FBI is an open source CIA installer for 3DS. It is not the first one, but so far, it is the one with the best features.
CIA files allow the installation of titles to the 3DS. Think of them like the .wad files for Wii. FBI lets you install/uninstall them. In the past, the tools that was used for this purpose was Nintendo copyrighted material. Big Red Menu was the first open source/legal CIA installer, but as it came in .cia format, you still had to use a Nintendo copyrighted tool once to install it.
FBI comes in 3 formats, a .cia file, a .3ds file and most important a .3dsx file. Yes, you guessed right, it can be launched through Ninjhax. You still have to patch service access to install .cia files through ninjhax. This post can help you do that.
Keep in mind that you can still run only clean (legit) .cia files when you run this through ninjhax or any other method which doesn’t patch signature checks.
Here is the official feature list:
Available as a CIA, 3DS, and 3DSX.
Install and uninstall applications from both the SD card and NAND.
Delete CIA files from the SD card.
Install or delete all of the CIA files in a directory at once.
Install CIA files over the network using sockfile.
Detailed error output, making it easier to figure out why an (un)installation failed.