Program: 134003
Project: 134003
Buggy source:
public void progress(){
  progressCounter++;
  if (player.isDead() || !player.isOnline()) {
    remove();
    return;
  }
  if (type != AbilityType.RELEASE) {
    if (!GeneralMethods.canBend(player.getName(),"String_Node_Str") || !player.hasPermission("String_Node_Str")) {
      remove();
      return;
    }
    String ability=GeneralMethods.getBoundAbility(player);
    if (ability == null || !ability.equalsIgnoreCase("String_Node_Str")) {
      remove();
      return;
    }
  }
  if (type == AbilityType.CLICK) {
    if (origin == null) {
      removeType(player,AbilityType.CLICK);
      Block block=BlockSource.getWaterSourceBlock(player,range,ClickType.LEFT_CLICK,true,true,WaterMethods.canPlantbend(player));
      if (block == null) {
        if (instances.contains(this)) {
          remove();
        }
        return;
      }
      instances.add(this);
      Block blockAbove=block.getRelative(BlockFace.UP);
      if (blockAbove.getType() != Material.AIR && !WaterMethods.isWaterbendable(blockAbove,player)) {
        remove();
        return;
      }
      origin=block.getLocation();
      if (!WaterMethods.isWaterbendable(block,player) || GeneralMethods.isRegionProtectedFromBuild(player,"String_Node_Str",origin)) {
        remove();
        return;
      }
      if (ICE_ONLY && !(block.getType() == Material.ICE || block.getType() == Material.SNOW || block.getType() == Material.PACKED_ICE)) {
        remove();
        return;
      }
    }
    if (player.getLocation().distance(origin) > range) {
      remove();
      return;
    }
 else     if (player.isSneaking()) {
      new WaterWave(player,AbilityType.SHIFT);
      return;
    }
    WaterMethods.playFocusWaterEffect(origin.getBlock());
  }
 else   if (type == AbilityType.SHIFT) {
    if (direction == null) {
      direction=player.getEyeLocation().getDirection();
    }
    if (!charging) {
      if (!containsType(player,AbilityType.SHIFT)) {
        removeType(player,AbilityType.CLICK);
        remove();
        return;
      }
      charging=true;
      anim=AnimateState.RISE;
      if (!getType(player,AbilityType.CLICK).isEmpty()) {
        WaterWave clickSpear=getType(player,AbilityType.CLICK).get(0);
        origin=clickSpear.origin.clone();
        currentLoc=origin.clone();
        if (WaterMethods.isPlant(origin.getBlock()))         new Plantbending(origin.getBlock());
      }
    }
    removeType(player,AbilityType.CLICK);
    if (!player.isSneaking()) {
      if (System.currentTimeMillis() - time > chargeTime) {
        WaterWave wwave=new WaterWave(player,AbilityType.RELEASE);
        wwave.anim=AnimateState.SHRINK;
        wwave.direction=direction;
      }
      remove();
      return;
    }
    double animSpeed=1.2;
    if (anim == AnimateState.RISE && currentLoc != null) {
      revertBlocks();
      currentLoc.add(0,animSpeed,0);
      Block block=currentLoc.getBlock();
      if (!(WaterMethods.isWaterbendable(block,player) || block.getType() == Material.AIR) || GeneralMethods.isRegionProtectedFromBuild(player,"String_Node_Str",block.getLocation())) {
        remove();
        return;
      }
      createBlock(block,Material.STATIONARY_WATER);
      if (currentLoc.distance(origin) > 2)       anim=AnimateState.TOWARDPLAYER;
    }
 else     if (anim == AnimateState.TOWARDPLAYER) {
      revertBlocks();
      Location eyeLoc=player.getTargetBlock((HashSet<Material>)null,2).getLocation();
      eyeLoc.setY(player.getEyeLocation().getY());
      Vector vec=GeneralMethods.getDirection(currentLoc,eyeLoc);
      currentLoc.add(vec.normalize().multiply(animSpeed));
      Block block=currentLoc.getBlock();
      if (!(WaterMethods.isWaterbendable(block,player) || block.getType() == Material.AIR) || GeneralMethods.isRegionProtectedFromBuild(player,"String_Node_Str",block.getLocation())) {
        remove();
        return;
      }
      createBlock(block,Material.STATIONARY_WATER);
      if (currentLoc.distance(eyeLoc) < 1.3) {
        anim=AnimateState.CIRCLE;
        Vector tempDir=player.getLocation().getDirection();
        tempDir.setY(0);
        direction=tempDir.normalize();
        revertBlocks();
      }
    }
 else     if (anim == AnimateState.CIRCLE) {
      drawCircle(120,5);
    }
  }
 else   if (type == AbilityType.RELEASE) {
    if (anim == AnimateState.SHRINK) {
      radius-=0.20;
      drawCircle(360,15);
      if (radius < 1) {
        revertBlocks();
        time=System.currentTimeMillis();
        anim=null;
      }
    }
 else {
      if ((System.currentTimeMillis() - time > flightTime && !AvatarState.isAvatarState(player)) || player.isSneaking()) {
        remove();
        return;
      }
      player.setFallDistance(0f);
      double currentSpeed=speed - (speed * (double)(System.currentTimeMillis() - time) / (double)flightTime);
      double nightSpeed=WaterMethods.waterbendingNightAugment(currentSpeed * 0.9,player.getWorld());
      currentSpeed=nightSpeed > currentSpeed ? nightSpeed : currentSpeed;
      if (AvatarState.isAvatarState(player))       currentSpeed=WaterMethods.waterbendingNightAugment(speed,player.getWorld());
      player.setVelocity(player.getEyeLocation().getDirection().normalize().multiply(currentSpeed));
      for (      Block block : GeneralMethods.getBlocksAroundPoint(player.getLocation().add(0,-1,0),waveRadius))       if (block.getType() == Material.AIR && !GeneralMethods.isRegionProtectedFromBuild(player,"String_Node_Str",block.getLocation())) {
        if (iceWave)         createBlockDelay(block,Material.ICE,(byte)0,2L);
 else         createBlock(block,Material.STATIONARY_WATER,(byte)0);
      }
      revertBlocksDelay(20L);
      if (iceWave && progressCounter % 3 == 0) {
        for (        Entity entity : GeneralMethods.getEntitiesAroundPoint(player.getLocation().add(0,-1,0),waveRadius * 1.5)) {
          if (entity != this.player && entity instanceof LivingEntity && !affectedEntities.contains(entity)) {
            affectedEntities.add(entity);
            final double aug=WaterMethods.getWaterbendingNightAugment(player.getWorld());
            GeneralMethods.damageEntity(player,entity,aug * damage,Element.Water,"String_Node_Str");
            final Player fplayer=this.player;
            final Entity fent=entity;
            new BukkitRunnable(){
              public void run(){
                createIceSphere(fplayer,fent,aug * 2.5);
              }
            }
.runTaskLater(ProjectKorra.plugin,6);
          }
        }
      }
    }
  }
}

Fixed version (ground truth):
public void progress(){
  progressCounter++;
  if (player.isDead() || !player.isOnline() || !origin.getWorld().equals(player.getWorld())) {
    remove();
    return;
  }
  if (type != AbilityType.RELEASE) {
    if (!GeneralMethods.canBend(player.getName(),"String_Node_Str") || !player.hasPermission("String_Node_Str")) {
      remove();
      return;
    }
    String ability=GeneralMethods.getBoundAbility(player);
    if (ability == null || !ability.equalsIgnoreCase("String_Node_Str")) {
      remove();
      return;
    }
  }
  if (type == AbilityType.CLICK) {
    if (origin == null) {
      removeType(player,AbilityType.CLICK);
      Block block=BlockSource.getWaterSourceBlock(player,range,ClickType.LEFT_CLICK,true,true,WaterMethods.canPlantbend(player));
      if (block == null) {
        if (instances.contains(this)) {
          remove();
        }
        return;
      }
      instances.add(this);
      Block blockAbove=block.getRelative(BlockFace.UP);
      if (blockAbove.getType() != Material.AIR && !WaterMethods.isWaterbendable(blockAbove,player)) {
        remove();
        return;
      }
      origin=block.getLocation();
      if (!WaterMethods.isWaterbendable(block,player) || GeneralMethods.isRegionProtectedFromBuild(player,"String_Node_Str",origin)) {
        remove();
        return;
      }
      if (ICE_ONLY && !(block.getType() == Material.ICE || block.getType() == Material.SNOW || block.getType() == Material.PACKED_ICE)) {
        remove();
        return;
      }
    }
    if (player.getLocation().distance(origin) > range) {
      remove();
      return;
    }
 else     if (player.isSneaking()) {
      new WaterWave(player,AbilityType.SHIFT);
      return;
    }
    WaterMethods.playFocusWaterEffect(origin.getBlock());
  }
 else   if (type == AbilityType.SHIFT) {
    if (direction == null) {
      direction=player.getEyeLocation().getDirection();
    }
    if (!charging) {
      if (!containsType(player,AbilityType.SHIFT)) {
        removeType(player,AbilityType.CLICK);
        remove();
        return;
      }
      charging=true;
      anim=AnimateState.RISE;
      if (!getType(player,AbilityType.CLICK).isEmpty()) {
        WaterWave clickSpear=getType(player,AbilityType.CLICK).get(0);
        origin=clickSpear.origin.clone();
        currentLoc=origin.clone();
        if (WaterMethods.isPlant(origin.getBlock()))         new Plantbending(origin.getBlock());
      }
    }
    removeType(player,AbilityType.CLICK);
    if (!player.isSneaking()) {
      if (System.currentTimeMillis() - time > chargeTime) {
        WaterWave wwave=new WaterWave(player,AbilityType.RELEASE);
        wwave.anim=AnimateState.SHRINK;
        wwave.direction=direction;
      }
      remove();
      return;
    }
    double animSpeed=1.2;
    if (anim == AnimateState.RISE && currentLoc != null) {
      revertBlocks();
      currentLoc.add(0,animSpeed,0);
      Block block=currentLoc.getBlock();
      if (!(WaterMethods.isWaterbendable(block,player) || block.getType() == Material.AIR) || GeneralMethods.isRegionProtectedFromBuild(player,"String_Node_Str",block.getLocation())) {
        remove();
        return;
      }
      createBlock(block,Material.STATIONARY_WATER);
      if (currentLoc.distance(origin) > 2)       anim=AnimateState.TOWARDPLAYER;
    }
 else     if (anim == AnimateState.TOWARDPLAYER) {
      revertBlocks();
      Location eyeLoc=player.getTargetBlock((HashSet<Material>)null,2).getLocation();
      eyeLoc.setY(player.getEyeLocation().getY());
      Vector vec=GeneralMethods.getDirection(currentLoc,eyeLoc);
      currentLoc.add(vec.normalize().multiply(animSpeed));
      Block block=currentLoc.getBlock();
      if (!(WaterMethods.isWaterbendable(block,player) || block.getType() == Material.AIR) || GeneralMethods.isRegionProtectedFromBuild(player,"String_Node_Str",block.getLocation())) {
        remove();
        return;
      }
      createBlock(block,Material.STATIONARY_WATER);
      if (currentLoc.distance(eyeLoc) < 1.3) {
        anim=AnimateState.CIRCLE;
        Vector tempDir=player.getLocation().getDirection();
        tempDir.setY(0);
        direction=tempDir.normalize();
        revertBlocks();
      }
    }
 else     if (anim == AnimateState.CIRCLE) {
      drawCircle(120,5);
    }
  }
 else   if (type == AbilityType.RELEASE) {
    if (anim == AnimateState.SHRINK) {
      radius-=0.20;
      drawCircle(360,15);
      if (radius < 1) {
        revertBlocks();
        time=System.currentTimeMillis();
        anim=null;
      }
    }
 else {
      if ((System.currentTimeMillis() - time > flightTime && !AvatarState.isAvatarState(player)) || player.isSneaking()) {
        remove();
        return;
      }
      player.setFallDistance(0f);
      double currentSpeed=speed - (speed * (double)(System.currentTimeMillis() - time) / (double)flightTime);
      double nightSpeed=WaterMethods.waterbendingNightAugment(currentSpeed * 0.9,player.getWorld());
      currentSpeed=nightSpeed > currentSpeed ? nightSpeed : currentSpeed;
      if (AvatarState.isAvatarState(player))       currentSpeed=WaterMethods.waterbendingNightAugment(speed,player.getWorld());
      player.setVelocity(player.getEyeLocation().getDirection().normalize().multiply(currentSpeed));
      for (      Block block : GeneralMethods.getBlocksAroundPoint(player.getLocation().add(0,-1,0),waveRadius))       if (block.getType() == Material.AIR && !GeneralMethods.isRegionProtectedFromBuild(player,"String_Node_Str",block.getLocation())) {
        if (iceWave)         createBlockDelay(block,Material.ICE,(byte)0,2L);
 else         createBlock(block,Material.STATIONARY_WATER,(byte)0);
      }
      revertBlocksDelay(20L);
      if (iceWave && progressCounter % 3 == 0) {
        for (        Entity entity : GeneralMethods.getEntitiesAroundPoint(player.getLocation().add(0,-1,0),waveRadius * 1.5)) {
          if (entity != this.player && entity instanceof LivingEntity && !affectedEntities.contains(entity)) {
            affectedEntities.add(entity);
            final double aug=WaterMethods.getWaterbendingNightAugment(player.getWorld());
            GeneralMethods.damageEntity(player,entity,aug * damage,Element.Water,"String_Node_Str");
            final Player fplayer=this.player;
            final Entity fent=entity;
            new BukkitRunnable(){
              public void run(){
                createIceSphere(fplayer,fent,aug * 2.5);
              }
            }
.runTaskLater(ProjectKorra.plugin,6);
          }
        }
      }
    }
  }
}