Rinnegatamante has released the first open source and legal CIA installer/uninstaller for the 3DS, here is a quote from the source:
Big Red Menu is the first CIA manager (installer/uninstaller) for 3DS completely legal and opensource.
It’s wrote in both C++ and LUA (Heavy edited LPP edition) and ACTUALLY works only AS CIA.
So to install Big Red Menu, you’ll require BigBlueMenu or devMenu but, after its installation, you can delete these Nintendo copyrighted tools and starts to use Big Red Menu.
Smealum for libctru
Aurelio for helping during the writing of the lua_uninstallCIA code.
Note: Big Red Menu doesn’t obscure any System CIA (devMenu for example hides DS_INTERNET and a lot of other NAND CIAs) so PAY ATTENTION when you uninstall NAND contents cause you can also corrupt 3DS NAND -> Brick.
Visit The Forum To Discuss The Story: [Released] Big Red Menu – Legal CIA Installer/Uninstaller