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 lists only SDMC CIAs to prevent users to brick their 3DS with some NAND CIAs importing.
Instead adding NAND and GAMECARD support is very easy.

A - Uninstall/Import CIA
Select - Switch between Imported CIA and SDMC
Start - Exit homebrew

Note that Big Red Menu will list only dirs and CIAs file from SDMC so you'll not lose time finding your CIAs to import.
For ORGANIZ3D users, style might be familiar