This bug clogs up my console/log and impacted the operations of my server quite a bit. I gunzipped the entire log directory and did a grep count on this;
grep -o '[Server thread\/WARN]: Keeping entity' * | wc -l
2453079
As you can see there are 2,453,079 hits! It really makes it unpleasant for me to monitor the server, and I am sure this had affected the other admins of vanilla servers as well.
Doing /kill uuid on all of those entities is not a feasible solution. There are simply too many players on my server with villager shops, iron golem farms, and etc. I cannot just kill hundreds of villagers and animals without breaking their farms and replace their villager with a new villager that sells the same items.
The amount of lines that we get spammed on the server console because of bug is pretty ridiculous. There were other problems with the server upgrades too. When I upgraded my server from 1.8 to 1.9, the ender dragon fight was broken even after deleting the DIM1 directory, so I had to manually edit the DragonFight attribute in level.dat to fix it. Please put more thoughts into the upgrading process.
This message has been spamming my server log heavily since I replace the minecraft_server.1.8.9.jar to 1.9 keeping the rest of the server files from the old version. I was able to kill some of the entities using /kill UUID command, but the same" keeping entity..." warning messages for that particular UUID still show up. Also, I was unable to kill most of the entities with the UUID that shows up in the warning message, because "That entity cannot be found". I've been seeing this error for any kind of entities including MinecartHopper, VillagerGolem, Villager, etc.
@Matti Ruohonen, thank you for the suggestion, but does the command remove-duplicate-uuids actually /kill the entity? I was wondering if this operation somehow reassigns an uuid to the entity with the duplicated one. If it does kill, then it is not a viable solution for me, because I just cannot destroy the villager shop, farms, and etc that my players spent years to build. If I could kill the entities then I could have just periodically piped the output of the grep command to console to kill, or used the MCEdit to clean it up.
Secondly, I have to admit I do not know anything about Forge or any mods, but I care very much about staying vanilla, and being able to update the server as soon as the new version comes out without worrying about any of the mods being outdated. For that reason I do not want to install mods of any kind.