Firebird2.5-superclassic on Ubuntu 16.04 LTS
Ok, so I found functions.sh in /usr/share/firebird2.5-common. Running this creates all of the maintenance scripts and logging files that need to be there. It also creates security2.fdb which stores the security info for users and sets up the password according to the SYSDBA.password file.  You will need to set up two environment variables before running this:

FB_VER


and

FB_FLAVOUR


These need to be set to the point release you are on, ex: 2.5 and the flavor you are running, ex: superclassic.

Note: Mark Rotteveel's solution seemed to work as well, but I think this would be deemed as the more acceptable method.