Usage (command prompt):
cxitool something.3dsx something.cxi
makerom -f cia -o something.cia -target t -i something.cxi:0:0

Help:
cxitool --help

Compiled on windows from: https://github.com/devkitPro/3dstools/tree/cxi-stuff using devkitpro's msys2 and gcc.c.