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I'm far from an expert, but I don't know of rclone doing versioning, or a continuous sync like syncthing. Also haven't used proton, so take my thoughts with a grain of salt.

Stage 1 Run rclone config to set up the proton remote. rclone config should take you through a wizard and will eventually ask you to authenticate somehow with the remote. Once that is done and saved, you'll exit the rclone config wizard and be back at the command line.

Then you would run a test command like: rclone ls :

If it worked, you should see a list of files/folders on Proton. If not, you'll have to go back to rclone config and edit the remote to fix whatever went wrong.

Stage 2

Test out copying the folders with a command something like: rclone copy localfile/folder remotename:remotepath

Do some testing to get the hang of the command, but it is pretty straightforward.

Stage 3

I don't know how many files or how big the files are, but I assume not too many and not too big. I also don't know which version of Linux you have, but I assume you have access to systemd, cron, or both.

You'll make a basic shell script that runs the command you practiced in stage 2. Easy peasy, put it in a text file with a shebang at the beginning, make it executable, and give it a go. It should run exactly how it did when you typed the command out manually.

Finally, you will write a systemd timer or a cron/crontab entry to execute that script at some frequency.

So just to summarize:

1. Setup the proton remote in rclone using rclone config
2. Test out copying files to proton through rclone
3. Write a basic shell script that runs the command to copy files from the desired local folders to the desired proton folders.
4. Use one of the tools on Linux that lets you schedule the execution of scripts to automate running your copy to proton script as frequently as makes sense to you.