There is a few variants of configuration:
1) Via global config file: /etc/cgitrc
2) Or via local config file, shipped in ./conf dir into webapp_dir. It has to
   be explicitly specified with CGIT_CONFIG env variable in your web server
   configuration.

If you would like to update the list of git repositories in cgit automatically,
you might consider adding something similar to the following as a cronjob:

"${MY_CGIBINDIR}/cgit.cgi --scan-tree=/git/repo-parent-path > /etc/cgit-repos"

Then add "include=/etc/cgit-repos" in /etc/cgitrc. This way it's simpler and
more convenient. You won't need to update your cgitrc every time you add a new
repository.