There is few points regarding this

To update database from linux shell console it's enough just execute it will update database and clear cache automatically

php cron.php -s site_admin -c cron/util/update_database

It's also possible to update database just by executing http request. To allow execute this update in chat configuraiton you have to enter ip from which request will come.

http://expample.com/index.php/system/autodbupdate

To update files I just recommend use git if you have checked out lhc itself. It will update all changes files from master branch. So you can every night execute git pull command first and then just above command.

git pull origin master

If you do not have ability to use git you can use this command to update all lhc at once. This update script is experimental and backup should be created first!

php cron.php -s site_admin -c cron/util/update_files