diff --git a/src/com/vividsolutions/jcs/conflate/polygonmatch/ChainMatcher.java b/src/com/vividsolutions/jcs/conflate/polygonmatch/ChainMatcher.java
index 605c4dd..ab4c8f3 100644
--- a/src/com/vividsolutions/jcs/conflate/polygonmatch/ChainMatcher.java
+++ b/src/com/vividsolutions/jcs/conflate/polygonmatch/ChainMatcher.java
@@ -36,6 +36,7 @@
 
 import com.vividsolutions.jump.feature.Feature;
 import com.vividsolutions.jump.feature.FeatureCollection;
+import com.vividsolutions.jump.feature.FeatureDataset;
 
 /**
  * Composes several FeatureMatchers into one. Candidate features are whittled
@@ -68,8 +69,7 @@ public ChainMatcher(FeatureMatcher[] matchers) {
    */
     @Override
   public Matches match(Feature target, FeatureCollection candidates) {
-    Matches survivors = new Matches(
-        candidates.getFeatureSchema(), candidates.getFeatures());
+    Matches survivors = new Matches(new FeatureDataset(candidates.getFeatures(), candidates.getFeatureSchema(), candidates.getEnvelope()));
     for (FeatureMatcher matcher : matchers) {
       survivors = matcher.match(target, survivors);
     }
diff --git a/src/com/vividsolutions/jcs/conflate/polygonmatch/DisambiguatingFCMatchFinder.java b/src/com/vividsolutions/jcs/conflate/polygonmatch/DisambiguatingFCMatchFinder.java
index 71288a5..4f72dd4 100644
--- a/src/com/vividsolutions/jcs/conflate/polygonmatch/DisambiguatingFCMatchFinder.java
+++ b/src/com/vividsolutions/jcs/conflate/polygonmatch/DisambiguatingFCMatchFinder.java
@@ -1,7 +1,10 @@
 package com.vividsolutions.jcs.conflate.polygonmatch;
+
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.SortedSet;
 
 import com.vividsolutions.jump.feature.Feature;
@@ -24,20 +27,26 @@ public Map<Feature, Matches> match(
         FeatureCollection targetFC,
         FeatureCollection candidateFC,
         TaskMonitor monitor) {
-        List<Feature> targets = new ArrayList<>();
-        List<Feature> candidates = new ArrayList<>();
-        List<Double> scores = new ArrayList<>();
-        SortedSet<DisambiguationMatch> matchSet = DisambiguationMatch.createDisambiguationMatches(matchFinder.match(targetFC, candidateFC, monitor), monitor);
+        final SortedSet<DisambiguationMatch> matchSet =
+                DisambiguationMatch.createDisambiguationMatches(matchFinder.match(targetFC, candidateFC, monitor), monitor);
+        final List<Feature> targets = new ArrayList<>(matchSet.size());
+        final List<Feature> candidates = new ArrayList<>(matchSet.size());
+        // These sets are here to avoid expensive ArrayList#contains calls
+        final Set<Feature> candidatesSet = new HashSet<>(matchSet.size());
+        final Set<Feature> targetsSet = new HashSet<>(matchSet.size());
+        final List<Double> scores = new ArrayList<>(matchSet.size());
         monitor.report("Discarding inferior matches");
         int j = 0;
         for (DisambiguationMatch match : matchSet) {
             monitor.report(++j, matchSet.size(), "matches");
-            if (targets.contains(match.getTarget()) || candidates.contains(match.getCandidate())) {
+            if (targetsSet.contains(match.getTarget()) || candidatesSet.contains(match.getCandidate())) {
                 continue;
             }
             targets.add(match.getTarget());
+            targetsSet.add(match.getTarget());
             candidates.add(match.getCandidate());
-            scores.add(Double.valueOf(match.getScore()));
+            candidatesSet.add(match.getCandidate());
+            scores.add(match.getScore());
         }
         //Re-add filtered-out targets, but with zero-score matches [Jon Aquino]
         Map<Feature, Matches> targetToMatchesMap =
@@ -46,7 +55,7 @@ public Map<Feature, Matches> match(
                 candidateFC.getFeatureSchema());
         for (int i = 0; i < targets.size(); i++) {
             Matches matches = new Matches(candidateFC.getFeatureSchema());
-            matches.add(candidates.get(i), scores.get(i).doubleValue());
+            matches.add(candidates.get(i), scores.get(i));
             targetToMatchesMap.put(targets.get(i), matches);
         }
         return targetToMatchesMap;
diff --git a/src/com/vividsolutions/jcs/conflate/polygonmatch/FeatureMatcher.java b/src/com/vividsolutions/jcs/conflate/polygonmatch/FeatureMatcher.java
index 79626fe..b9d5c63 100644
--- a/src/com/vividsolutions/jcs/conflate/polygonmatch/FeatureMatcher.java
+++ b/src/com/vividsolutions/jcs/conflate/polygonmatch/FeatureMatcher.java
@@ -58,6 +58,6 @@ public interface FeatureMatcher {
    * @return the matching features, and a score for each. (Implementors should
    * document how they do their scoring).
    */
-  public Matches match(Feature target, FeatureCollection candidates);
+  Matches match(Feature target, FeatureCollection candidates);
 
 }
diff --git a/src/com/vividsolutions/jcs/conflate/polygonmatch/IndependentCandidateMatcher.java b/src/com/vividsolutions/jcs/conflate/polygonmatch/IndependentCandidateMatcher.java
index 80b8d8b..f8137d7 100644
--- a/src/com/vividsolutions/jcs/conflate/polygonmatch/IndependentCandidateMatcher.java
+++ b/src/com/vividsolutions/jcs/conflate/polygonmatch/IndependentCandidateMatcher.java
@@ -31,9 +31,12 @@
  */
 package com.vividsolutions.jcs.conflate.polygonmatch;
 
+import java.util.Collections;
+
 import org.locationtech.jts.geom.Geometry;
 import com.vividsolutions.jump.feature.Feature;
 import com.vividsolutions.jump.feature.FeatureCollection;
+import com.vividsolutions.jump.feature.FeatureDataset;
 
 /**
  * Base class of FeatureMatchers that compare the target to each candidate
@@ -46,7 +49,9 @@ public IndependentCandidateMatcher() {
 
     @Override
   public Matches match(Feature target, FeatureCollection candidates) {
-    Matches matches = new Matches(candidates.getFeatureSchema());
+    final FeatureDataset fds = new FeatureDataset(Collections.emptySet(), candidates.getFeatureSchema(),
+            candidates.getEnvelope());
+    final Matches matches = new Matches(fds);
     for (Feature candidate : candidates) {
       double score = match(target.getGeometry(), candidate.getGeometry());
       if (score > 0) { matches.add(candidate, score); }
diff --git a/src/com/vividsolutions/jcs/conflate/polygonmatch/Matches.java b/src/com/vividsolutions/jcs/conflate/polygonmatch/Matches.java
index 5575fbb..ba60095 100644
--- a/src/com/vividsolutions/jcs/conflate/polygonmatch/Matches.java
+++ b/src/com/vividsolutions/jcs/conflate/polygonmatch/Matches.java
@@ -32,8 +32,9 @@
 package com.vividsolutions.jcs.conflate.polygonmatch;
 
 import java.util.AbstractMap;
-import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
@@ -41,7 +42,8 @@
 import java.util.Set;
 
 import org.locationtech.jts.geom.Envelope;
-import org.locationtech.jts.util.Assert;
+import org.locationtech.jts.util.AssertionFailedException;
+
 import com.vividsolutions.jump.feature.Feature;
 import com.vividsolutions.jump.feature.FeatureCollection;
 import com.vividsolutions.jump.feature.FeatureDataset;
@@ -53,13 +55,14 @@
  */
 public class Matches extends AbstractMap<Feature, Double> implements FeatureCollection, Cloneable {
     private final Set<Map.Entry<Feature, Double>> entrySet = new HashSet<>();
+    private int size;
     /**
      * Creates a Matches object.
      * @param schema metadata applicable to the features that will be stored in
      * this Matches object
      */
     public Matches(FeatureSchema schema) {
-        dataset = new FeatureDataset(schema);
+        this(schema, Collections.emptyList());
     }
 
     @Override
@@ -78,14 +81,28 @@ protected Matches clone() {
      * @param features added to the Matches, each with the max score (1.0)
      */
     public Matches(FeatureSchema schema, List<Feature> features) {
-        this(schema);
-        for (Feature match : features) {
-            add(match, 1);
-        }
+        // We want to ensure that the dataset won't have a ton of ArrayList#grow calls
+        // So we initialize the dataset with all the data
+        this.dataset = new FeatureDataset(features.size(), schema, null);
+        this.scores = new double[features.size()];
+        addAll(features, 1, true);
+    }
+
+    /**
+     * Creates a Matches object, initialized with the given Dataset.
+     * @param featureDataset The dataset to use for initialization
+     */
+    public Matches(FeatureDataset featureDataset) {
+        // We want to ensure that the dataset won't have a ton of ArrayList#grow calls
+        // So we initialize the dataset with all the data
+        this.scores = new double[featureDataset.size()];
+        this.dataset = new FeatureDataset(featureDataset);
+
+        addAll(featureDataset, 1, false);
     }
 
     private final FeatureDataset dataset;
-    private final List<Double> scores = new ArrayList<>();
+    private double[] scores;
 
     /**
      * This method is not supported, because added features need to be associated
@@ -94,7 +111,7 @@ public Matches(FeatureSchema schema, List<Feature> features) {
      * @see #add(Feature, double)
      */
     @Override
-	public void add(Feature feature) {
+    public void add(Feature feature) {
         throw new UnsupportedOperationException("Use #add(feature, score) instead");
     }
 
@@ -103,10 +120,16 @@ public void add(Feature feature) {
      * with a score. Use #add(Feature, double) instead.
      */
     @Override
-	public void addAll(Collection<? extends Feature> features) {
+    public void addAll(Collection<? extends Feature> features) {
         throw new UnsupportedOperationException("Use #add(feature, score) instead");
     }
 
+    private void addAll(Iterable<? extends Feature> features, double score, boolean addToDataset) {
+        for (Feature feature : features) {
+            add(feature, score, addToDataset);
+        }
+    }
+
     /**
      * This method is not supported, because added features need to be associated
      * with a score. Use #add(Feature, double) instead.
@@ -122,7 +145,7 @@ public void add(int index, Feature feature) {
      * have matches removed.
      */
     @Override
-	public Collection<Feature> remove(Envelope envelope) {
+    public Collection<Feature> remove(Envelope envelope) {
         //If we decide to implement this, remember to remove the corresponding
         //score. [Jon Aquino]
         throw new UnsupportedOperationException();
@@ -133,7 +156,7 @@ public Collection<Feature> remove(Envelope envelope) {
      * have matches removed.
      */
     @Override
-	public void clear() {
+    public void clear() {
         //If we decide to implement this, remember to remove the corresponding
         //score. [Jon Aquino]
         throw new UnsupportedOperationException();
@@ -162,7 +185,7 @@ private synchronized Set<Entry<Feature, Double>> updateEntrySet() {
      * have matches removed.
      */
     @Override
-	public void removeAll(Collection<Feature> features) {
+    public void removeAll(Collection<Feature> features) {
         //If we decide to implement this, remember to remove the corresponding
         //score. [Jon Aquino]
         throw new UnsupportedOperationException();
@@ -174,7 +197,7 @@ public void removeAll(Collection<Feature> features) {
      * @param feature a feature to remove
      */
     @Override
-	public void remove(Feature feature) {
+    public void remove(Feature feature) {
         //If we decide to implement this, remember to remove the corresponding
         //score. [Jon Aquino]
         throw new UnsupportedOperationException();
@@ -185,20 +208,36 @@ public void remove(Feature feature) {
      * @param score the confidence of the match, ranging from 0 to 1
      */
     public void add(Feature feature, double score) {
-        Assert.isTrue(0 <= score && score <= 1, "Score = " + score);
+        add(feature, score, true);
+    }
+
+    private void add(Feature feature, double score, boolean addToDataset) {
+        // We want to avoid the string concatenation here, if we don't need it.
+        // It is *very* expensive when run with large datasets.
+        // This used to be an Assert.isTrue statement
+        if (0 > score || score > 1) {
+            throw new AssertionFailedException("Score = " + score);
+        }
         if (score == 0) {
             return;
         }
-        scores.add(score);
-        dataset.add(feature);
+        scoreAdd(size++, score);
+        if (addToDataset) dataset.add(feature);
         if (score > topScore) {
             topScore = score;
             topMatch = feature;
         }
     }
 
+    private void scoreAdd(int index, double score) {
+        if (this.scores.length < index + 1) {
+            this.scores = Arrays.copyOf(this.scores, index + 1);
+        }
+        this.scores[index] = score;
+    }
+
     private Feature topMatch;
-    private double topScore = 0;
+    private double topScore;
 
     public double getTopScore() {
         return topScore;
@@ -217,26 +256,26 @@ public Feature getTopMatch() {
      * @return the confidence of the ith match
      */
     public double getScore(int i) {
-        return scores.get(i);
+        return scores[i];
     }
 
     @Override
-	public FeatureSchema getFeatureSchema() {
+    public FeatureSchema getFeatureSchema() {
         return dataset.getFeatureSchema();
     }
 
     @Override
-	public Envelope getEnvelope() {
+    public Envelope getEnvelope() {
         return dataset.getEnvelope();
     }
 
     @Override
-	public int size() {
+    public int size() {
         return dataset.size();
     }
 
     @Override
-	public boolean isEmpty() {
+    public boolean isEmpty() {
         return dataset.isEmpty();
     }
 
@@ -245,17 +284,17 @@ public Feature getFeature(int index) {
     }
 
     @Override
-	public List<Feature> getFeatures() {
+    public List<Feature> getFeatures() {
         return dataset.getFeatures();
     }
 
     @Override
-	public Iterator<Feature> iterator() {
+    public Iterator<Feature> iterator() {
         return dataset.iterator();
     }
 
     @Override
-	public List<Feature> query(Envelope envelope) {
+    public List<Feature> query(Envelope envelope) {
         return dataset.query(envelope);
     }
 }
diff --git a/src/com/vividsolutions/jcs/conflate/polygonmatch/WindowMatcher.java b/src/com/vividsolutions/jcs/conflate/polygonmatch/WindowMatcher.java
index 1cd76cc..626919c 100644
--- a/src/com/vividsolutions/jcs/conflate/polygonmatch/WindowMatcher.java
+++ b/src/com/vividsolutions/jcs/conflate/polygonmatch/WindowMatcher.java
@@ -37,6 +37,7 @@
 import org.locationtech.jts.geom.Envelope;
 import com.vividsolutions.jump.feature.Feature;
 import com.vividsolutions.jump.feature.FeatureCollection;
+import com.vividsolutions.jump.feature.FeatureDataset;
 import com.vividsolutions.jump.geom.EnvelopeUtil;
 
 /**
@@ -79,6 +80,6 @@ public WindowMatcher() {}
   public Matches match(Feature target, FeatureCollection candidates) {
     Envelope window = new Envelope(target.getGeometry().getEnvelopeInternal());
     window = EnvelopeUtil.expand(window, buffer);
-    return new Matches(candidates.getFeatureSchema(), candidates.query(window));
+    return new Matches(new FeatureDataset(candidates.query(window), candidates.getFeatureSchema(), window));
   }
 }
diff --git a/src/com/vividsolutions/jump/feature/FeatureDataset.java b/src/com/vividsolutions/jump/feature/FeatureDataset.java
index cf99299..e0742bd 100644
--- a/src/com/vividsolutions/jump/feature/FeatureDataset.java
+++ b/src/com/vividsolutions/jump/feature/FeatureDataset.java
@@ -55,8 +55,31 @@ public class FeatureDataset implements FeatureCollection {
      * @param featureSchema the types of the attributes of the features in this collection
      */
     public FeatureDataset(Collection<Feature> newFeatures, FeatureSchema featureSchema) {
-        features = new ArrayList<>(newFeatures);
+        this(newFeatures, featureSchema, null);
+    }
+
+    /**
+     * Creates a FeatureDataset, initialized with a group of Features.
+     * @param newFeatures an initial group of features to add to this FeatureDataset
+     * @param featureSchema the types of the attributes of the features in this collection
+     * @param envelope The expected envelope for the features
+     */
+    public FeatureDataset(Collection<Feature> newFeatures, FeatureSchema featureSchema, Envelope envelope) {
+        this.features = new ArrayList<>(newFeatures);
+        this.featureSchema = featureSchema;
+        this.envelope = envelope != null ? envelope.copy() : null;
+    }
+
+    /**
+     * Creates a FeatureDataset, with an initial list size for features
+     * @param newFeatures The expected size of the features
+     * @param featureSchema the types of the attributes of the features in this collection
+     * @param envelope The expected envelope for this dataset
+     */
+    public FeatureDataset(int newFeatures, FeatureSchema featureSchema, Envelope envelope) {
+        this.features = new ArrayList<>(newFeatures);
         this.featureSchema = featureSchema;
+        this.envelope = envelope == null ? null : envelope.copy();
     }
 
     /**
@@ -64,7 +87,18 @@ public FeatureDataset(Collection<Feature> newFeatures, FeatureSchema featureSche
      * @param featureSchema the types of the attributes of the features in this collection
      */
     public FeatureDataset(FeatureSchema featureSchema) {
-        this(new ArrayList<Feature>(), featureSchema);
+        this(new ArrayList<>(), featureSchema);
+    }
+
+    /**
+     * Clone another dataset
+     * @param otherDataset The dataset to clone
+     */
+    public FeatureDataset(FeatureDataset otherDataset) {
+        this(otherDataset.getFeatures(), otherDataset.getFeatureSchema());
+        if (otherDataset.envelope != null) {
+            this.envelope = otherDataset.envelope.copy();
+        }
     }
 
     public Feature getFeature(int index) {
@@ -72,7 +106,7 @@ public Feature getFeature(int index) {
     }
 
     @Override
-	public FeatureSchema getFeatureSchema() {
+    public FeatureSchema getFeatureSchema() {
         return featureSchema;
     }
 
@@ -81,7 +115,7 @@ public FeatureSchema getFeatureSchema() {
      * later change a Feature's geometry using Feature#setGeometry.
      */
     @Override
-	public Envelope getEnvelope() {
+    public Envelope getEnvelope() {
         if (envelope == null) {
             envelope = new Envelope();
 
@@ -95,12 +129,12 @@ public Envelope getEnvelope() {
     }
 
     @Override
-	public List<Feature> getFeatures() {
+    public List<Feature> getFeatures() {
         return Collections.unmodifiableList(features);
     }
 
     @Override
-	public boolean isEmpty() {
+    public boolean isEmpty() {
         return size() == 0;
     }
 
@@ -112,7 +146,7 @@ public boolean isEmpty() {
     //<<TODO:DESIGN>> Perhaps return value should be a Set, not a List, because order
     //doesn't matter. [Jon Aquino]
     @Override
-	public List<Feature> query(Envelope envelope) {
+    public List<Feature> query(Envelope envelope) {
         if (!envelope.intersects(getEnvelope())) {
             return new ArrayList<>();
         }
@@ -131,7 +165,7 @@ public List<Feature> query(Envelope envelope) {
     }
 
     @Override
-	public void add(Feature feature) {
+    public void add(Feature feature) {
         features.add(feature);
         if (envelope != null) {
             envelope.expandToInclude(feature.getGeometry().getEnvelopeInternal());
@@ -152,7 +186,7 @@ public boolean contains(Feature feature) {
      * @param env
      */
     @Override
-	public Collection<Feature> remove(Envelope env) {
+    public Collection<Feature> remove(Envelope env) {
         Collection<Feature> features = query(env);
         removeAll(features);
 
@@ -160,7 +194,7 @@ public Collection<Feature> remove(Envelope env) {
     }
 
     @Override
-	public void remove(Feature feature) {
+    public void remove(Feature feature) {
         features.remove(feature);
         invalidateEnvelope();
     }
@@ -169,18 +203,18 @@ public void remove(Feature feature) {
      * Removes all features from this collection.
      */
     @Override
-	public void clear() {
+    public void clear() {
         invalidateEnvelope();
         features.clear();
     }
 
     @Override
-	public int size() {
+    public int size() {
         return features.size();
     }
 
     @Override
-	public Iterator<Feature> iterator() {
+    public Iterator<Feature> iterator() {
         return features.iterator();
     }
 
@@ -189,7 +223,7 @@ public void invalidateEnvelope() {
     }
 
     @Override
-	public void addAll(Collection<? extends Feature> features) {
+    public void addAll(Collection<? extends Feature> features) {
         this.features.addAll(features);
         if (envelope != null) {
             for (Feature feature : features) {
@@ -199,7 +233,7 @@ public void addAll(Collection<? extends Feature> features) {
     }
 
     @Override
-	public void removeAll(Collection<Feature> features) {
+    public void removeAll(Collection<Feature> features) {
         this.features.removeAll(features);
         invalidateEnvelope();
     }
diff --git a/src/org/openstreetmap/josm/plugins/conflation/command/ConflateMatchCommand.java b/src/org/openstreetmap/josm/plugins/conflation/command/ConflateMatchCommand.java
index 3fbf110..60a2d1a 100644
--- a/src/org/openstreetmap/josm/plugins/conflation/command/ConflateMatchCommand.java
+++ b/src/org/openstreetmap/josm/plugins/conflation/command/ConflateMatchCommand.java
@@ -38,6 +38,7 @@
 import org.openstreetmap.josm.plugins.utilsplugin2.replacegeometry.ReplaceGeometryException;
 import org.openstreetmap.josm.plugins.utilsplugin2.replacegeometry.ReplaceGeometryUtils;
 import org.openstreetmap.josm.tools.ImageProvider;
+import org.openstreetmap.josm.tools.Logging;
 import org.openstreetmap.josm.tools.UserCancelException;
 import org.openstreetmap.josm.tools.Utils;
 
@@ -195,7 +196,8 @@ public static Command buildReplaceGeometryCommand(OsmPrimitive subjectObject, Os
         TagMap savedSubjectTags = saveAndRemoveTagsNotInCollection(subjectObject, tagCollection);
         Command command = null;
         try {
-            command = ReplaceGeometryUtils.buildReplaceCommand(subjectObject, referenceObject);
+            command = ReplaceGeometryUtils.buildReplaceCommand(subjectObject, referenceObject,
+                    CombinePrimitiveResolverDialog.Strategy.KEEP_NON_CONFLICTING);
         } catch (ReplaceGeometryException ex) {
             AutoScaleAction.zoomTo(Arrays.asList(subjectObject, referenceObject));
             JOptionPane.showMessageDialog(MainApplication.getMainFrame(),
@@ -230,8 +232,10 @@ public static List<Command> buildTagMergingCommand(SimpleMatch match, SimpleMatc
             return CombinePrimitiveResolverDialog.launchIfNecessary(
                     match.getMergingTagCollection(settings),
                     Arrays.asList(match.getReferenceObject(), match.getSubjectObject()),
-                    Collections.singleton(match.getSubjectObject()));
+                    Collections.singleton(match.getSubjectObject()),
+                    CombinePrimitiveResolverDialog.Strategy.KEEP_NON_CONFLICTING);
         } catch (UserCancelException e) {
+            Logging.trace(e);
             return null;
         } finally {
             restoreRelationsData(savedRelationsData);