Minecraft has some poorly-explained "security" fix every few months. That worries me.
You can mitigate some of that craziness by running minecraft java instances from a script that is constrained by Linux's apparmor.
If you use Ubuntu or Debian, and only wish to use these startup scripts and security profiles, then the personal package archive at
https://code.launchpad.net/~cmiller/+archive/ubuntu/ppa
or
ppa:cmiller/ppa
will be perfect for you. Commits into Github percolate to that PPA in hours.
If you are not lucky enough to use Debian based distro, you can instead install these files in the appropriate locations. Then,
$ sudo apparmor_parser -a /etc/apparmor.d/usr.bin/minecraft-{server,client}
$ sudo aa-enforce /usr/bin/minecraft-{server,client}
After the first time, you don't have to do these.
Then, run "minecraft-server" or "minecraft-client".
Your data is kept in ~/.minecraft.
If you create different "level-names" in your server.properties, it must start with "world".
First time you run it, run
$ dmesg |grep apparmor= |grep minecraft-