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That would just add to the time it takesHow about making it work like this: The CFW looks for two files--first it looks for arm9aurei.bin, and if that is not present it looks for arm9loaderhax.bin. Instead of a hardcoded path, it picks whichever one it finds first.
If you're not using a boot manager, you install it as arm9loaderhax.bin and when it reboots it sees that arm9aurei.bin isn't found so it reboots using arm9loaderhax.bin. If you are using a boot manager, you install it as arm9aurei.bin and when it reboots it finds that and reboots using that as the path.
Alternatively, how about a config option where the user can specify "reboot as this filename"? If the user is using a boot manager, he installs it as the alternate filename, and if not he installs it as arm9loaderhax.bin. (Of course it would fail if he installs it as arm9loaderhax.bin and forgets to take the option out of the config.)
Side note, for anyone who can't use zippyshare and needs the patcher
http://gbatemp.net/index.php?posts/6252216