What to do:
If you were running 1.3 before via the 'trunk' link from subversion, you should switch to the new 1.3 branch, lest you end up running alpha/broken 1.4 code without meaning to. To do this do the following:
svn switch https://evilnet.svn.sourceforge.net/svnroot/evilnet/branches/nefarious-1.3 svn update
make clean make make install
Then you can restart your ircd whenever.
Note: 1.3 uses a completely different ircd.conf syntax!
Users of the old released version of nefarious, 1.2, should start fresh with a new source tree, you can follow the directions I updated to 1.3 here. It is fairly important that all afternet servers get updated soon, as there are some minor annoyances with a mixed network which we hope to not have to content with much longer.