I've been working on a cool new thing (Supster ruined the surprise)
I've tested it a bit and everything seems to work as expected, but I want to be sure.
In the meantime, this is a test build:
http://www118.zippyshare.com/v/ebSTFhJ9/file.html
Basically, no more flags. There's a configuration menu which can be called by holding SELECT on boot. It appears automatically the first time you boot the new version, there you can toggle the options that were "flags" previously. You can remove the "lastbootcfg" file as that is now bundled in the new "config.bin" (which holds the configuration too). Then, AuReiNand now actually prints error messages before shutting down (I hope we'll have less noobs XD), I moved the emunand.bin and reboot.bin to a "patches" folder (which seems more logical), I hopefully made the FIRM patching slightly faster (only applies if you don't use pre-patched FIRMs) by removing two memory searches, and finally AuReiNand will auto-delete the pre-patched FIRMs when you switch to/from(?) A9LH or, in the future, new patches are added.