EDIT: rxTools is now open sourced and has sig patches. Go check that out here.

Credits to @Roxas75 for rxTools in the first place and all the others that have worked on it.

The original thread is here. IF YOU HAVE ANY QUESTIONS, PLEASE CHECK HERE FIRST.

Credit to @Apache Thunder for testing stuff while my 3ds is away.

Here's a video of it working, recorded by Apache Thunder on my Youtube account:

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This one was recorded by MegaShaymin with his Cap Card:

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And of course, here is the link: https://mega.co.nz/#!XY1DHZSC!e_0sGG7R65-P_1pwAA1RQcWn7Z0zgjRneZqHCjcHwbk

This version has TWL and AGB title support, but lacks sm4sh and mh4u support: https://mega.co.nz/#!HQdxyJqL!HcNL0FqJ_6FkA-Rf5D94_1OBtOGpfuWLmmKBFCuBr50
NOTE if you have unlinked NANDs: For a GBA or DSi title to run, it needs to exist on sysnand. You can run them on emunand if they are also installed on sysnand.

Here's a thread that can explain how to update from your current PBT/Pasta/Palantine 'CFW': http://gbatemp.net/threads/how-to-switch-from-pbt-pasta-palantine-cfw-to-rxtools-sig-patched.390624

There's a tutorial by @VerseHell here: http://gbatemp.net/threads/rxtools-with-signatures-patched-out.390607/page-50#post-5535527 and another here: http://gbatemp.net/goto/post?id=5540327#post-5540327 to inject FBI without downgrading (Works for 2DS).

Go here if you want to decrypt, unpack, and edit rxTools: http://gbatemp.net/threads/rxtools-with-signatures-patched-out.390607/page-55#post-5535962

Here are some neat little tricks:

You can xor 0B 3C E6 39 4D 9F 5B 4C @ 0x26754 of rxTools, and that'll display "RX-S" and "RX-E" which you can edit and re-xor to have whatever you want displayed in System settings. (Personally I revert "RX-S" back to "Ver.")

You can chop off the last 0x110000 bytes of rxTools.dat, that's a little over a mb.

You can write 72 5B 48 14 0C F4 5D 93 A2 6C 35 FF 29 83 53 41 @ 0x40A31 to have the slot 0x25 keyX load from the first 0x10 bytes of rxTools.dat. You'll have to paste the key in yourself, of course. (This kills mset compatibility, so don't do it if you intend to use mset.)

I'll make changes to it if needed.