Update for latest atmosphere, sysmodule registration and bug fixes

Changelog

• Fixes so the Toolbox works with latest libnx and Atmosphere again

• The flags folder will now be created before trying to create a boot2.flag file

• Third-party sysmodules can now create a toolbox.json file in their folder to make them be loadable by the toolbox

  • To use this feature, create a toolbox.json file in your sysmodule's /atmosphere/contents/ folder with the following format:

{
	"name"  : "sys-something",
	"tid"   : "0100000000000999",
	"requires_reboot": false
}

• The atmosphere config files will now be created and filled if none was found
• Allow inputs from any controller, for consistency with hbmenu v3.2.0

All you can see here was the work of @cathery so a huge thanks to them <3