games/minecraft-server: fix issues that resulted from recent upgrade

• Fix version reference in server script
• Remove blank sample files
• Add note in pkg-message how to upgrade from version 1.4.6
• Note in pkg-deinstall files files might exist in $ETCDIR as well (even though pkg also mentions this)

PR: 194312
Reported by: Helge Oldach
Final fix by: maintainer (Jonathan Price)