When it comes to manually updating a Contao installation, you can either upload the whole Contao download archive to the server (replacing files) or you can upload only the files that have been modified since the last update (synchronizing files). Either way, you should always back up the following files and folders - just in case there is an error or you accidentally override them:
This will back up your local configuration, your custom templates and your files.
Replacing the files of a Contao installation is pretty simple. Just unpack the Contao download archive on the server or extract it on your local computer and upload the files with an FTP client. Then restore the files that you have backed up and remove potential leftovers from earlier Contao versions.
If you have installed any third-party extensions, make sure to backup and restore them, too, or do not overwrite them at all. Otherwise you will have to reinstall the modules and depending on the extension you might eventually lose data!
To synchronize a Contao installation, you can either use the Unix diff utility or an FTP program. Unix utilities are typically used by server administrators only, so they will not be explained here. To synchronize files via FTP, open WinSCP and connect to the server. Backup the files mentioned above and then navigate to the Contao directory and click the "Synchronize files" button.
Review the options carefully and make sure to choose "Preview changes", so you can check which files will be updated. Then confirm each file in the preview window and double check the files that are marked for deletion! Click "OK" to start the synchronization process.
Updating the database
After you have updated the Contao files, you need to update the database, too. Fortunately, the Contao install tool will do most of the work for you. Just open it and enter your password, then scroll down to the database section and confirm the changes.
Purge the internal cache
Finally you should also rebuild the internal cache (for DCA and language files). In the backend go to "Maintenance" and check "Purge the internal cache" in the "Purge data" section. Confirm the action by clicking on "Purge data".
You will now receive a message in the header asking to rebuild the internal cache. Click on "Build the cache" to cache the internal files.