluginManager());
-
-			final Result<? extends Object> exportResult = framework.getTaskManager().execute(exportTask, description +": writing .g");
-
-			if (exportResult.getOutcome() != Outcome.FINISHED) {
-				if (exportResult.getOutcome() == Outcome.CANCELLED) {
-					return Result.cancelled();
+			boolean printStdout = PetrifyUtilitySettings.getPrintStdout();
+			boolean printStderr = PetrifyUtilitySettings.getPrintStderr();
+			ExternalProcessTask task = new ExternalProcessTask(command, directory, printStdout, printStderr);
+			SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor); 
+			Result<? extends ExternalProcessResult> res = task.run(mon);
+
+			if (res.getOutcome() == Outcome.CANCELLED) {
+				return new Result<TransformationResult>(Outcome.CANCELLED);
+			} else {
+				final Outcome outcome;
+				STGModel outStg = null;
+				if (res.getReturnValue().getReturnCode() == 0) {
+					outcome = Outcome.FINISHED;
 				} else {
-					return Result.exception(exportResult.getCause());
+					outcome = Outcome.FAILED;
 				}
-			}
-
-			PetrifyTask petrifyTask = new PetrifyTask(parameters, modelFile.getAbsolutePath());
-
-			final Result<? extends ExternalProcessResult> petrifyResult 
-					= framework.getTaskManager().execute(petrifyTask, description + ": executing Petrify");
-
-			if (petrifyResult.getOutcome() == Outcome.FINISHED) {
 				try {
-					ByteArrayInputStream in = new ByteArrayInputStream(petrifyResult.getReturnValue().getOutput());
-					final STGModel outStg = new DotGImporter().importSTG(in);
-					return Result.finished(new TransformationResult(null, outStg));
+					String out = (outFile.exists() ? FileUtils.readAllText(outFile) : "");
+					ByteArrayInputStream outStream = new ByteArrayInputStream(out.getBytes());
+					outStg = new DotGImporter().importSTG(outStream);
 				} catch (DeserialisationException e) {
 					return Result.exception(e);
 				}
-
-			} else {
-				if(petrifyResult.getOutcome() == Outcome.FAILED) {
-					return Result.failed(new TransformationResult(petrifyResult, null));
-				} else {
-					return Result.cancelled();
-				}
+				TransformationResult result = new TransformationResult(res, outStg);
+				return new Result<TransformationResult>(outcome, result);
 			}
 		} catch (Throwable e) {
-			return Result.exception(e);
+			throw new RuntimeException(e);
 		} finally {
-			FileUtils.deleteFile(modelFile, CommonDebugSettings.getKeepTemporaryFiles());
-		}
-	}
-	
+			FileUtils.deleteFile(directory, CommonDebugSettings.getKeepTemporaryFiles());
+		}
+	}
+	
+	private File getInputFile(Model model, File directory) {
+		final Framework framework = Framework.getInstance();
+		UUID format = null;
+		String extension = null;
+		if (model instanceof PetriNetModel) {
+			format = Format.STG;
+			extension = ".g";
+		} else if (model instanceof Fsm) {
+			format = Format.SG;
+			extension = ".sg";
+		}
+		if (format == null) {
+			throw new RuntimeException("This tool is not applicable to " + model.getDisplayName() + " model.");
+		}
+
+		File modelFile = new File(directory, "original" + extension);
+		try {
+			ExportTask exportTask = Export.createExportTask(model, modelFile, format, framework.getPluginManager());
+			final Result<? extends Object> exportResult = framework.getTaskManager().execute(exportTask, "Exporting model");
+			if (exportResult.getOutcome() != Outcome.FINISHED) {
+				modelFile = null;
+			}
+		} catch (SerialisationException e) {
+			throw new RuntimeException("Unable to export the model.");
+		}
+		return modelFile;
+	}
+
+	
+	@Override
+	public void processFinished(int returnCode) {
+	}
+
+	@Override
+	public void errorData(byte[] data) {
+		System.out.print(data);
+	}
+
+	@Override
+	public void outputData(byte[] data) {
+		System.out.print(data);
+	}
+
 }
 
=== modified file 'PolicyNetPlugin/src/org/workcraft/plugins/policy/tasks/CheckDeadlockTask.java'
--- PolicyNetPlugin/src/org/workcraft/plugins/policy/tasks/CheckDeadlockTask.java	2016-01-09 22:12:07 +0000
+++ PolicyNetPlugin/src/org/workcraft/plugins/policy/tasks/CheckDeadlockTask.java	2016-01-15 17:12:28 +0000
@@ -57,7 +57,7 @@
 			monitor.progressUpdate(0.10);
 			
 			File netFile = new File(directory, "net" + exporter.getExtenstion());
-			ExportTask exportTask = new ExportTask(exporter, model, netFile.getCanonicalPath());
+			ExportTask exportTask = new ExportTask(exporter, model, netFile.getAbsolutePath());
 			SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor);
 			Result<? extends Object> exportResult = framework.getTaskManager().execute(
 					exportTask, "Exporting .g", mon);
@@ -72,7 +72,7 @@
 			monitor.progressUpdate(0.20);
 			
 			File unfoldingFile = new File(directory, "unfolding" + PunfUtilitySettings.getUnfoldingExtension(true));
-			PunfTask punfTask = new PunfTask(netFile.getCanonicalPath(), unfoldingFile.getCanonicalPath());
+			PunfTask punfTask = new PunfTask(netFile.getAbsolutePath(), unfoldingFile.getAbsolutePath());
 			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(
 					punfTask, "Unfolding .g", mon);
 			
@@ -86,7 +86,7 @@
 			monitor.progressUpdate(0.70);
 
 			MpsatTask mpsatTask = new MpsatTask(settings.getMpsatArguments(directory), 
-					unfoldingFile.getCanonicalPath(), directory, true);
+					unfoldingFile.getAbsolutePath(), directory, true);
 			Result<? extends ExternalProcessResult> mpsatResult = framework.getTaskManager().execute(
 					mpsatTask, "Running deadlock checking [MPSat]", mon);
 			
 
=== modified file 'PunfPlugin/src/org/workcraft/plugins/punf/PunfUtilitySettings.java'
--- PunfPlugin/src/org/workcraft/plugins/punf/PunfUtilitySettings.java	2015-12-30 23:43:20 +0000
+++ PunfPlugin/src/org/workcraft/plugins/punf/PunfUtilitySettings.java	2016-01-15 17:12:28 +0000
@@ -36,14 +36,20 @@
 	
 	private static final String keyCommand = prefix + ".command";
 	private static final String keyExtraArgs = prefix + ".args";
+	private static final String keyPrintStdout= prefix + ".printStdout";
+	private static final String keyPrintStderr= prefix + ".printStderr";
 	private static final String keyUsePnmlUnfolding = prefix + ".usePnmlUnfolding";
 	
 	private static final String defaultCommand = (DesktopApi.getOs().isWindows() ? "tools\\UnfoldingTools\\punf.exe" : "tools/UnfoldingTools/punf");
 	private static final String defaultExtraArgs = "-r";
+	private static final Boolean defaultPrintStdout = true;
+	private static final Boolean defaultPrintStderr = true;
 	private static final Boolean defaultUsePnmlUnfolding = true;
 
 	private static String command = defaultCommand;
 	private static String extraArgs = defaultExtraArgs;
+	private static Boolean printStdout = defaultPrintStdout;
+	private static Boolean printStderr = defaultPrintStderr;
 	private static Boolean usePnmlUnfolding = defaultUsePnmlUnfolding;
 
 	public PunfUtilitySettings() {
@@ -68,6 +74,26 @@
 		});
 
 		properties.add(new PropertyDeclaration<PunfUtilitySettings, Boolean>(
+				this, "Output stdout", Boolean.class, true, false, false) {
+			protected void setter(PunfUtilitySettings object, Boolean value) {
+				setPrintStdout(value);
+			}
+			protected Boolean getter(PunfUtilitySettings object) {
+				return getPrintStdout();
+			}
+		});
+
+		properties.add(new PropertyDeclaration<PunfUtilitySettings, Boolean>(
+				this, "Output stderr", Boolean.class, true, false, false) {
+			protected void setter(PunfUtilitySettings object, Boolean value) {
+				setPrintStderr(value);
+			}
+			protected Boolean getter(PunfUtilitySettings object) {
+				return getPrintStderr();
+			}
+		});
+
+		properties.add(new PropertyDeclaration<PunfUtilitySettings, Boolean>(
 				this, "Use PNML-based unfolding (where possible)", Boolean.class, true, false, false) {
 			protected void setter(PunfUtilitySettings object, Boolean value) {
 				setUsePnmlUnfolding(value);
@@ -88,12 +114,16 @@
 		setCommand(config.getString(keyCommand, defaultCommand));
 		setExtraArgs(config.getString(keyExtraArgs, defaultExtraArgs));
 		setUsePnmlUnfolding(config.getBoolean(keyUsePnmlUnfolding, defaultUsePnmlUnfolding));
+		setPrintStdout(config.getBoolean(keyPrintStdout, defaultPrintStdout));
+		setPrintStderr(config.getBoolean(keyPrintStderr, defaultPrintStderr));
 	}
 
 	@Override
 	public void save(Config config) {
 		config.set(keyCommand, getCommand());
 		config.set(keyExtraArgs, getExtraArgs());
+		config.setBoolean(keyPrintStdout, getPrintStdout());
+		config.setBoolean(keyPrintStderr, getPrintStderr());
 		config.setBoolean(keyUsePnmlUnfolding, getUsePnmlUnfolding());
 	}
 	
@@ -123,6 +153,22 @@
 		extraArgs = value;
 	}
 
+	public static Boolean getPrintStdout() {
+		return printStdout;
+	}
+
+	public static void setPrintStdout(Boolean value) {
+		printStdout = value;
+	}
+
+	public static Boolean getPrintStderr() {
+		return printStderr;
+	}
+
+	public static void setPrintStderr(Boolean value) {
+		printStderr = value;
+	}
+
 	public static Boolean getUsePnmlUnfolding() {
 		return usePnmlUnfolding;
 	}
@@ -138,5 +184,5 @@
 	public static String getToolSuffix(boolean tryPnml) {
 		return (tryPnml && getUsePnmlUnfolding() ? "" : "-mci");
 	}
-	
+
 }
 
=== modified file 'PunfPlugin/src/org/workcraft/plugins/punf/tasks/PunfTask.java'
--- PunfPlugin/src/org/workcraft/plugins/punf/tasks/PunfTask.java	2016-01-09 22:12:07 +0000
+++ PunfPlugin/src/org/workcraft/plugins/punf/tasks/PunfTask.java	2016-01-15 17:12:28 +0000
@@ -38,8 +38,11 @@
 		// Built-in arguments
 		command.add("-m=" + outputPath);
 		command.add(inputPath);
-
-		Result<? extends ExternalProcessResult> res = new ExternalProcessTask(command).run(monitor);
+		
+		boolean printStdout = PunfUtilitySettings.getPrintStdout();
+		boolean printStderr = PunfUtilitySettings.getPrintStderr();
+		ExternalProcessTask task = new ExternalProcessTask(command, null, printStdout, printStderr);
+		Result<? extends ExternalProcessResult> res = task.run(monitor);
 		
 		if (res.getOutcome() != Outcome.FINISHED) {
 			return res;
 
=== modified file 'WorkcraftCore/src/org/workcraft/Config.java'
--- WorkcraftCore/src/org/workcraft/Config.java	2014-07-25 16:19:39 +0000
+++ WorkcraftCore/src/org/workcraft/Config.java	2016-01-15 17:12:28 +0000
@@ -190,51 +190,51 @@
 			group.put(k[1], value);
 		}
 	}
-
-	public void load(String fileName) {
-		DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
-		Document xmldoc;
-		DocumentBuilder db;
-
-		try {
-			db = dbf.newDocumentBuilder();
-			xmldoc = db.parse(new File(fileName));
-		} catch (ParserConfigurationException e) {
-			e.printStackTrace();
-			return;
-		} catch (IOException e) {
-			return;
-		} catch (SAXException e) {
-			e.printStackTrace();
-			return;
-		}
-
-		Element xmlroot = xmldoc.getDocumentElement();
-		NodeList nl =  xmlroot.getChildNodes(), nl2;
-		for (int i=0; i<nl.getLength(); i++) {
-			if (! (nl.item(i) instanceof Element)) {
+
+	public void load(String fileName) {
+		DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+		Document xmldoc;
+		DocumentBuilder db;
+
+		try {
+			db = dbf.newDocumentBuilder();
+			xmldoc = db.parse(new File(fileName));
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+			return;
+		} catch (IOException e) {
+			return;
+		} catch (SAXException e) {
+			e.printStackTrace();
+			return;
+		}
+
+		Element xmlroot = xmldoc.getDocumentElement();
+		NodeList nl =  xmlroot.getChildNodes(), nl2;
+		for (int i=0; i<nl.getLength(); i++) {
+			if (! (nl.item(i) instanceof Element)) {
 				continue;
-			}
-			Element e = (Element)nl.item(i);
-
-			if (e.getTagName().equals("var")) {
-				set(e.getAttribute("name"),  e.getAttribute("value"));
-			} else {
-				if (e.getTagName().equals("group")) {
-					String name = e.getAttribute("name");
-					nl2 = e.getChildNodes();
-					for (int j=0; j<nl2.getLength(); j++) {
-						if (! (nl2.item(j) instanceof Element)) {
-							continue;
-						}
-						Element e2 = (Element)nl2.item(j);
-						if (e2.getTagName().equals("var"))
-							set(name+"."+e2.getAttribute("name"),  e2.getAttribute("value"));
-					}
+			}
+			Element e = (Element)nl.item(i);
+
+			if (e.getTagName().equals("var")) {
+				set(e.getAttribute("name"),  e.getAttribute("value"));
+			} else {
+				if (e.getTagName().equals("group")) {
+					String name = e.getAttribute("name");
+					nl2 = e.getChildNodes();
+					for (int j=0; j<nl2.getLength(); j++) {
+						if (! (nl2.item(j) instanceof Element)) {
+							continue;
+						}
+						Element e2 = (Element)nl2.item(j);
+						if (e2.getTagName().equals("var"))
+							set(name+"."+e2.getAttribute("name"),  e2.getAttribute("value"));
+					}
 				}
-			}
-		}
-	}
+			}
+		}
+	}
 
 	public void save(String fileName) {
 		DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
 
=== modified file 'WorkcraftCore/src/org/workcraft/Framework.java'
--- WorkcraftCore/src/org/workcraft/Framework.java	2015-11-27 18:45:40 +0000
+++ WorkcraftCore/src/org/workcraft/Framework.java	2016-01-15 17:12:28 +0000
@@ -228,9 +228,15 @@
 		return instance;
 	}
 
+	public void resetConfig() {
+		config = new Config();
+		for (PluginInfo<? extends Settings> info : pluginManager.getPlugins(Settings.class)) {
+			info.getSingleton().load(config);
+		}
+	}
+
 	public void loadConfig(String fileName) {
 		config.load(fileName);
-
 		for (PluginInfo<? extends Settings> info : pluginManager.getPlugins(Settings.class)) {
 			info.getSingleton().load(config);
 		}
@@ -240,7 +246,6 @@
 		for (PluginInfo<? extends Settings> info : pluginManager.getPlugins(Settings.class)) {
 			info.getSingleton().save(config);
 		}
-
 		config.save(fileName);
 	}
 
 
=== modified file 'WorkcraftCore/src/org/workcraft/gui/AboutDialog.java'
--- WorkcraftCore/src/org/workcraft/gui/AboutDialog.java	2014-11-14 23:43:09 +0000
+++ WorkcraftCore/src/org/workcraft/gui/AboutDialog.java	2016-01-15 17:12:28 +0000
@@ -98,7 +98,7 @@
 	    });
 	    
 		okButton = new JButton();
-		okButton.setPreferredSize(new Dimension(100, 20));
+		okButton.setPreferredSize(new Dimension(100, 25));
 		okButton.setText("OK");
 		okButton.addActionListener(new java.awt.event.ActionListener() {
 			public void actionPerformed(java.awt.event.ActionEvent e) {
 
=== modified file 'WorkcraftCore/src/org/workcraft/gui/CreateWorkDialog.java'
--- WorkcraftCore/src/org/workcraft/gui/CreateWorkDialog.java	2015-10-15 16:52:53 +0000
+++ WorkcraftCore/src/org/workcraft/gui/CreateWorkDialog.java	2016-01-15 17:12:28 +0000
@@ -196,7 +196,7 @@
 		buttonsPane = new JPanel(new FlowLayout(FlowLayout.CENTER, 10, 10));
 
 		okButton = new JButton();
-		okButton.setPreferredSize(new Dimension(100, 20));
+		okButton.setPreferredSize(new Dimension(100, 25));
 		okButton.setEnabled(false);
 		okButton.setText("OK");
 		okButton.addActionListener(new java.awt.event.ActionListener() {
@@ -206,7 +206,7 @@
 		});
 
 		cancelButton = new JButton();
-		cancelButton.setPreferredSize(new Dimension(100, 20));
+		cancelButton.setPreferredSize(new Dimension(100, 25));
 		cancelButton.setText("Cancel");
 		cancelButton.addActionListener(new java.awt.event.ActionListener() {
 			public void actionPerformed(java.awt.event.ActionEvent e) {
@@ -216,11 +216,11 @@
 
 		buttonsPane.add(okButton);
 		buttonsPane.add(cancelButton);
-
 		contentPane.add(splitPane, BorderLayout.CENTER);
-		contentPane.add(buttonsPane, BorderLayout.SOUTH);
+		contentPane.add(buttonsPane, BorderLayout.SOUTH);
+		getRootPane().setDefaultButton(okButton);
 
-	    getRootPane().registerKeyboardAction(new ActionListener() {
+		getRootPane().registerKeyboardAction(new ActionListener() {
 	    	@Override
 	    	public void actionPerformed(ActionEvent e) {
 				ok();  
 
=== modified file 'WorkcraftCore/src/org/workcraft/gui/propertyeditor/Settings.java'
--- WorkcraftCore/src/org/workcraft/gui/propertyeditor/Settings.java	2014-08-05 22:17:32 +0000
+++ WorkcraftCore/src/org/workcraft/gui/propertyeditor/Settings.java	2016-01-15 17:12:28 +0000
@@ -24,8 +24,8 @@
 import org.workcraft.Config;
 
 public interface Settings extends Properties  {
-	public void save (Config config);
-	public void load (Config config);
+	public void save(Config config);
+	public void load(Config config);
 	
 	public String getSection();
 	public String getName();
 
=== modified file 'WorkcraftCore/src/org/workcraft/gui/propertyeditor/SettingsEditorDialog.java'
--- WorkcraftCore/src/org/workcraft/gui/propertyeditor/SettingsEditorDialog.java	2015-10-16 17:25:11 +0000
+++ WorkcraftCore/src/org/workcraft/gui/propertyeditor/SettingsEditorDialog.java	2016-01-15 17:12:28 +0000
@@ -26,6 +26,7 @@
 import java.awt.FlowLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.util.ArrayList;
@@ -35,13 +36,16 @@
 
 import javax.swing.BorderFactory;
 import javax.swing.JButton;
+import javax.swing.JComponent;
 import javax.swing.JDialog;
 import javax.swing.JFrame;
+import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JSplitPane;
 import javax.swing.JTable;
 import javax.swing.JTree;
+import javax.swing.KeyStroke;
 import javax.swing.event.TreeSelectionEvent;
 import javax.swing.event.TreeSelectionListener;
 import javax.swing.tree.DefaultMutableTreeNode;
@@ -49,6 +53,7 @@
 import javax.swing.tree.TreePath;
 import javax.swing.tree.TreeSelectionModel;
 
+import org.workcraft.Config;
 import org.workcraft.Framework;
 import org.workcraft.PluginManager;
 import org.workcraft.gui.MainWindow;
@@ -62,10 +67,15 @@
 	private JSplitPane splitPane;
 	private JPanel buttonsPane;
 	private JButton okButton;
+	private JButton cancelButton;
+	private JButton restoreButton;
 	private DefaultMutableTreeNode sectionRoot;
 	private JTree sectionTree;
 	private final PropertyEditorTable propertiesTable;
 	
+	private Settings currentPage;
+	private Config currentConfig;
+	
 	static class SettingsPageNode {
 		private Settings page;
 		
@@ -111,7 +121,7 @@
 		initComponents();
 		loadSections();
 	}
-	
+
 	public DefaultMutableTreeNode getSectionNode (DefaultMutableTreeNode node, String section) {
 		int dotPos = section.indexOf('.');
 		  
@@ -172,6 +182,7 @@
 			final TreePath treePath = sectionTree.getPathForRow(i);		
 			sectionTree.expandPath(treePath);
 		}
+		setObject(null);
 	}
 
 	private ArrayList<Settings> getSortedPluginSettings(Collection<PluginInfo<? extends Settings>> plugins) {
@@ -204,12 +215,17 @@
 		return settings;
 	}
 	
-	private void setObject(Settings p) {
-		if (p == null) {
-			propertiesTable.setObject(null);
+	private void setObject(Settings page) {
+		if (page == null) {
+			currentConfig = null;
+			restoreButton.setText("Restore defaults (all)");
 		} else {
-			propertiesTable.setObject(p);
+			currentConfig = new Config();
+			page.save(currentConfig);
+			restoreButton.setText("Restore defaults");
 		}
+		currentPage = page;
+		propertiesTable.setObject(currentPage);
 	}
 
 	private void initComponents() {
@@ -227,7 +243,8 @@
 			public void valueChanged(TreeSelectionEvent e) {
 				Object userObject = ((DefaultMutableTreeNode)e.getPath().getLastPathComponent()).getUserObject();
 				if (userObject instanceof SettingsPageNode) {
-					setObject( ((SettingsPageNode) userObject).getPage() );					
+					Settings page = ((SettingsPageNode) userObject).getPage();
+					setObject(page);					
 				} else {
 					setObject(null);
 				}
@@ -251,24 +268,85 @@
 		splitPane.setResizeWeight(0.1);
 
 		okButton = new JButton();
-		okButton.setPreferredSize(new Dimension(100, 20));
+		okButton.setPreferredSize(new Dimension(100, 25));
 		okButton.setText("OK");
 		okButton.addActionListener(new ActionListener() {
 			public void actionPerformed(ActionEvent e) {
 				ok();
 			}
 		});
+
+		cancelButton = new JButton();
+		cancelButton.setPreferredSize(new Dimension(100, 25));
+		cancelButton.setText("Cancel");
+		cancelButton.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				cancel();
+			}
+		});
+
+		restoreButton = new JButton();
+		restoreButton.setPreferredSize(new Dimension(170, 25));
+		restoreButton.setText("Restore defaults");
+		restoreButton.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				restore();
+			}
+		});
 		
 		buttonsPane = new JPanel(new FlowLayout(FlowLayout.CENTER, 10, 10));
 		buttonsPane.add(okButton);
+		buttonsPane.add(cancelButton);
+		buttonsPane.add(restoreButton);
 		contentPane.add(splitPane, BorderLayout.CENTER);
 		contentPane.add(buttonsPane, BorderLayout.SOUTH);
 		getRootPane().setDefaultButton(okButton);
+		
+	    getRootPane().registerKeyboardAction(new ActionListener() {
+	    	@Override
+	    	public void actionPerformed(ActionEvent e) {
+				ok();  
+	    	}
+	    },
+	    KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, 0),
+	    JComponent.WHEN_IN_FOCUSED_WINDOW);
+
+	    getRootPane().registerKeyboardAction(new ActionListener() {
+	    	@Override
+	    	public void actionPerformed(ActionEvent e) {
+				cancel();  
+	    	}
+	    },
+	    KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0),
+	    JComponent.WHEN_IN_FOCUSED_WINDOW);
 	}
 
 	private void ok() {
 		setObject(null);	
 		setVisible(false);
 	}
+
+	private void cancel() {
+		if ((currentPage != null) && (currentConfig != null)) {
+			currentPage.load(currentConfig);
+		}
+		setObject(null);	
+		setVisible(false);
+	}
+
+	private void restore() {
+		if (currentPage != null) {
+			currentPage.load(new Config());
+			setObject(currentPage);
+		} else {
+			final Framework framework = Framework.getInstance();
+			int answer = JOptionPane.showConfirmDialog(framework.getMainWindow(),
+					"This will reset all the settings to defaults.\nContinue?",
+					"Please confirm", JOptionPane.YES_NO_OPTION);
+			if (answer == JOptionPane.YES_OPTION) {
+				framework.resetConfig();
+			}
+		}
+	}
 	
 }
 
=== modified file 'WorkcraftCore/src/org/workcraft/interop/ExternalProcess.java'
--- WorkcraftCore/src/org/workcraft/interop/ExternalProcess.java	2015-07-31 15:05:52 +0000
+++ WorkcraftCore/src/org/workcraft/interop/ExternalProcess.java	2016-01-15 17:12:28 +0000
@@ -32,34 +32,31 @@
 
 public class ExternalProcess {
 	
-	abstract static class StreamReaderThread extends Thread
-	{
+	abstract static class StreamReaderThread extends Thread {
 		private final ReadableByteChannel channel;
 		private final ByteBuffer buffer = ByteBuffer.allocate(1024);
 		
-		public StreamReaderThread(ReadableByteChannel channel)
-		{
+		public StreamReaderThread(ReadableByteChannel channel) {
 			this.channel = channel;
 		}
 		
 		abstract void handleData(byte [] data);
 
+		@Override
 		public void run() {
 			while (true)
 				try {
 					buffer.rewind();
 					int result = channel.read(buffer);
-
-					if (result == -1) 
+					if (result == -1) { 
 						return;
-					
-					if (result == 0)
+					}
+					if (result == 0) {
 						continue;
-
+					}
 					buffer.rewind();
 					byte[] data = new byte[result];
 					buffer.get(data);
-
 					handleData(data);
 				} catch (IOException e) {
 //					e.printStackTrace(); -- This exception is mostly caused by the process termination and spams the user with information about exceptions that should
@@ -70,29 +67,27 @@
 	}
 	
 	class InputReaderThread extends StreamReaderThread {
-		
-		InputReaderThread()
-		{
+		InputReaderThread() {
 			super(inputStream);
 		}
-		
-		void handleData(byte[] data) {
+		@Override
+		void handleData(byte[] data) {
 			outputData(data);
 		}
 	}
 	
 	class ErrorReaderThread extends StreamReaderThread {
-		ErrorReaderThread()
-		{
+		ErrorReaderThread() {
 			super(errorStream);
 		}
-
+		@Override
 		void handleData(byte[] data) {
 			errorData(data);
 		}
 	}
 
 	class WaiterThread extends Thread {
+		@Override
 		public void run() {
 			try {
 				process.waitFor();
@@ -112,7 +107,7 @@
 
 	private LinkedList<ExternalProcessListener> listeners = new LinkedList<ExternalProcessListener>();
 
-	public ExternalProcess (String[] command, String workingDirectoryPath) {
+	public ExternalProcess(String[] command, String workingDirectoryPath) {
 		processBuilder = new ProcessBuilder(command);
 		processBuilder.directory(workingDirectoryPath == null? null : new File(workingDirectoryPath));
 	}
@@ -122,19 +117,21 @@
 	}
 
 	private void outputData(byte[] data) {
-		for (ExternalProcessListener l : listeners)
-			l.outputData(data);
+		for (ExternalProcessListener l : listeners) {
+			l.outputData(data);
+		}
 	}
 
 	private void errorData(byte[] data) {
-		for (ExternalProcessListener l : listeners)
-			l.errorData(data);
+		for (ExternalProcessListener l : listeners) {
+			l.errorData(data);
+		}
 	}
 
 	private void processFinished() {
 		for (ExternalProcessListener l : listeners){
 			l.processFinished(process.exitValue());
-		}
+		}
 		finished = true;
 	}
 
@@ -143,15 +140,13 @@
 	}
 
 	public void start() throws IOException {
-		if (isRunning())
+		if (isRunning()) {
 			return;
-
+		}
 		process = processBuilder.start();
-		
 		outputStream = Channels.newChannel(process.getOutputStream());
 		errorStream = Channels.newChannel(process.getErrorStream());
 		inputStream = Channels.newChannel(process.getInputStream());
-		
 		if (outputStream == null) {
 			throw new RuntimeException("No output stream!");
 		}
@@ -161,8 +156,9 @@
 	}
 
 	public void cancel() {
-		if (isRunning())
-			process.destroy();
+		if (isRunning()) {
+			process.destroy();
+		}
 	}
 
 	public void writeData(byte[] data) {
 
=== modified file 'WorkcraftCore/src/org/workcraft/interop/SynchronousExternalProcess.java'
--- WorkcraftCore/src/org/workcraft/interop/SynchronousExternalProcess.java	2009-09-22 21:01:45 +0000
+++ WorkcraftCore/src/org/workcraft/interop/SynchronousExternalProcess.java	2016-01-15 17:12:28 +0000
@@ -25,19 +25,20 @@
 import java.util.LinkedList;
 
 public class SynchronousExternalProcess {
-	class SynchronousListener implements ExternalProcessListener {
+	class SynchronousListener implements ExternalProcessListener {
+		@Override
 		public void errorData(byte[] data) {
 			synchronized (errorData) {
 				errorData.add(data);
 			}
 		}
-
+		@Override
 		public void outputData(byte[] data) {
 			synchronized (outputData) {
 				outputData.add(data);
 			}
 		}
-
+		@Override
 		public void processFinished(int returnCode) {
 			SynchronousExternalProcess.this.returnCode = returnCode;
 			finished = true;
@@ -90,18 +91,18 @@
 		return returnCode;
 	}
 	
-	private static byte [] mergeChunksToArray (LinkedList<byte[]> chunks) {
+	private static byte [] mergeChunksToArray(LinkedList<byte[]> chunks) {
 		int len = 0;
-		for (byte[] dataChunk : chunks)
+		for (byte[] dataChunk : chunks) {
 			len += dataChunk.length;
-		
+		}
 		byte [] result = new byte[len];
-	
 		int cur = 0;
-		for (byte[] dataChunk : chunks)
-			for(int i=0;i<dataChunk.length;i++)
-				result[cur++] = dataChunk[i];
-		
+		for (byte[] dataChunk : chunks) {
+			for(int i=0;i<dataChunk.length;i++) {
+				result[cur++] = dataChunk[i];
+			}
+		}
 		return result;
 	}
 	
@@ -111,5 +112,6 @@
 	
 	public byte [] getErrorData() {
 		return mergeChunksToArray(errorData);
-	}
+	}
+	
 }
 
=== modified file 'WorkcraftCore/src/org/workcraft/plugins/layout/DotLayoutTool.java'
--- WorkcraftCore/src/org/workcraft/plugins/layout/DotLayoutTool.java	2015-12-26 23:27:09 +0000
+++ WorkcraftCore/src/org/workcraft/plugins/layout/DotLayoutTool.java	2016-01-15 17:12:28 +0000
@@ -204,7 +204,7 @@
 			args.add(layout.getAbsolutePath());
 			args.add(original.getAbsolutePath());
 			
-			Task<ExternalProcessResult> task = new ExternalProcessTask(args, directory);
+			Task<ExternalProcessResult> task = new ExternalProcessTask(args, directory, false, false);
 			final Framework framework = Framework.getInstance();
 			Result<? extends ExternalProcessResult> res = framework.getTaskManager().execute(task, "Laying out the graph...");
 			
 
=== modified file 'WorkcraftCore/src/org/workcraft/plugins/shared/tasks/ExternalProcessTask.java'
--- WorkcraftCore/src/org/workcraft/plugins/shared/tasks/ExternalProcessTask.java	2016-01-05 20:25:07 +0000
+++ WorkcraftCore/src/org/workcraft/plugins/shared/tasks/ExternalProcessTask.java	2016-01-15 17:12:28 +0000
@@ -14,6 +14,10 @@
 
 public class ExternalProcessTask implements Task<ExternalProcessResult>, ExternalProcessListener {
 	private List<String> args;
+	private final File workingDir;
+	private boolean printStdout;
+	private boolean printStderr;
+	private boolean hasNewLine = false;
 	
 	private volatile boolean finished;
 	private volatile int returnCode;
@@ -23,15 +27,11 @@
 	private DataAccumulator stdoutAccum = new DataAccumulator();
 	private DataAccumulator stderrAccum = new DataAccumulator();
 
-	private final File workingDir;
-	
-	public ExternalProcessTask(List<String> args) {
-		this(args, null);
-	}
-			
-	public ExternalProcessTask(List<String> args, File workingDir) {
+	public ExternalProcessTask(List<String> args, File workingDir, boolean printStdout, boolean printStderr) {
 		this.args = args;
 		this.workingDir = workingDir;
+		this.printStdout = printStdout;
+		this.printStderr = printStderr;
 	}
 	
 	@Override
@@ -68,7 +68,9 @@
 		if (userCancelled) {
 			return Result.cancelled();
 		}
-		ExternalProcessResult result = new ExternalProcessResult(returnCode, stdoutAccum.getData(), stderrAccum.getData(), Collections.<String, byte[]>emptyMap());
+		ExternalProcessResult result = new ExternalProcessResult(
+				returnCode, stdoutAccum.getData(), stderrAccum.getData(), 
+				Collections.<String, byte[]>emptyMap());
 		
 		return Result.finished(result);
 	}
@@ -91,6 +93,19 @@
 	}
 
 	@Override
+	public void outputData(byte[] data) {
+		try {
+			stdoutAccum.write(data);
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
+		monitor.stdout(data);
+		if (printStdout) {
+			printData(data);
+		}
+	}
+
+	@Override
 	public void errorData(byte[] data) {
 		try {
 			stderrAccum.write(data);
@@ -98,22 +113,26 @@
 			throw new RuntimeException(e);
 		}
 		monitor.stderr(data);
-	}
-
-	@Override
-	public void outputData(byte[] data) {
-		try {
-			stdoutAccum.write(data);
-		} catch (IOException e) {
-			throw new RuntimeException(e);
+		if (printStderr) {
+			printData(data);
 		}
-		monitor.stdout(data);
+
 	}
 
 	@Override
 	public void processFinished(int returnCode) {
 		this.returnCode = returnCode;
 		this.finished = true;
+		if ( !hasNewLine ) {
+			System.out.println();
+			hasNewLine = true;
+		}
+	}
+
+	private void printData(byte[] data) {
+		String s = new String(data);
+		System.out.print(s);
+		hasNewLine = (s.endsWith("\n"));
 	}
 	
 }
 
=== modified file 'WorkcraftCore/src/org/workcraft/tasks/DummyProgressMonitor.java'
--- WorkcraftCore/src/org/workcraft/tasks/DummyProgressMonitor.java	2010-02-14 17:59:01 +0000
+++ WorkcraftCore/src/org/workcraft/tasks/DummyProgressMonitor.java	2016-01-15 17:12:28 +0000
@@ -1,8 +1,9 @@
 package org.workcraft.tasks;
 
 public class DummyProgressMonitor<T> implements ProgressMonitor<T> {
+	
 	@Override
-	public void finished(Result<? extends T> result, String description) {
+	public void progressUpdate(double completion) {
 	}
 
 	@Override
@@ -15,10 +16,11 @@
 	}
 
 	@Override
-	public void progressUpdate(double completion) {
-	}
-
-	@Override
 	public void stderr(byte[] data) {
 	}
+
+	@Override
+	public void finished(Result<? extends T> result, String description) {
+	}
+	
 }