It is coming back! http://hax3d.com/forums/index.php?threads/wip-downlow-the-automatic-3ds-homebrew-installer.26/
You will soon be able to do it all from your 3DS. http://hax3d.com/forums/index.php?threads/wip-compil3d.32/
Delete the old 3dscraft. Extract this to your 3ds folder and run fixer.3dsx(the one with the 3dscraft SMDH in HBL).
EDIT: And after running the homebrew, press A.