Currently 3T writes settings and other things into the user home directory under .3T, .swt and .cache (on macOS; possibly different on other systems). This clutters the home directory and is therefore generally discouraged.

On macOS specifically, Apple user interface guidelines dictate that settings should go into the folder ~/Library/Preferences, and cache files should go into ~/Library/Caches. Similarly, on Linux the generally agreed-on guideline is to adhere to the XDG Base Directory Specification.