<this is a crude guide to upgrade, needs to be expanded/redone>

...make a database dump

• cd /var/www
• cp -R HaCi HaCi-backup
• tar zxvf HaCi_0.961.tar.gz
• ...check ownership of files (logs must be www-data or whatever your apache runs as)
• diff -ubr HaCi-backup HaCi
• ...edit back the changes you had done (typically: add back your CSS layout definition to internal.conf)
• restart apache (remember mod_perl is cached!)

done!