Settings
The Settings
dialog can be opened with the top right "cog" button of the toolbar:

Here is what the Settings
window looks like:

Settings description
Images
Persistent images
When enabled, the images will be persistent across application restart.
Programming
Skip memory verification after programming
When enabled, the programmed image will not be verified and thus there is no guaranty that the firmware will run properly. Speeds up the programming process by ~40%. Never disable for production use.
Auto programming
When enabled, the "Auto-programming" feature will be enabled by default at application startup. Useful for production centers.
SAM-BA
Use cutom SAM-BA
When enabled, you must specify the path to a compatible SAM-BA application directory. The specified version of SAM-BA will be used.
Under the hood
The Programming Tool has been built with Flutter.
ATMEL SAM-BA Command Line Tool is used by the Programming Tool. The SAM-BA application is delivered within the Programming Tool and is part of the application resources.