Add (or move) optionselect preferences for the file manager to the file manager settings
When you open the file manager, there is a pop up that asks you to select what directory to go to and if you want to see hidden files. There's the option to save your answers and use them every time without prompting.
There's also a "settings" link at the top left of the file manager. It would be nice if the options in the pop up could also have defaults set here - including the "use the pop up every time" option. :)