Server upgrade from 1.8.x to 15w31b results in "duplicate UUID" error.

This issue is similar to MC-82945 though it isn't about a multiplayer existing server upgrade.

The server runs fine in 1.8.1 or 1.8.8 (the only versions tested). When the server is shut down and .jar replaced with the snapshot I am greeted with the following in my console:

server console log

$ java -Xmx1024M -Xms1024M -jar minecraft_server.jar 
[00:18:16] [Server thread/INFO]: Starting minecraft server version 15w31b
[00:18:16] [Server thread/INFO]: Loading properties
[00:18:16] [Server thread/INFO]: Default game type: SURVIVAL
[00:18:16] [Server thread/INFO]: Generating keypair
[00:18:17] [Server thread/INFO]: Starting Minecraft server on *:25565
[00:18:17] [Server thread/INFO]: Using default channel type
[00:18:17] [Server thread/INFO]: Preparing level "world"
[00:18:17] [Server thread/INFO]: Preparing start region for level 0
[00:18:19] [Server thread/INFO]: Preparing spawn area: 0%
[00:18:20] [Server thread/INFO]: Preparing spawn area: 12%
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 794facd5-8bcd-47df-9530-9c68ae63fb5b
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID ec546c6e-c0ba-4d4f-a5a2-9171541711c7
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 742fc0f3-3f52-4322-9291-60b150310faf
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 71a19447-7f8e-4026-8eba-173b556da0e7
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID a3b8e2eb-7af9-4291-90ce-a066495f4602
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 24aca33e-545f-4129-a06c-93c571071ba7
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID ec546c6e-c0ba-4d4f-a5a2-9171541711c7
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID ad0c32ab-b563-4a44-a600-567b0f9554a0
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 0dfe9dcb-e1e3-4234-8860-44ced737fd51
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 558251e4-6442-4add-815a-0e0b439aa1ac
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 3b1f1853-cd0b-4d83-b34f-2949ebe2e701
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID c95dfd66-09af-49cb-b495-e5a276eac571
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 22dca54a-80e9-4519-ad4a-edfcb361cf43
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID f771d6f9-1544-4534-b973-d10f04474c60
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID dab90c3b-e5e0-4c96-a768-2fd09116e9f4
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 8e4eb971-64c5-4977-bd0e-c0bf868b98c3
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID bcb3a04b-41d7-4829-96c2-a16036be355c
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 4f13f0d8-5fb9-4ad8-9bc7-dfd067f94340
[00:18:21] [Server thread/WARN]: Tried to add entity with duplicate UUID 666e9c94-0dc0-4eae-8324-4e0e48a83353
[00:18:22] [Server thread/INFO]: Preparing spawn area: 57%
[00:18:23] [Server thread/INFO]: Preparing spawn area: 85%
[00:18:23] [Server thread/INFO]: Done (6.103s)! For help, type "help" or "?"
[00:18:23] [Server thread/INFO]: Starting GS4 status listener
[00:18:23] [Query Listener #1/INFO]: Query running on 0.0.0.0:25565
[00:19:15] [Server thread/WARN]: Tried to add entity with duplicate UUID 58a6a389-390f-45fe-a223-e9f1e030662d
[00:19:15] [Server thread/WARN]: Tried to add entity with duplicate UUID e341134b-e7ce-4aa1-90e1-6efa96d8650b
[00:19:15] [Server thread/WARN]: Tried to add entity with duplicate UUID 14cd33d0-cd34-4d6a-ac27-3b697a709be7
[00:19:15] [Server thread/WARN]: Tried to add entity with duplicate UUID 90483a77-9600-45b4-9f6f-5aa6ad43d8d6
[00:19:15] [Server thread/WARN]: Tried to add entity with duplicate UUID bb3c4b14-fad5-4f72-90cb-859dfe684933
[00:19:15] [Server thread/WARN]: Tried to add entity with duplicate UUID 062928ff-2603-42c9-ad5b-db2a4dfe2c78
[00:19:15] [Server thread/WARN]: Tried to add entity with duplicate UUID 8cf1458d-dd2d-4d20-a1e9-9b3ff0b026d5
stop
[00:19:26] [Server thread/INFO]: Stopping the server
[00:19:26] [Server thread/INFO]: Stopping server
[00:19:26] [Server thread/INFO]: Saving players
[00:19:26] [Server thread/INFO]: Saving worlds
[00:19:26] [Server thread/INFO]: Saving chunks for level 'world'/Overworld
[00:19:26] [Server thread/INFO]: Saving chunks for level 'world'/Nether
[00:19:26] [Server thread/INFO]: Saving chunks for level 'world'/The End
[00:19:27] [Server Shutdown Thread/INFO]: Stopping server
[00:19:27] [Server Shutdown Thread/INFO]: Saving players
$ java -version
java version "1.6.0_65"

Players are not able to log into the server either as it produces an error at login and kicks them out. This might be a client issue so I'll create another bug report for this issue. I'm putting it here since it might be related. Example:

console log

[00:00:57] [User Authenticator #1/INFO]: UUID of player turtle2472 is xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
[00:00:57] [Server thread/INFO]: turtle2472[/127.0.0.1:56545] logged in with entity id 874 at (146.3491359054718, 109.0, 1168.487930355481)
[00:00:57] [Server thread/INFO]: turtle2472 joined the game
[00:01:00] [Server thread/INFO]: turtle2472 lost connection: TranslatableComponent{key='disconnect.genericReason', args=[Internal Exception: java.io.IOException: Broken pipe], siblings=[], style=Style{hasParent=false, color=null, bold=null, italic=null, underlined=null, obfuscated=null, clickEvent=null, hoverEvent=null, insertion=null}}
[00:01:00] [Server thread/INFO]: turtle2472 left the game