Where your data lives

WindowsLinux
Mortar's data (profiles, mods, downloads, backups, settings, logs)%LOCALAPPDATA%\Mortar$XDG_DATA_HOME/mortar, usually ~/.local/share/mortar
Your saves%APPDATA%\StardewValley\Saves~/.config/StardewValley/Saves

The Mortar menu's Open data folder opens the first row.

To move the data, stop the game, open Settings › Storage and choose Move…. Mortar copies everything to an empty folder you pick, checks it, removes the old one and restarts. A file named portable beside the program keeps all data in a data folder next to it (not in a Flatpak or a read-only folder).