All the same, permissions seems to be a prominent issue in your error logs.
Caused by: codechicken.lib.configuration.ConfigFile$ConfigException: java.io.FileNotFoundException: /var/games/minecraft/servers/stoneblock21/config/avaritia.cfg (Permission denied)
Caused by: java.io.FileNotFoundException: /var/games/minecraft/servers/stoneblock21/config/avaritia.cfg (Permission denied)
2019-01-24 02:12:04,330 main ERROR Cannot access RandomAccessFile java.io.FileNotFoundException: logs/latest.log (Permission denied) java.io.FileNotFoundException: logs/latest.log (Permission denied)
2019-01-24 02:12:04,345 main ERROR Cannot access RandomAccessFile java.io.FileNotFoundException: logs/debug.log (Permission denied) java.io.FileNotFoundException: logs/debug.log (Permission denied)
2019-01-24 02:12:08,157 main ERROR Cannot access RandomAccessFile java.io.FileNotFoundException: logs/latest.log (Permission denied) java.io.FileNotFoundException: logs/latest.log (Permission denied)
2019-01-24 02:12:08,165 main ERROR Cannot access RandomAccessFile java.io.FileNotFoundException: logs/debug.log (Permission denied) java.io.FileNotFoundException: logs/debug.log (Permission denied)
[02:12:13] [main/ERROR] [BetterFps]: Could not save the config file
java.io.FileNotFoundException: config/betterfps.json (Permission denied)
[02:12:27] [Server thread/ERROR] [LLibrary Core]: Failed to save debug patched class for net.minecraft.server.MinecraftServer
java.io.FileNotFoundException: llibrary/debug/net.minecraft.server.MinecraftServer.class (Permission denied)
[02:12:33] [Server thread/INFO] [STDERR]: [com.setycz.chickens.common.LogUtil:setup:122]: java.io.FileNotFoundException: ./logs/chickens/chickens-latest.log (Permission denied)
[02:12:51] [Server thread/ERROR] [FML]: Error while saving config /config/enderio/enderio.cfg.
java.io.IOException: Permission denied
[02:12:51] [Server thread/ERROR] [FML]: Error while saving config /config/enderio/enderio.cfg.
java.io.IOException: Permission denied
Caused by: codechicken.lib.configuration.ConfigFile$ConfigException: java.io.FileNotFoundException: /var/games/minecraft/servers/stoneblock21/config/avaritia.cfg (Permission denied)
Caused by: java.io.FileNotFoundException: /var/games/minecraft/servers/stoneblock21/config/avaritia.cfg (Permission denied)
These occurences of Permission Denied are in line with the thought that there is improper ownership of these files. There’s also a pattern that many of these files would not be created by Vanilla, which means the ls -la you show where the files are all mc:mc makes sense that mc was the user that created them, but another user (perhaps sudo'd?) created the other files farther in the structure.
Of course, easy to confirm what Java is saying the issue is:
ls -la /var/games/minecraft/servers/stoneblock21/config
ls -la /var/games/minecraft/servers/stoneblock21/logs
Let us know what you see, and then we can use that to finally solve this.
If it’s not all mc:mc here (or even if it is, we just need another chown.