Desktop sync
You can keep your remote folders in sync with your local ones, or the other way around with the desktop sync apps.
The apps are available from the download page: https://filerun.com/download
On the first run, you will be asked to provide your FileRun installation URL, your FileRun username and password. You can either sync your entire account, or choose particular folders.
You can also use third-party software via FileRun's WebDAV interface.
Tips for performance
Try to use the “Connect app” option from the web user interface to generate credentials to be used from the desktop app, instead of using the same credentials that you use to access the web interface. (Enabling third-party authentication will considerably slow sync down, because WebDAV is a stateless protocol, authentication happens with each and every request. Your third-party authentication server might be flooded when synching folders with many small files.)
Disable “Instant e-mail notification” from the Control Panel Email section. Use this instead.
Add the following inside the configuration file. Note that it will disable e-mail notifications which are sent to other FileRun users when you download files which are found in other user's folders.
$config['app']['logging']['skip_provide_download'] = true;
Troubleshooting
If you are getting “The server did not acknowledge the last chunk (No e-tag was present)” while using Cloudflare, you will need to disable the Cloudflare proxies, disable “Rocket Loader” or any other speed enhancers. They will speed up FileRun the same way one can speed up an F1 car by pushing it from behind.