2. This works for me with .cia packing (in example on LoZ OoT 3D):

Code:

makerom [B]-f cia[/B] -rsf oot.rsf -target t -content loz-oot.cxi:0:0 [B]-content manual.cfa:1:1[/B] -o loz-oot[B].cia[/B]

Full .bat file (which builds loz-oot.cxi first):

Code:

makerom -f ncch -rsf oot.rsf -target t -desc app:1 -icon exefs\icon.bin -banner exefs\banner.bin -exefslogo -code exefs\code.bin -exheader exheader.bin -romfs romfs.bin -o loz-oot.cxi
makerom -f cia -rsf oot.rsf -target t -content loz-oot.cxi:0:0 -content manual.cfa:1:1 -o loz-oot.cia
pause

I use this makerom (x86) - 662 Kb (678 274 bytes).
3DSguy's v0.13, IIRC.

Didn't try to build .cci (3DS) with manual, though.