/clear turns items held by mouse into ghost items

The bug

Using /clear while an inventory is open and you are holding an item with your mouse causes an inventory desync and turns this item into a "ghost" item. You can place it in your inventory, but using it will fail in Creative mode and in Adventure and Survival mode additionally removes the item.

Expected would be that /clear successfully clears the held item client-side as well.

How to reproduce

1. Put a repeating command block down with

   /clear @p torch
   

2. Switch to Creative mode

   /gamemode creative
   

3. Grab a stack of torches for example from your Creative inventory and put it in your hotbar
4. Try placing down torches
   → The torches are not placed

Code analysis (outdated for 1.13+)

The following is based on a decompiled version of Minecraft 1.8 using MCP. All method and class names are the ones used in the decompiled version.

The reason for this is a piece of code in the public void processCommand(ICommandSender sender, String[] args) method of the net.minecraft.command.CommandClearInventory class that only updates the held item once the /clear command was used, if the player is not in Creative mode:

public void processCommand(ICommandSender sender, String[] args) throws CommandException
{
	EntityPlayerMP var3 = args.length == 0 ? getCommandSenderAsPlayer(sender) : getPlayer(sender, args[0]);
	
	// ...
	
	if (args.length >= 2 && var4 == null)
	{
		throw new CommandException("commands.clear.failure", new Object[] {var3.getName()});
	}
	else
	{
		int var8 = var3.inventory.func_174925_a(var4, var5, var6, var7);
		var3.inventoryContainer.detectAndSendChanges();

		//This prevents the update
		if (!var3.capabilities.isCreativeMode)
		{
			var3.updateHeldItem();
		}

		//...
	}
}