Updating the free version is fairly simple but manual. This guide is with screenshots from windows, but it works exactly the same on linux (remember the extra step you may need, the chmod +x command or the manual running of the terminal command, refer to the download page for these instructions if you need a refresher).
Download the latest game version from the download page.
Extract the downloaded folder. DO NOT RUN THE GAME FROM THE NEW FOLDER YOU JUST DOWNLOADED! You should now have 2 folders, one with the old game install, and one with the new one you just downloaded. The following steps will allow you to keep your settings and save files.
If you start the game from the folder of the new one you just downloaded, and then follow the next steps, your settings and some saves (fortunately not your levels though) will be reset!
Put these folders side by side in your file explorer, like this:
You will now need to overwrite the old game folder with the new one. Go into the new folder, Control + A to select all, and copy. Then head into the old folder, and paste. File explorer will give you a warning about overwriting files, this is exactly what you want. The files that are the same / have changed (the game files) will be overwritten with the new ones. Your custom levels (and your settings, as long as you followed the bullet point in step 2), don't exist as files in the newly downloaded game folder, and as such should be ignored by the overwrite. To be extra safe, just make another copy of your old game folder before doing this and store it somewhere else.
Below is a gif of this process, if it doesn't load download it to view it.