See Upgrading from older versions (Keeping Track) for the upgrade process from 3.x to 4.x.
If you are running a 3.x version, please consider upgrading to 4.0. There are some security concerns about the 3.1xx code that have gone with 4.0. Furthermore, the gnats 3 branch is not maintained anymore due to lack of capacity.
The default format of the reports has not changed during the transition from 3.113.1 to 4.0, though you may add more fields to 4.0 reports (and leave out others). The format of the index file is now binary.
However, you have to change the e-mail aliases because the meaning of the -d option to the client programs has changed: It took the directory of the gnats database in 3.1xx, and now takes its name (plus, it is now installed into the libexec directory instead of the lib directory). I.e., you must change the aliases:
# GNATS 3 aliases:
ourdb-query: "|/usr/local/lib/gnats/mail-query -d /usr/local/gnats/db2"
ourdb-bugs: "|/usr/local/lib/gnats/queue-pr -d /usr/local/gnats/db2 -q"
to
# GNATS 4 aliases:
ourdb-query: "|/usr/local/libexec/gnats/mail-query -d ourdb"
ourdb-bugs: "|/usr/local/libexec/gnats/queue-pr -d ourdb -q"
Also note that the client/server protocol has changed from 3.1xx to 4.0; you cannot run clients from one version with the server from the other version.