21 files changed, 188 insertions, 154 deletions

diff --git a/subprojects/frontend/src/graph/RelationName.tsx b/subprojects/frontend/src/graph/RelationName.tsx
index ec26fb21..e651cb87 100644
--- a/subprojects/frontend/src/graph/RelationName.tsx
+++ b/subprojects/frontend/src/graph/RelationName.tsx
@@ -9,7 +9,7 @@ import { observer } from 'mobx-react-lite';
 
 import { RelationMetadata } from '../xtext/xtextServiceResults';
 
-const Error = styled('span', {
+const ErrorPredicateName = styled('span', {
   name: 'RelationName-Error',
 })(({ theme }) => ({
   color: theme.palette.error.main,
@@ -36,7 +36,7 @@ const FormattedName = observer(function FormattedName({
     return <b>{name}</b>;
   }
   if (detail.type === 'predicate' && detail.error) {
-    return <Error>{name}</Error>;
+    return <ErrorPredicateName>{name}</ErrorPredicateName>;
   }
   return name;
 });
diff --git a/subprojects/store-dse-visualization/build.gradle.kts b/subprojects/store-dse-visualization/build.gradle.kts
index abad0491..ab9ed336 100644
--- a/subprojects/store-dse-visualization/build.gradle.kts
+++ b/subprojects/store-dse-visualization/build.gradle.kts
@@ -10,4 +10,5 @@ plugins {
 
 dependencies {
         api(project(":refinery-store-query"))
+        implementation(libs.slf4j.api)
 }
diff --git a/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/ModelVisualizerBuilder.java b/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/ModelVisualizerBuilder.java
index 1ee41cc3..e122f55c 100644
--- a/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/ModelVisualizerBuilder.java
+++ b/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/ModelVisualizerBuilder.java
@@ -9,6 +9,7 @@ import tools.refinery.store.adapter.ModelAdapterBuilder;
 import tools.refinery.visualization.internal.FileFormat;
 
 public interface ModelVisualizerBuilder extends ModelAdapterBuilder {
+        ModelVisualizerBuilder withDotBinaryPath(String dotBinaryPath);
         ModelVisualizerBuilder withOutputPath(String outputPath);
         ModelVisualizerBuilder withFormat(FileFormat format);
         ModelVisualizerBuilder saveDesignSpace();
diff --git a/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerAdapterImpl.java b/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerAdapterImpl.java
index a6a3dc69..ef10dd30 100644
--- a/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerAdapterImpl.java
+++ b/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerAdapterImpl.java
@@ -5,6 +5,8 @@
  */
 package tools.refinery.visualization.internal;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import tools.refinery.store.map.Version;
 import tools.refinery.store.model.Interpretation;
 import tools.refinery.store.model.Model;
@@ -20,13 +22,13 @@ import java.util.*;
 import java.util.stream.Collectors;
 
 public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
+        private static final Logger LOG = LoggerFactory.getLogger(ModelVisualizerAdapterImpl.class);
+
         private final Model model;
-        private final ModelVisualizerStoreAdapter storeAdapter;
+        private final ModelVisualizerStoreAdapterImpl storeAdapter;
         private final Map<AnySymbol, Interpretation<?>> allInterpretations;
         private final StringBuilder designSpaceBuilder = new StringBuilder();
         private final Map<Version, Integer> states = new HashMap<>();
-        private int transitionCounter = 0;
-        private Integer numberOfStates = 0;
         private final String outputPath;
         private final Set<FileFormat> formats;
         private final boolean renderDesignSpace;
@@ -41,7 +43,7 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
                         false, "0"
         );
 
-        public ModelVisualizerAdapterImpl(Model model, ModelVisualizerStoreAdapter storeAdapter) {
+        public ModelVisualizerAdapterImpl(Model model, ModelVisualizerStoreAdapterImpl storeAdapter) {
                 this.model = model;
                 this.storeAdapter = storeAdapter;
                 this.outputPath = storeAdapter.getOutputPath();
@@ -257,8 +259,8 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
 
                 try (FileWriter writer = new FileWriter(file)) {
                         writer.write(dot);
-                } catch (Exception e) {
-                        e.printStackTrace();
+                } catch (IOException e) {
+                        LOG.error("Failed to write dot file", e);
                         return false;
                 }
                 return true;
@@ -270,14 +272,15 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
 
         private boolean renderDot(String dot, FileFormat format, String filePath) {
                 try {
-                        Process process = new ProcessBuilder("dot", "-T" + format.getFormat(), "-o", filePath).start();
+                        Process process = new ProcessBuilder(storeAdapter.getDotBinaryPath(), "-T" + format.getFormat(),
+                                        "-o", filePath).start();
 
                         OutputStream osToProcess = process.getOutputStream();
                         PrintWriter pwToProcess = new PrintWriter(osToProcess);
                         pwToProcess.write(dot);
                         pwToProcess.close();
                 } catch (IOException e) {
-                        e.printStackTrace();
+                        LOG.error("Failed to render dot", e);
                         return false;
                 }
                 return true;
diff --git a/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerBuilderImpl.java b/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerBuilderImpl.java
index 9ba2abe8..db4f37b4 100644
--- a/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerBuilderImpl.java
+++ b/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerBuilderImpl.java
@@ -13,16 +13,24 @@ import java.util.LinkedHashSet;
 import java.util.Set;
 
 public class ModelVisualizerBuilderImpl
-                extends AbstractModelAdapterBuilder<ModelVisualizeStoreAdapterImpl>
+                extends AbstractModelAdapterBuilder<ModelVisualizerStoreAdapterImpl>
                 implements ModelVisualizerBuilder {
+        private String dotBinaryPath = "dot";
         private String outputPath;
         private boolean saveDesignSpace = false;
         private boolean saveStates = false;
         private final Set<FileFormat> formats = new LinkedHashSet<>();
 
         @Override
-        protected ModelVisualizeStoreAdapterImpl doBuild(ModelStore store) {
-                return new ModelVisualizeStoreAdapterImpl(store, outputPath, formats, saveDesignSpace, saveStates);
+        protected ModelVisualizerStoreAdapterImpl doBuild(ModelStore store) {
+                return new ModelVisualizerStoreAdapterImpl(store, dotBinaryPath, outputPath, formats, saveDesignSpace, saveStates);
+        }
+
+        @Override
+        public ModelVisualizerBuilder withDotBinaryPath(String dotBinaryPath) {
+                checkNotConfigured();
+                this.dotBinaryPath = dotBinaryPath;
+                return this;
         }
 
         @Override
diff --git a/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizeStoreAdapterImpl.java b/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerStoreAdapterImpl.java
index 04be22d6..c2ad4d87 100644
--- a/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizeStoreAdapterImpl.java
+++ b/subprojects/store-dse-visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerStoreAdapterImpl.java
@@ -12,16 +12,18 @@ import tools.refinery.visualization.ModelVisualizerStoreAdapter;
 
 import java.util.Set;
 
-public class ModelVisualizeStoreAdapterImpl implements ModelVisualizerStoreAdapter {
+public class ModelVisualizerStoreAdapterImpl implements ModelVisualizerStoreAdapter {
         private final ModelStore store;
+        private final String dotBinaryPath;
         private final String outputPath;
         private final boolean renderDesignSpace;
         private final boolean renderStates;
         private final Set<FileFormat> formats;
 
-        public ModelVisualizeStoreAdapterImpl(ModelStore store, String outputPath, Set<FileFormat> formats,
-                                                                                  boolean renderDesignSpace, boolean renderStates) {
+        public ModelVisualizerStoreAdapterImpl(ModelStore store, String dotBinaryPath, String outputPath,
+                                                                                   Set<FileFormat> formats, boolean renderDesignSpace, boolean renderStates) {
                 this.store = store;
+                this.dotBinaryPath = dotBinaryPath;
                 this.outputPath = outputPath;
                 this.formats = formats;
                 this.renderDesignSpace = renderDesignSpace;
@@ -38,6 +40,10 @@ public class ModelVisualizeStoreAdapterImpl implements ModelVisualizerStoreAdapt
                 return new ModelVisualizerAdapterImpl(model, this);
         }
 
+        String getDotBinaryPath() {
+                return dotBinaryPath;
+        }
+
         @Override
         public String getOutputPath() {
                 return outputPath;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstExplorer.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstExplorer.java
index 5e2f8fa9..ce3efb21 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstExplorer.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstExplorer.java
@@ -16,7 +16,11 @@ public class BestFirstExplorer extends BestFirstWorker {
         public BestFirstExplorer(BestFirstStoreManager storeManager, Model model, int id) {
                 super(storeManager, model);
                 this.id = id;
-                this.random = new Random(id);
+                // The use of a non-cryptographic random generator is safe here, because we only use it to direct the state
+                // space exploration.
+                @SuppressWarnings("squid:S2245")
+                var randomGenerator = new Random(id);
+                this.random = randomGenerator;
         }
 
         private boolean shouldRun() {
diff --git a/subprojects/viatra-runtime-localsearch/build.gradle.kts b/subprojects/viatra-runtime-localsearch/build.gradle.kts
index 31c0c634..d0259d95 100644
--- a/subprojects/viatra-runtime-localsearch/build.gradle.kts
+++ b/subprojects/viatra-runtime-localsearch/build.gradle.kts
@@ -6,6 +6,10 @@
 
 plugins {
         id("tools.refinery.gradle.java-library")
+        // Vendor code from Eclipse VIATRA is maintained by the VIATRA project,
+        // so we don't need to keep track of coverage ourselves.
+        // Our own modifications are covered by tests in the `store-query-viatra` subproject.
+        id("tools.refinery.gradle.skip-coverage")
 }
 
 dependencies {
diff --git a/subprojects/viatra-runtime-rete-recipes/build.gradle.kts b/subprojects/viatra-runtime-rete-recipes/build.gradle.kts
index b1b11b4e..b0d0139a 100644
--- a/subprojects/viatra-runtime-rete-recipes/build.gradle.kts
+++ b/subprojects/viatra-runtime-rete-recipes/build.gradle.kts
@@ -10,6 +10,10 @@ plugins {
         id("tools.refinery.gradle.java-library")
         id("tools.refinery.gradle.mwe2")
         id("tools.refinery.gradle.sonarqube")
+        // Vendor code from Eclipse VIATRA is maintained by the VIATRA project,
+        // so we don't need to keep track of coverage ourselves.
+        // Our own modifications are covered by tests in the `store-query-viatra` subproject.
+        id("tools.refinery.gradle.skip-coverage")
 }
 
 dependencies {
diff --git a/subprojects/viatra-runtime-rete/build.gradle.kts b/subprojects/viatra-runtime-rete/build.gradle.kts
index 7e795a90..560e8854 100644
--- a/subprojects/viatra-runtime-rete/build.gradle.kts
+++ b/subprojects/viatra-runtime-rete/build.gradle.kts
@@ -6,6 +6,10 @@
 
 plugins {
         id("tools.refinery.gradle.java-library")
+        // Vendor code from Eclipse VIATRA is maintained by the VIATRA project,
+        // so we don't need to keep track of coverage ourselves.
+        // Our own modifications are covered by tests in the `store-query-viatra` subproject.
+        id("tools.refinery.gradle.skip-coverage")
 }
 
 dependencies {
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/matcher/RetePatternMatcher.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/matcher/RetePatternMatcher.java
index 38fe7c2f..5f0f1892 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/matcher/RetePatternMatcher.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/matcher/RetePatternMatcher.java
@@ -31,10 +31,8 @@ import tools.refinery.viatra.runtime.rete.single.TransformerNode;
 import tools.refinery.viatra.runtime.rete.traceability.RecipeTraceInfo;
 
 import java.util.Collection;
-import java.util.List;
 import java.util.Map;
 import java.util.Optional;
-import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 /**
@@ -78,14 +76,6 @@ public class RetePatternMatcher extends TransformerNode implements IQueryResultP
         return productionNode;
     }
 
-    public Tuple matchOneRandomly(Object[] inputMapping, boolean[] fixed) {
-        List<Tuple> allMatches = matchAll(inputMapping, fixed).collect(Collectors.toList());
-        if (allMatches == null || allMatches.isEmpty())
-            return null;
-        else
-            return allMatches.get((int) (Math.random() * allMatches.size()));
-    }
-
     /**
      * @since 2.0
      */
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ConnectionFactory.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ConnectionFactory.java
index b261d19d..bd4d9bf2 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ConnectionFactory.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ConnectionFactory.java
@@ -132,17 +132,16 @@ class ConnectionFactory {
      * @return a replacement for the secondary Indexers, if needed
      */
     private Slots avoidActiveNodeConflict(final RecipeTraceInfo primarySlot, final RecipeTraceInfo secondarySlot) {
-        Slots result = new Slots() {
-            {
-                primary = (IterableIndexer) resolveIndexer((ProjectionIndexerRecipe) primarySlot.getRecipe());
-                secondary = resolveIndexer((IndexerRecipe) secondarySlot.getRecipe());
-            }
-        };
-        if (activeNodeConflict(result.primary, result.secondary))
-            if (result.secondary instanceof IterableIndexer)
-                result.secondary = resolveActiveIndexer(secondarySlot);
-            else
-                result.primary = (IterableIndexer) resolveActiveIndexer(primarySlot);
+        Slots result = new Slots();
+        result.primary = (IterableIndexer) resolveIndexer((ProjectionIndexerRecipe) primarySlot.getRecipe());
+        result.secondary = resolveIndexer((IndexerRecipe) secondarySlot.getRecipe());
+        if (activeNodeConflict(result.primary, result.secondary)) {
+                        if (result.secondary instanceof IterableIndexer) {
+                                result.secondary = resolveActiveIndexer(secondarySlot);
+                        } else {
+                                result.primary = (IterableIndexer) resolveActiveIndexer(primarySlot);
+                        }
+                }
         return result;
     }
 
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/Network.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/Network.java
index 64f59ff3..61030ff2 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/Network.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/Network.java
@@ -3,23 +3,12 @@
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v. 2.0 which is available at
  * http://www.eclipse.org/legal/epl-v20.html.
- * 
+ *
  * SPDX-License-Identifier: EPL-2.0
  *******************************************************************************/
 
 package tools.refinery.viatra.runtime.rete.network;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.concurrent.locks.Lock;
-import java.util.concurrent.locks.ReadWriteLock;
-import java.util.concurrent.locks.ReentrantReadWriteLock;
-
 import tools.refinery.viatra.runtime.matchers.tuple.Tuple;
 import tools.refinery.viatra.runtime.matchers.util.CollectionsFactory;
 import tools.refinery.viatra.runtime.matchers.util.Direction;
@@ -30,9 +19,15 @@ import tools.refinery.viatra.runtime.rete.remote.Address;
 import tools.refinery.viatra.runtime.rete.traceability.RecipeTraceInfo;
 import tools.refinery.viatra.runtime.rete.util.Options;
 
+import java.util.*;
+import java.util.Map.Entry;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReadWriteLock;
+import java.util.concurrent.locks.ReentrantReadWriteLock;
+
 /**
  * @author Gabor Bergmann
- * 
+ *
  */
 public class Network {
     final int threads;
@@ -43,7 +38,7 @@ public class Network {
     private int nextContainer = 0;
 
     // the following fields exist only if threads > 0
-    protected Map<ReteContainer, Long> globalTerminationCriteria = null;
+    protected final Map<ReteContainer, Long> globalTerminationCriteria;
     protected Map<ReteContainer, Long> reportedClocks = null;
     protected Lock updateLock = null; // grab during normal update operations
     protected Lock structuralChangeLock = null; // grab if the network structure
@@ -104,9 +99,10 @@ public class Network {
             structuralChangeLock = rwl.writeLock();
             for (int i = 0; i < threads; ++i)
                 containers.add(new ReteContainer(this, true));
-        } else
-            containers.add(new ReteContainer(this, false));
-
+        } else {
+                        containers.add(new ReteContainer(this, false));
+                        globalTerminationCriteria = null;
+                }
         headContainer = containers.get(0);
     }
 
@@ -138,7 +134,7 @@ public class Network {
 
     /**
      * Internal message delivery method.
-     * 
+     *
      * @pre threads > 0
      */
     private void sendUpdate(Address<? extends Receiver> receiver, Direction direction, Tuple updateElement) {
@@ -151,7 +147,7 @@ public class Network {
 
     /**
      * Internal message delivery method for single-threaded operation
-     * 
+     *
      * @pre threads == 0
      */
     private void sendUpdateSingleThreaded(Address<? extends Receiver> receiver, Direction direction,
@@ -162,7 +158,7 @@ public class Network {
 
     /**
      * Internal message delivery method.
-     * 
+     *
      * @pre threads > 0
      */
     private void sendUpdates(Address<? extends Receiver> receiver, Direction direction,
@@ -180,7 +176,7 @@ public class Network {
      * Sends an update message to the receiver node, indicating a newly found or lost partial matching. The node may
      * reside in any of the containers associated with this network. To be called from a user thread during normal
      * operation, NOT during construction.
-     * 
+     *
      * @since 2.4
      */
     public void sendExternalUpdate(Address<? extends Receiver> receiver, Direction direction, Tuple updateElement) {
@@ -201,10 +197,10 @@ public class Network {
      * Sends an update message to the receiver node, indicating a newly found or lost partial matching. The node may
      * reside in any of the containers associated with this network. To be called from a user thread during
      * construction.
-     * 
+     *
      * @pre: structuralChangeLock MUST be grabbed by the sequence (but not necessarily this thread, as the sequence may
      *       span through network calls, that's why it's not enforced here )
-     * 
+     *
      * @return the value of the target container's clock at the time when the message was accepted into its message
      *         queue
      * @since 2.4
@@ -222,10 +218,10 @@ public class Network {
      * Sends multiple update messages atomically to the receiver node, indicating a newly found or lost partial
      * matching. The node may reside in any of the containers associated with this network. To be called from a user
      * thread during construction.
-     * 
+     *
      * @pre: structuralChangeLock MUST be grabbed by the sequence (but not necessarily this thread, as the sequence may
      *       span through network calls, that's why it's not enforced here )
-     * 
+     *
      * @since 2.4
      */
     public void sendConstructionUpdates(Address<? extends Receiver> receiver, Direction direction,
@@ -241,7 +237,7 @@ public class Network {
     /**
      * Establishes connection between a supplier and a receiver node, regardless which container they are in. Not to be
      * called remotely, because this method enforces the structural lock.
-     * 
+     *
      * @param supplier
      * @param receiver
      * @param synchronise
@@ -262,7 +258,7 @@ public class Network {
     /**
      * Severs connection between a supplier and a receiver node, regardless which container they are in. Not to be
      * called remotely, because this method enforces the structural lock.
-     * 
+     *
      * @param supplier
      * @param receiver
      * @param desynchronise
@@ -282,9 +278,9 @@ public class Network {
 
     /**
      * Containers use this method to report whenever they run out of messages in their queue.
-     * 
+     *
      * To be called from the thread of the reporting container.
-     * 
+     *
      * @pre threads > 0.
      * @param reportingContainer
      *            the container reporting the emptiness of its message queue.
@@ -328,7 +324,7 @@ public class Network {
     /**
      * Waits until all rete update operations are settled in all containers. Returns immediately, if no updates are
      * pending.
-     * 
+     *
      * To be called from any user thread.
      */
     public void waitForReteTermination() {
@@ -338,7 +334,7 @@ public class Network {
                     try {
                         globalTerminationCriteria.wait();
                     } catch (InterruptedException e) {
-
+                                                Thread.currentThread().interrupt();
                     }
                 }
             }
@@ -350,10 +346,10 @@ public class Network {
      * Waits to execute action until all rete update operations are settled in all containers. Runs action and returns
      * immediately, if no updates are pending. The given action is guaranteed to be run when the terminated state still
      * persists.
-     * 
+     *
      * @param action
      *            the action to be run when reaching the steady-state.
-     * 
+     *
      *            To be called from any user thread.
      */
     public void waitForReteTermination(Runnable action) {
@@ -363,7 +359,7 @@ public class Network {
                     try {
                         globalTerminationCriteria.wait();
                     } catch (InterruptedException e) {
-
+                                                Thread.currentThread().interrupt();
                     }
                 }
                 action.run();
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ReteContainer.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ReteContainer.java
index 79e0526d..d058417f 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ReteContainer.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ReteContainer.java
@@ -514,6 +514,7 @@ public final class ReteContainer {
                             try {
                                 externalMessageLock.wait();
                             } catch (InterruptedException e) {
+                                                                Thread.currentThread().interrupt();
                                 if (killed)
                                     return;
                             }
@@ -565,7 +566,9 @@ public final class ReteContainer {
                                         + group.getRepresentative() + " has already been processed!");
                     }
 
-                    group.deliverMessages();
+                                        if (group != null) {
+                                                group.deliverMessages();
+                                        }
 
                     lastGroup = group;
                 }
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/communication/CommunicationTracker.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/communication/CommunicationTracker.java
index d244e644..9c2fbb9a 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/communication/CommunicationTracker.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/communication/CommunicationTracker.java
@@ -8,33 +8,15 @@
  *******************************************************************************/
 package tools.refinery.viatra.runtime.rete.network.communication;
 
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.PriorityQueue;
-import java.util.Queue;
-import java.util.Set;
-
-import tools.refinery.viatra.runtime.rete.itc.alg.incscc.IncSCCAlg;
-import tools.refinery.viatra.runtime.rete.itc.alg.misc.topsort.TopologicalSorting;
-import tools.refinery.viatra.runtime.rete.itc.graphimpl.Graph;
 import tools.refinery.viatra.runtime.matchers.tuple.TupleMask;
 import tools.refinery.viatra.runtime.rete.aggregation.IAggregatorNode;
 import tools.refinery.viatra.runtime.rete.boundary.ExternalInputEnumeratorNode;
 import tools.refinery.viatra.runtime.rete.eval.RelationEvaluatorNode;
-import tools.refinery.viatra.runtime.rete.index.DualInputNode;
-import tools.refinery.viatra.runtime.rete.index.ExistenceNode;
-import tools.refinery.viatra.runtime.rete.index.Indexer;
-import tools.refinery.viatra.runtime.rete.index.IndexerListener;
-import tools.refinery.viatra.runtime.rete.index.IterableIndexer;
-import tools.refinery.viatra.runtime.rete.index.SpecializedProjectionIndexer;
-import tools.refinery.viatra.runtime.rete.network.IGroupable;
-import tools.refinery.viatra.runtime.rete.network.NetworkStructureChangeSensitiveNode;
-import tools.refinery.viatra.runtime.rete.network.Node;
-import tools.refinery.viatra.runtime.rete.network.ProductionNode;
-import tools.refinery.viatra.runtime.rete.network.Receiver;
-import tools.refinery.viatra.runtime.rete.network.ReteContainer;
+import tools.refinery.viatra.runtime.rete.index.*;
+import tools.refinery.viatra.runtime.rete.itc.alg.incscc.IncSCCAlg;
+import tools.refinery.viatra.runtime.rete.itc.alg.misc.topsort.TopologicalSorting;
+import tools.refinery.viatra.runtime.rete.itc.graphimpl.Graph;
+import tools.refinery.viatra.runtime.rete.network.*;
 import tools.refinery.viatra.runtime.rete.network.communication.timely.TimelyIndexerListenerProxy;
 import tools.refinery.viatra.runtime.rete.network.communication.timely.TimelyMailboxProxy;
 import tools.refinery.viatra.runtime.rete.network.mailbox.FallThroughCapableMailbox;
@@ -43,6 +25,8 @@ import tools.refinery.viatra.runtime.rete.network.mailbox.timeless.BehaviorChang
 import tools.refinery.viatra.runtime.rete.single.TransitiveClosureNode;
 import tools.refinery.viatra.runtime.rete.single.TrimmerNode;
 
+import java.util.*;
+
 /**
  * An instance of this class is associated with every {@link ReteContainer}. The tracker serves two purposes: <br>
  * (1) It allows RETE nodes to register their communication dependencies on-the-fly. These dependencies can be
@@ -263,7 +247,10 @@ public abstract class CommunicationTracker {
 
     public CommunicationGroup getAndRemoveFirstGroup() {
         final CommunicationGroup group = groupQueue.poll();
-        group.isEnqueued = false;
+                if (group == null) {
+                        throw new IllegalStateException("Group queue must not be empty");
+                }
+                group.isEnqueued = false;
         return group;
     }
 
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/util/OrderingCompareAgent.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/util/OrderingCompareAgent.java
index 8b147cf6..6d0d813a 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/util/OrderingCompareAgent.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/util/OrderingCompareAgent.java
@@ -3,7 +3,7 @@
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v. 2.0 which is available at
  * http://www.eclipse.org/legal/epl-v20.html.
- * 
+ *
  * SPDX-License-Identifier: EPL-2.0
  *******************************************************************************/
 
@@ -13,9 +13,9 @@ import java.util.Comparator;
 
 /**
  * Comparing agent for an ordering. Terminology: the "preferred" item will register as LESS.
- * 
+ *
  * @author Gabor Bergmann
- * 
+ *
  */
 public abstract class OrderingCompareAgent<T> {
     protected T a;
@@ -25,7 +25,7 @@ public abstract class OrderingCompareAgent<T> {
      * @param a
      * @param b
      */
-    public OrderingCompareAgent(T a, T b) {
+    protected OrderingCompareAgent(T a, T b) {
         super();
         this.a = a;
         this.b = b;
@@ -77,16 +77,21 @@ public abstract class OrderingCompareAgent<T> {
     protected static <U> int preferLess(Comparable<U> c1, U c2) {
         return c1.compareTo(c2);
     }
-    
+
     protected static <U> int preferLess(U c1, U c2, Comparator<U> comp) {
         return comp.compare(c1, c2);
     }
 
     protected static <U> int preferMore(Comparable<U> c1, U c2) {
-        return -c1.compareTo(c2);
+        return reverse(c1.compareTo(c2));
     }
+
     protected static <U> int preferMore(U c1, U c2, Comparator<U> comp) {
-        return -comp.compare(c1, c2);
+        return reverse(comp.compare(c1, c2));
     }
 
+        private static int reverse(int value) {
+                return Integer.compare(0, value);
+        }
+
 }
diff --git a/subprojects/viatra-runtime/build.gradle.kts b/subprojects/viatra-runtime/build.gradle.kts
index c4bd9129..05c2b754 100644
--- a/subprojects/viatra-runtime/build.gradle.kts
+++ b/subprojects/viatra-runtime/build.gradle.kts
@@ -6,6 +6,10 @@
 
 plugins {
         id("tools.refinery.gradle.java-library")
+        // Vendor code from Eclipse VIATRA is maintained by the VIATRA project,
+        // so we don't need to keep track of coverage ourselves.
+        // Our own modifications are covered by tests in the `store-query-viatra` subproject.
+        id("tools.refinery.gradle.skip-coverage")
 }
 
 dependencies {
diff --git a/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/internal/apiimpl/ViatraQueryEngineImpl.java b/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/internal/apiimpl/ViatraQueryEngineImpl.java
index 5317a79e..84ac8f7d 100644
--- a/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/internal/apiimpl/ViatraQueryEngineImpl.java
+++ b/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/internal/apiimpl/ViatraQueryEngineImpl.java
@@ -74,7 +74,7 @@ public final class ViatraQueryEngineImpl extends AdvancedViatraQueryEngine
     /**
      * The context of the engine, provided by the scope.
      */
-    private IEngineContext engineContext;
+    private final IEngineContext engineContext;
 
     /**
      * Initialized matchers for each query
@@ -85,7 +85,7 @@ public final class ViatraQueryEngineImpl extends AdvancedViatraQueryEngine
     /**
      * The RETE and other pattern matcher implementations of the VIATRA Query Engine.
      */
-    private volatile Map<IQueryBackendFactory, IQueryBackend> queryBackends = new HashMap<>();
+    private final Map<IQueryBackendFactory, IQueryBackend> queryBackends = Collections.synchronizedMap(new HashMap<>());
 
     /**
      * The current engine default hints
diff --git a/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/context/common/JavaTransitiveInstancesKey.java b/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/context/common/JavaTransitiveInstancesKey.java
index eb972c2d..400a6ab9 100644
--- a/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/context/common/JavaTransitiveInstancesKey.java
+++ b/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/context/common/JavaTransitiveInstancesKey.java
@@ -3,7 +3,7 @@
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v. 2.0 which is available at
  * http://www.eclipse.org/legal/epl-v20.html.
- * 
+ *
  * SPDX-License-Identifier: EPL-2.0
  *******************************************************************************/
 package tools.refinery.viatra.runtime.matchers.context.common;
@@ -12,22 +12,22 @@ package tools.refinery.viatra.runtime.matchers.context.common;
 
 /**
  * Instance tuples are of form (x), where object x is an instance of the given Java class or its subclasses.
- * <p> Fine print 1: classes with the same name are considered equivalent. 
- * Can be instantiated with class name, even if the class itself is not loaded yet; but if the class is available, passing it in the constructor is beneficial to avoid classloading troubles.  
- * <p> Fine print 2: primitive types (char, etc.) are transparently treated as their wrapper class (Character, etc.). 
+ * <p> Fine print 1: classes with the same name are considered equivalent.
+ * Can be instantiated with class name, even if the class itself is not loaded yet; but if the class is available, passing it in the constructor is beneficial to avoid classloading troubles.
+ * <p> Fine print 2: primitive types (char, etc.) are transparently treated as their wrapper class (Character, etc.).
  * <p> Non-enumerable type, can only be checked.
  * <p> Stateless type (objects can't change their type)
  * @author Bergmann Gabor
  *
 */
 public class JavaTransitiveInstancesKey extends BaseInputKeyWrapper<String> {
-    
+
     /**
      * The actual Class whose (transitive) instances this relation contains. Can be null at compile time, if only the name is available.
-     * Can be a primitive.  
+     * Can be a primitive.
      */
     private Class<?> cachedOriginalInstanceClass;
-    
+
     /**
      * Same as {@link #cachedOriginalInstanceClass}, but primitive classes are replaced with their wrapper classes (e.g. int --> java.lang.Integer).
      */
@@ -37,17 +37,17 @@ public class JavaTransitiveInstancesKey extends BaseInputKeyWrapper<String> {
      * Preferred constructor.
      */
     public JavaTransitiveInstancesKey(Class<?> instanceClass) {
-        this(primitiveTypeToWrapperClass(instanceClass).getName());
+        this(getName(instanceClass));
         this.cachedOriginalInstanceClass = instanceClass;
     }
-    
+
     /**
      * Call this constructor only in contexts where the class itself is not available for loading, e.g. it has not yet been compiled.
      */
     public JavaTransitiveInstancesKey(String className) {
         super(className);
     }
-    
+
 
     /**
      * Returns null if class cannot be loaded.
@@ -66,7 +66,7 @@ public class JavaTransitiveInstancesKey extends BaseInputKeyWrapper<String> {
 
     /**
      * @return non-null instance class
-     * @throws ClassNotFoundException 
+     * @throws ClassNotFoundException
      */
     private Class<?> forceGetOriginalInstanceClass() throws ClassNotFoundException {
         if (cachedOriginalInstanceClass == null) {
@@ -74,10 +74,10 @@ public class JavaTransitiveInstancesKey extends BaseInputKeyWrapper<String> {
         }
         return cachedOriginalInstanceClass;
     }
-    
+
     /**
      * @return non-null instance class, wrapped if primitive class
-     * @throws ClassNotFoundException 
+     * @throws ClassNotFoundException
      */
     public Class<?> forceGetWrapperInstanceClass() throws ClassNotFoundException {
         forceGetOriginalInstanceClass();
@@ -85,12 +85,12 @@ public class JavaTransitiveInstancesKey extends BaseInputKeyWrapper<String> {
     }
     /**
      * @return non-null instance class, wrapped if primitive class
-     * @throws ClassNotFoundException 
+     * @throws ClassNotFoundException
      */
     public Class<?> forceGetInstanceClass() throws ClassNotFoundException {
         return forceGetWrapperInstanceClass();
     }
-    
+
     /**
      * @return instance class, wrapped if primitive class, null if class cannot be loaded
      */
@@ -106,16 +106,19 @@ public class JavaTransitiveInstancesKey extends BaseInputKeyWrapper<String> {
     public Class<?> getInstanceClass()  {
         return getWrapperInstanceClass();
     }
-    
+
     private void resolveClassInternal() throws ClassNotFoundException {
         cachedOriginalInstanceClass = Class.forName(wrappedKey);
     }
-    
+
     @Override
     public String getPrettyPrintableName() {
         getWrapperInstanceClass();
-        return cachedWrapperInstanceClass == null ? wrappedKey == null ? "<null>" : wrappedKey : cachedWrapperInstanceClass.getName();
-    }
+                if (cachedWrapperInstanceClass == null) {
+                        return wrappedKey == null ? "<null>" : wrappedKey;
+                }
+                return cachedWrapperInstanceClass.getName();
+        }
 
     @Override
     public String getStringID() {
@@ -126,12 +129,12 @@ public class JavaTransitiveInstancesKey extends BaseInputKeyWrapper<String> {
     public int getArity() {
         return 1;
     }
-    
+
     @Override
     public boolean isEnumerable() {
         return false;
     }
-    
+
     @Override
     public String toString() {
         return this.getPrettyPrintableName();
@@ -161,5 +164,11 @@ public class JavaTransitiveInstancesKey extends BaseInputKeyWrapper<String> {
         return instanceClass;
     }
 
-
+        private static String getName(Class<?> instanceClass) {
+                Class<?> wrapperClass = primitiveTypeToWrapperClass(instanceClass);
+                if (wrapperClass == null) {
+                        return "<null>";
+                }
+                return wrapperClass.getName();
+        }
 }
diff --git a/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/psystem/rewriters/VariableMappingExpressionEvaluatorWrapper.java b/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/psystem/rewriters/VariableMappingExpressionEvaluatorWrapper.java
index 10337979..e0e17b5e 100644
--- a/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/psystem/rewriters/VariableMappingExpressionEvaluatorWrapper.java
+++ b/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/psystem/rewriters/VariableMappingExpressionEvaluatorWrapper.java
@@ -3,24 +3,24 @@
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v. 2.0 which is available at
  * http://www.eclipse.org/legal/epl-v20.html.
- * 
+ *
  * SPDX-License-Identifier: EPL-2.0
  *******************************************************************************/
 package tools.refinery.viatra.runtime.matchers.psystem.rewriters;
 
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
 import tools.refinery.viatra.runtime.matchers.psystem.IExpressionEvaluator;
 import tools.refinery.viatra.runtime.matchers.psystem.IValueProvider;
 import tools.refinery.viatra.runtime.matchers.psystem.PVariable;
 import tools.refinery.viatra.runtime.matchers.util.Preconditions;
 
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
 /**
  * A wrapper for {@link IExpressionEvaluator} which is capable of correctly mapping variable names used by the
  * expression.
- * 
+ *
  * @author Grill Balázs
  *
  */
@@ -28,10 +28,10 @@ class VariableMappingExpressionEvaluatorWrapper implements IExpressionEvaluator
 
     private final IExpressionEvaluator wrapped;
     private final Map<String, String> variableMapping;
-    
+
     public VariableMappingExpressionEvaluatorWrapper(IExpressionEvaluator wrapped,
             Map<PVariable, PVariable> variableMapping) {
-        
+
         // Support to rewrap an already wrapped expression.
         boolean rewrap = wrapped instanceof VariableMappingExpressionEvaluatorWrapper;
         this.wrapped = rewrap ? ((VariableMappingExpressionEvaluatorWrapper)wrapped).wrapped : wrapped;
@@ -46,7 +46,7 @@ class VariableMappingExpressionEvaluatorWrapper implements IExpressionEvaluator
         for (PVariable originalVar : variableMapping.keySet()) {
             names.put(originalVar.getName(), originalVar);
         }
-        
+
         // In case of rewrapping, current names are contained by the previous mapping
         Map<String, String> previousMapping = null;
         if (rewrap){
@@ -55,6 +55,8 @@ class VariableMappingExpressionEvaluatorWrapper implements IExpressionEvaluator
 
         // Populate mapping
         for (String inputParameterName : this.wrapped.getInputParameterNames()) {
+                        // {@code previousMapping} can't be {@code null} if {@code rewrap} is {@code true}.
+                        @SuppressWarnings("squid:S2259")
             String parameterName = rewrap ? previousMapping.get(inputParameterName) : inputParameterName;
             Preconditions.checkArgument(parameterName != null);
             PVariable original = names.get(parameterName);
diff --git a/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/util/EclipseCollectionsLongSetMemory.java b/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/util/EclipseCollectionsLongSetMemory.java
index fceb54fc..ce3efa92 100644
--- a/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/util/EclipseCollectionsLongSetMemory.java
+++ b/subprojects/viatra-runtime/src/main/java/tools/refinery/viatra/runtime/matchers/util/EclipseCollectionsLongSetMemory.java
@@ -3,20 +3,21 @@
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v. 2.0 which is available at
  * http://www.eclipse.org/legal/epl-v20.html.
- * 
+ *
  * SPDX-License-Identifier: EPL-2.0
  *******************************************************************************/
 package tools.refinery.viatra.runtime.matchers.util;
 
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.Set;
-
 import org.eclipse.collections.api.LongIterable;
 import org.eclipse.collections.api.iterator.LongIterator;
 import org.eclipse.collections.api.set.primitive.LongSet;
 import org.eclipse.collections.impl.set.mutable.primitive.LongHashSet;
 
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.Set;
+
 /**
  * @author Gabor Bergmann
  * @since 2.0
@@ -31,7 +32,7 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
     @Override
     public boolean addSigned(Long value, int count) {
         if (count == 1) return addOne(value);
-        else if (count == -1) return removeOne(value); 
+        else if (count == -1) return removeOne(value);
         else throw new IllegalStateException();
     }
 
@@ -40,7 +41,7 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
         // Kept for binary compatibility
         return ISetMemory.super.removeOne(value);
     }
-    
+
     /**
      * @since 2.3
      */
@@ -58,7 +59,7 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
     public int getCount(Long value) {
         return super.contains(value) ? 1 : 0;
     }
-    
+
     @Override
     public int getCountUnsafe(Object value) {
         return value instanceof Long ? getCount((Long) value) : 0;
@@ -68,7 +69,7 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
     public boolean containsNonZero(Long value) {
         return super.contains(value);
     }
-    
+
     @Override
     public boolean containsNonZeroUnsafe(Object value) {
         return value instanceof Long && containsNonZero((Long) value);
@@ -83,18 +84,18 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
     public Set<Long> distinctValues() {
         return new SetWrapper(this);
     }
-    
+
     @Override
     public boolean isEmpty() {
         return super.isEmpty();
     }
-    
+
     /**
      * Helper for iterating a LongIterable
      */
     public static Iterator<Long> iteratorOf(LongIterable wrapped) {
         return new Iterator<Long>() {
-            LongIterator longIterator = wrapped.longIterator();
+            private final LongIterator longIterator = wrapped.longIterator();
 
             @Override
             public boolean hasNext() {
@@ -103,11 +104,14 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
 
             @Override
             public Long next() {
+                                if (!longIterator.hasNext()) {
+                                        throw new NoSuchElementException("next() called, but the iterator is exhausted");
+                                }
                 return longIterator.next();
             }
         };
     }
-    
+
     @Override
     public int hashCode() {
         return IMemoryView.hashCode(this);
@@ -117,7 +121,7 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
         return IMemoryView.equals(this, obj);
     }
 
-    
+
     /**
      * Helper that presents a primitive collection as a Set view
      * @author Gabor Bergmann
@@ -171,7 +175,7 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
         public <T> T[] toArray(T[] a) {
             int k = 0;
             LongIterator iterator = wrapped.longIterator();
-            while (iterator.hasNext()) 
+            while (iterator.hasNext())
                 a[k++] = (T) Long.valueOf(iterator.next());
             return a;
         }
@@ -205,8 +209,8 @@ public class EclipseCollectionsLongSetMemory extends LongHashSet implements ISet
         public void clear() {
             throw new UnsupportedOperationException();
         }
-        
-        
+
+
     }
 
 }