Bukkit

@NathanWolf

Hm, I am currently not sure what could cause this..
I am calling:

if (!itemMeta1.getItemFlags().equals(itemMeta2.getItemFlags())) {
    return "differing item hide flags";
}

This method was added in spigot's craftbukkit recently. If you are running 1_8_R2, as your log says, then this method should be available there..
I just tested this code on my test server and it run fine (though I am 14 versions behind currently).
You could try if you can reliable trigger this error on your server if you setup a trade which involve items with metadata and then attempt to trade a matching item (so it has to execute all item meta comparison code first).

Maybe also try with a different spigot/craftbukkit build, in case something was messed up in your build for some reason.

@res83

If you are using citizens you can create npc shopkeepers and you can change their skin and the item hold in hand via citizens commands.
The shopkeeper plugin doesn't have this functionality.

@Goldtank

What? This is a craftbukkit plugin. You can run it everywhere where craftbukkit is running.

v1.50 for MC 1.6.2, 1.7.x, 1.8.x

• Added support for craftbukkit/spigot 1.8.3.
• Experimental: Unlocked a bunch of remaining living entity types for use as shopkeeper objects: bat, blaze, cave_spider, spider, ender_dragon, wither, enderman, ghast, giant, horse, magma_cube, slime, pig_zombie, silverfish, squid (no MC 1.8 entities yet) Those are highly experimental! They are disabled by default in the configuration: you might need to remove the 'disabled-living-shops' section in your config in order to let it regenerate with the new default values.
  Some of those entities (currently: bat, ender_dragon, wither, enderman, silverfish) get the new NoAI entity tag set in order to prevent the biggest issues with them: As this new tag is only available on MC 1.8 you should only enabled those if you are running on MC 1.8.x.

Currently known issues with those new entity types (there might be more issues.. usage on own risk):

• chicken: Still lays eggs.
• bat: Without the NoAI tag it flies around. If NoAI tag is available (MC 1.8) the bat is sleeping, but starts the flying animation if being hit by something.
• blaze: Without the NoAI tag it randolyl starts flying upwards.
• enderdragon: Without NoAI tag, it flies around, towards players, and pushes entities around. Shows boss bar.
• wither: Without NoAI tag, it makes noise. Shows boss bar.
• enderman: Teleports away / goes invisible when being hit by a projectile. Starts starring animation.
• silverfish: Without NoAI tag it is rotating wierdly depending on where the player is standing (possibly because it tries to rotate towards the player). Is constantly showing the movement animation.

@AetharanLevesque

Well, that's not possible right now and I currently have no plans adding something like that..

@AetharanLevesque

There is no mechanism built-in with which you can grant certain players access to the shopkeeper.
You could given everyone the shopkeeper.bypass permission node. This however would give them a bunch of other bypasses as well: they could modify the shopkeeper, remove it, set it for hire, transfer it, and they could bypass the 'prevent-shop-creation-item-regular-usage' setting from the config.

Not sure what sense the shopkeepers would have on your server when everyone has access to the chest anyways..

@Jikoo_K

v1.49 for MC 1.6.2, 1.7.x, 1.8.x

• Tiny internal change: The shopkeepers are kept ordered in the internal storage. This might fix potential issues of the newly added list command, which requires that the internal storage order does not change while the player is selecting another page for displaying.
• Fixed/Added: Entity shopkeepers are now unaffected by splash potion effects.

v1.48 for MC 1.6.2, 1.7.x, 1.8.x

• Changed: Being less strict with the argument count of commands now: If the first argument matches an exisitng command, we handle this command, even if the argument count doesn't match the required amount of arguments. Previously it attempted to spawn a shopkeeper via command in some situations, if it didn't find a command that exactly matched.
• Changed: Ignoring the player's naming chat event, if the affected shopkeeper is no longer existing.
• Changed (API): Deprecated getting all shopkeepers by chunks.
• Changed (API): All API methods now return unmodifiable collections.
• Changed (API): The permission nodes were moved into ShopkeepersAPI.

• Added command: /shopkeeper list [player|admin] [page] - Lists the players own shops (if no player/'admin' is specified), the shops of a specified player or all admin shops. The shops are divided into pages.
• Added permissions node: shopkeeper.list.own (default: true) - Allows listing the own shops via command.
• Added permissions node: shopkeeper.list.others (default: op) - Allows listing the shops of other players via command.
• Added permissions node: shopkeeper.list.admin (default: op) - Allows listing all admin shops via command.

• Added command: /shopkeeper remove [player|all|admin] - Removes the players own shops (if no player/'admin' is specified), the shops of a specified player, all player shops, or all admin shops. The command needs to be confirmed by the player via '/shopkeeper confirm'
• Added permissions node: shopkeeper.remove.own (default: op) - Allows removing the own shops via command.
• Added permissions node: shopkeeper.remove.others (default: op) - Allows removing the shops of other players via command.
• Added permissions node: shopkeeper.remove.all (default: op) - Allows removing the shops of all players at once via command.
• Added permissions node: shopkeeper.remove.admin (default: op) - Allows removing all admin shops via command.

Create a backup of your save.yml file and make sure that the permissions are setup correctly and actually work correctly before using, because the newly added remove commands are potentially dangerous.