3DS:
Fixed configuration override after updating Checkpoint version.

Switch:
* Fix compatibility with certain games and CFWs. Now Checkpoint is fully compatible with custom firmwares using fs_mitm, layeredfs and other modules massively relying on file operations.
* * Confirmed working on both hekate, Atmosphere and ReiNX using said modules.
* * Other CFWs may be compatible as well, even if not directly tested.
* * The issue was caused by a poorly optimized function to recursively delete folders, which has been now replaced by the one available on JKSV, too.
* Fixed configuration override after updating Checkpoint version.
* Avoid using a separate thread to populate titles.
* Default selected button for the homebrew keyboard is now OK (thanks @fennectech).