Test case to reproduce ITC issue

descent_2.ecore

 <?xml version="1.0" encoding="UTF-8"?>
<ecore:EPackage xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:ecore="http://www.eclipse.org/emf/2002/Ecore" name="descent" nsURI="http://descent/1.0" nsPrefix="descent">
  <eClassifiers xsi:type="ecore:EClass" name="TestClass"/>
  <eSubpackages name="jitd" nsURI="http://jitd.descent/1.0" nsPrefix="jitd">
    <eClassifiers xsi:type="ecore:EClass" name="Game">
      <eStructuralFeatures xsi:type="ecore:EReference" name="dungeon" lowerBound="1"
          eType="#//jitd/dungeon/Dungeon" containment="true" eOpposite="#//jitd/dungeon/Dungeon/game"/>
      <eStructuralFeatures xsi:type="ecore:EReference" name="gameDecks" lowerBound="1"
          eType="#//jitd/GameDecks" containment="true" eOpposite="#//jitd/GameDecks/game"/>
    </eClassifiers>
    <eClassifiers xsi:type="ecore:EClass" name="GameDecks">
      <eStructuralFeatures xsi:type="ecore:EReference" name="game" lowerBound="1"
          eType="#//jitd/Game" eOpposite="#//jitd/Game/gameDecks"/>
    </eClassifiers>
    <eSubpackages name="dungeon" nsURI="http://dungeon.jitd.descent/1.0" nsPrefix="dungeon">
      <eClassifiers xsi:type="ecore:EClass" name="Dungeon">
        <eStructuralFeatures xsi:type="ecore:EReference" name="game" lowerBound="1"
            eType="#//jitd/Game" eOpposite="#//jitd/Game/dungeon"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="rooms" lowerBound="1"
            upperBound="-1" eType="#//jitd/dungeon/Room" containment="true" eOpposite="#//jitd/dungeon/Room/dungeon"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="connections" upperBound="-1"
            eType="#//jitd/dungeon/RoomConnection" containment="true"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="entitiesOnBoard" upperBound="-1"
            eType="#//jitd/dungeon/OnBoardEntity" containment="true" eOpposite="#//jitd/dungeon/OnBoardEntity/dungeon"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="Room">
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="name" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EString"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="dungeon" lowerBound="1"
            eType="#//jitd/dungeon/Dungeon" eOpposite="#//jitd/dungeon/Dungeon/rooms"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="directedConnections"
            lowerBound="1" upperBound="-1" eType="#//jitd/dungeon/OrientationToConnectionPointMap"
            containment="true" eOpposite="#//jitd/dungeon/OrientationToConnectionPointMap/room"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="coordinateToTileMap"
            upperBound="-1" eType="#//jitd/dungeon/CoordinateToTileMap" containment="true"
            eOpposite="#//jitd/dungeon/CoordinateToTileMap/room"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="RoomCoordinate">
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="x" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EInt"
            defaultValueLiteral="-1"/>
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="y" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EInt"
            defaultValueLiteral="-1"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="Tile">
        <eStructuralFeatures xsi:type="ecore:EReference" name="entitiesOnTile" upperBound="-1"
            eType="#//jitd/dungeon/OnBoardEntity" eOpposite="#//jitd/dungeon/OnBoardEntity/location"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="tileMap" lowerBound="1"
            eType="#//jitd/dungeon/CoordinateToTileMap" eOpposite="#//jitd/dungeon/CoordinateToTileMap/tile"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="RoomConnectionPoint">
        <eStructuralFeatures xsi:type="ecore:EReference" name="connection" lowerBound="1"
            eType="#//jitd/dungeon/RoomConnection" eOpposite="#//jitd/dungeon/RoomConnection/connectedPoints"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="connectedTiles" lowerBound="2"
            upperBound="2" eType="#//jitd/dungeon/RoomCoordinate" containment="true"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="connectionPointMap"
            lowerBound="1" eType="#//jitd/dungeon/OrientationToConnectionPointMap"
            eOpposite="#//jitd/dungeon/OrientationToConnectionPointMap/connection"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="RoomConnection">
        <eStructuralFeatures xsi:type="ecore:EReference" name="connectedPoints" lowerBound="2"
            upperBound="2" eType="#//jitd/dungeon/RoomConnectionPoint" eOpposite="#//jitd/dungeon/RoomConnectionPoint/connection"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EEnum" name="Orientation">
        <eLiterals name="NORTH"/>
        <eLiterals name="NORTHEAST" value="1"/>
        <eLiterals name="EAST" value="2"/>
        <eLiterals name="SOUTHEAST" value="3"/>
        <eLiterals name="SOUTH" value="4"/>
        <eLiterals name="SOUTHWEST" value="5"/>
        <eLiterals name="WEST" value="6"/>
        <eLiterals name="NORTHWEST" value="7"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="CoordinateToTileMap">
        <eStructuralFeatures xsi:type="ecore:EReference" name="tile" lowerBound="1"
            eType="#//jitd/dungeon/Tile" containment="true" eOpposite="#//jitd/dungeon/Tile/tileMap"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="coordinate" lowerBound="1"
            eType="#//jitd/dungeon/RoomCoordinate" containment="true"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="room" lowerBound="1"
            eType="#//jitd/dungeon/Room" eOpposite="#//jitd/dungeon/Room/coordinateToTileMap"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="OrientationToConnectionPointMap">
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="key" eType="#//jitd/dungeon/Orientation"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="connection" lowerBound="1"
            eType="#//jitd/dungeon/RoomConnectionPoint" containment="true" eOpposite="#//jitd/dungeon/RoomConnectionPoint/connectionPointMap"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="room" lowerBound="1"
            eType="#//jitd/dungeon/Room" eOpposite="#//jitd/dungeon/Room/directedConnections"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="OnBoardEntity" abstract="true">
        <eStructuralFeatures xsi:type="ecore:EReference" name="location" lowerBound="1"
            eType="#//jitd/dungeon/Tile" eOpposite="#//jitd/dungeon/Tile/entitiesOnTile"/>
        <eStructuralFeatures xsi:type="ecore:EReference" name="dungeon" lowerBound="1"
            eType="#//jitd/dungeon/Dungeon" eOpposite="#//jitd/dungeon/Dungeon/entitiesOnBoard"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="Monster" eSuperTypes="#//jitd/dungeon/OnBoardEntity">
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="orientation" eType="#//jitd/dungeon/Orientation"
            defaultValueLiteral=""/>
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="master" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EBoolean"/>
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="woundsLost" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EInt"
            defaultValueLiteral="0"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="Glyph" eSuperTypes="#//jitd/dungeon/OnBoardEntity">
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="activated" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EBoolean"
            defaultValueLiteral="false"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="Rock" eSuperTypes="#//jitd/dungeon/OnBoardEntity"/>
      <eClassifiers xsi:type="ecore:EClass" name="Pit" eSuperTypes="#//jitd/dungeon/OnBoardEntity"/>
      <eClassifiers xsi:type="ecore:EClass" name="EventMarker" eSuperTypes="#//jitd/dungeon/OnBoardEntity"/>
      <eClassifiers xsi:type="ecore:EClass" name="Water" eSuperTypes="#//jitd/dungeon/OnBoardEntity"/>
      <eClassifiers xsi:type="ecore:EClass" name="Hero" eSuperTypes="#//jitd/dungeon/OnBoardEntity">
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="currentWounds" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EInt"/>
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="currentFatigue" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EInt"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EClass" name="TreasureChest" eSuperTypes="#//jitd/dungeon/OnBoardEntity">
        <eStructuralFeatures xsi:type="ecore:EAttribute" name="treasureType" eType="#//jitd/dungeon/TreasureType"/>
      </eClassifiers>
      <eClassifiers xsi:type="ecore:EEnum" name="TreasureType">
        <eLiterals name="BRONZE" literal="BRONZE"/>
        <eLiterals name="SILVER" value="1" literal="SILVER"/>
        <eLiterals name="GOLD" value="2" literal="GOLD"/>
      </eClassifiers>
    </eSubpackages>
  </eSubpackages>
</ecore:EPackage>

StrangeDeletionTest.xtend

import org.eclipse.viatra2.patternlanguage.eMFPatternLanguage.PatternModel
import org.eclipse.viatra2.patternlanguage.core.patternLanguage.PatternLanguageFactory
import org.eclipse.viatra2.patternlanguage.eMFPatternLanguage.EMFPatternLanguageFactory
import org.eclipse.emf.ecore.EcorePackage
import org.junit.Test
import org.junit.runner.RunWith
import org.eclipse.xtext.junit4.XtextRunner
import org.eclipse.xtext.junit4.InjectWith
import org.eclipse.viatra2.emf.incquery.testing.core.injector.EMFPatternLanguageInjectorProvider
import org.eclipse.emf.common.util.URI
import org.eclipse.viatra2.emf.incquery.runtime.util.XmiModelUtil
import org.eclipse.viatra2.emf.incquery.triggerengine.util.PatternToMatchMultimap
import org.eclipse.viatra2.emf.incquery.runtime.extensibility.MatcherFactoryRegistry
import org.eclipse.viatra2.emf.incquery.base.api.IQueryResultUpdateListener
import org.eclipse.viatra2.emf.incquery.runtime.api.IPatternMatch
import org.eclipse.viatra2.emf.incquery.runtime.api.IncQueryMatcher
import org.eclipse.viatra2.emf.incquery.runtime.api.IMatcherFactory
import org.eclipse.emf.ecore.resource.impl.ResourceSetImpl
import javax.inject.Inject
import org.apache.log4j.Logger
import java.util.logging.Logging
import org.eclipse.viatra2.emf.incquery.runtime.api.IncQueryEngine
import org.eclipse.emf.ecore.EPackage
import org.eclipse.emf.ecore.util.EcoreUtil
import org.eclipse.viatra2.emf.incquery.base.api.NavigationHelper
import org.eclipse.viatra2.emf.incquery.base.api.IncQueryBaseFactory
import org.eclipse.emf.ecore.EClass
import org.eclipse.emf.ecore.EcoreFactory
import java.util.Collection

@RunWith(typeof(XtextRunner))
@InjectWith(typeof(EMFPatternLanguageInjectorProvider))
class PatternBuilderTest {
  
  @Inject Logger logger
  
  @Test
  def callbackTest(){
    val resourceset = XmiModelUtil::prepareXtextResource
    val pr = resourceset.createResource(URI::createFileURI("D:/temp/test/test.eiq"))   
    
    pr.load(null)
    val pm = pr.contents.get(0) as PatternModel
    
    val rs = new ResourceSetImpl
    val mr = rs.createResource(URI::createFileURI("D:/temp/test/descent_2.ecore"))
    mr.load(null)
    
    val matchers = newArrayList()
    val callback = new TestCallback
    
    val CALLBACK = true
    
    pm.patterns.forEach[
      val factory = MatcherFactoryRegistry::getOrCreateMatcherFactory(it) as IMatcherFactory<IncQueryMatcher<IPatternMatch>>
      val matcher = factory.getMatcher(rs)
      matcher.addCallbackAfterUpdates(callback)
      matchers.add(matcher);
    ]
    
    val start = System::nanoTime
    
    val end = System::nanoTime - start
      logger.warn("[Callback] Total time on resource load: " + end + ", Count: " + callback.count)

    val navHelper = IncQueryBaseFactory::instance.createNavigationHelper(rs, false, logger);
    navHelper.registerEClasses(newHashSet(EcorePackage::eINSTANCE.EClass))
    val eclasses = navHelper.getAllInstances(EcorePackage::eINSTANCE.EClass)
    val start2 = System::nanoTime
    
    eclasses.forEach[
      val ec = it as EClass
      if(ec.EPackage != EcorePackage::eINSTANCE){
        ec.EPackage.EClassifiers.remove(it)
      }
    ]      
    val end2 = System::nanoTime - start2
      logger.warn("[Callback] Total time on model modification: " + end2 + ", Count: " + callback.count)
  
  }
}

class TestCallback implements Runnable{
  
  int count = 0
  
  override run() {
    count = count + 1
  }
  
  def getCount(){
    return count;
  }
  
}

test.eiq

import "http://www.eclipse.org/emf/2002/Ecore"

pattern reference(Source: EClass, reference: EReference, Target: EClass){
  find eAllReferences(PH_Source,reference);
  ETypedElement.eType(reference,PH_Target);
  neg find isAggregation(reference);
  find thisAndAllSuperTypes(Source, PH_Source);
  find thisAndAllSuperTypes(Target, PH_Target);
  neg find isEcore(Source);
}

pattern canTransitivelyContain(Source : EClass, Target : EClass) {
  find canContain+(Source, Target);
}

pattern canContain(Source: EClass, Target : EClass) {
  find eAllContainments(Source,reference);
  neg find isEcore(Source);
  EReference.eType(reference, Target);
}

@QueryExplorer(display = false)
pattern isEcore(Element){
  EClassifier.ePackage(Element,EP);
  EPackage(EP);
  EPackage.nsURI(EP,"http://www.eclipse.org/emf/2002/Ecore");
}

@QueryExplorer(display = false)
pattern isAggregation(ref:EReference){
  EReference.containment(ref,true);
}

// well-behaving ecore patterns

@QueryExplorer(display = false)
private pattern eStructuralFeatures(This : EClass, Target : EStructuralFeature){
  EClass.eStructuralFeatures(This, Target);
}

@QueryExplorer(display = false)
private pattern eGenericSuperTypes(This : EClass, Target : EGenericType){
  EClass.eGenericSuperTypes(This, Target);
}

@QueryExplorer(display = false)
pattern eAllGenericSuperTypes(This : EClass, Target : EGenericType){
  find eSuperTypes+(This, Type);
  find eGenericSuperTypes(Type, Target);
} or {
  find eGenericSuperTypes(This, Target);
}

@QueryExplorer(display = false)
private pattern eRawType(This : EGenericType, Target : EClass){
  EGenericType.eRawType(This, Target);
}

@QueryExplorer(display = false)
pattern eSuperTypes(This : EClass, Target : EClass){
  find eGenericSuperTypes(This, GenericType);
  find eRawType(GenericType, Target);
}

@QueryExplorer(display = false)
pattern eAllSuperTypes(This : EClass, Target : EClass){
  find eAllGenericSuperTypes(This, GenericType);
  find eRawType(GenericType, Target);
}

@QueryExplorer(display = false)
private pattern thisAndAllSuperTypes(This : EClass, Target : EClass){
  find eAllSuperTypes(This, Target);
} or {
  This == Target;
}

@QueryExplorer(display = false)
pattern eAllStructuralFeatures(This : EClass, Target : EStructuralFeature){
  find thisAndAllSuperTypes(This, Type);
  find eStructuralFeatures(Type, Target);
}

@QueryExplorer(display = false)
pattern eAllReferences(This : EClass, Target : EReference){
  find eAllStructuralFeatures(This, Target);
}

@QueryExplorer(display = false)
pattern eAllContainments(This : EClass, Target : EReference){
  find eAllReferences(This, Target);
  EReference.containment(Target, true);
}

TransitiveClosureNode

TC init[141]: T(ECI@6f8f7fe2 (name: Dungeon) foobar;ECI@3e48983b (name: RoomConnection) foobar;)
TC init[141]: T(ECI@6f8f7fe2 (name: Dungeon) foobar;ECI@5b56becd (name: Room) foobar;)
TC init[141]: T(ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;ECI@2998a407 (name: RoomConnectionPoint) foobar;)
TC init[141]: T(ECI@1997ce1a (name: CoordinateToTileMap) foobar;ECI@701e8c16 (name: Tile) foobar;)
TC init[141]: T(ECI@5b56becd (name: Room) foobar;ECI@1997ce1a (name: CoordinateToTileMap) foobar;)
TC init[141]: T(ECI@33d650f6 (name: Game) foobar;ECI@7968f44a (name: GameDecks) foobar;)
TC init[141]: T(ECI@6f8f7fe2 (name: Dungeon) foobar;ECI@330d8014 (name: OnBoardEntity) (instanceClassName: null) (abstract: true, interface: false);)
TC init[141]: T(ECI@5b56becd (name: Room) foobar;ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;)
TC init[141]: T(ECI@33d650f6 (name: Game) foobar;ECI@6f8f7fe2 (name: Dungeon) foobar;)
TC init[141]: T(ECI@1997ce1a (name: CoordinateToTileMap) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC init[141]: T(ECI@2998a407 (name: RoomConnectionPoint) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)

TC IN[141]: REVOKE !!! T(ECI@1997ce1a (name: CoordinateToTileMap) foobar;ECI@701e8c16 (name: Tile) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@1997ce1a (name: CoordinateToTileMap) foobar;ECI@701e8c16 (name: Tile) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@5b56becd (name: Room) foobar;ECI@701e8c16 (name: Tile) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@6f8f7fe2 (name: Dungeon) foobar;ECI@701e8c16 (name: Tile) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@33d650f6 (name: Game) foobar;ECI@701e8c16 (name: Tile) foobar;)
TC IN[141]: REVOKE !!! T(ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;ECI@2998a407 (name: RoomConnectionPoint) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;ECI@2998a407 (name: RoomConnectionPoint) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@5b56becd (name: Room) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@5b56becd (name: Room) foobar;ECI@2998a407 (name: RoomConnectionPoint) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@6f8f7fe2 (name: Dungeon) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@6f8f7fe2 (name: Dungeon) foobar;ECI@2998a407 (name: RoomConnectionPoint) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@33d650f6 (name: Game) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@33d650f6 (name: Game) foobar;ECI@2998a407 (name: RoomConnectionPoint) foobar;)
TC IN[141]: REVOKE !!! T(ECI@5b56becd (name: Room) foobar;ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@5b56becd (name: Room) foobar;ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@6f8f7fe2 (name: Dungeon) foobar;ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@33d650f6 (name: Game) foobar;ECI@b3a0261 (name: OrientationToConnectionPointMap) foobar;)
TC IN[141]: REVOKE !!! T(ECI@2998a407 (name: RoomConnectionPoint) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@2998a407 (name: RoomConnectionPoint) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC IN[141]: REVOKE !!! T(ECI@1997ce1a (name: CoordinateToTileMap) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@1997ce1a (name: CoordinateToTileMap) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@5b56becd (name: Room) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@6f8f7fe2 (name: Dungeon) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)
TC OUT[141]: REVOKE !!! T(ECI@33d650f6 (name: Game) foobar;ECI@69b4b9d2 (name: RoomCoordinate) foobar;)