The command line gives you everything that the GUI can do (plus some other commands), but it's a bit more laborious, you can use the Windows CMD window (capcli.exe), the MacOS terminal (capcli.MacOs) and the Linux shell (capcli.Linux), they all work the same I've tried to list the command in the order you might use them.
CapCLI>
commands:
help
Not always that much help as I haven't kept it up to date - I'll come back to this
loadrom /path/to ROM
Loads a file as if it was a Kickstart file, if you have a hash file for the kickstart then it will also understand all the individual components
roms
List the roms that you have loaded (or created)
rom [n]
Display the current ROM (if you don't give a number) or switch to "ROM n" if you do, the ROM numbers are given by the "roms" command
savecomponent [n]
Extracts a component (n) to your current savepath, if you don't specify a number, then it will save them all, this is similar to the "romsplit" tool
newrom [size]
Create a new (empty) ROM, valid sizes are nnnn (a number of bytes), nk (n kb, e.g. 512k - the most useful), nm (n mb, e.g. 1m)
add /path/to/component
Add a component (like one you saved earlier, or any loadable, romable library)
add [kickity-split|size|checksum|vectors]
Add a standard component, note these aren't library components so don't have relocs, it's best to add these before you add any libraries
saverom [filename]
Saves the current ROM, note this is just the current ROM, no byteswap or split, if you want to do more complex things like multiple ROM banks for dual eprom machines with byte swap etc. then you need to create a rom profile and save that instead, this just saves the raw data of one ROM bank.
romprofile [single|dual|cd32] [ROM numbers]
This defines which ROMs you want to select and the number of ROMs (i.e. your particular physical Amiga).
So, an A600 with a $F8 ROM and a $E0 ROM could be "romprofile single 0 1" (assuming you have two ROMs loaded)
saveprofile [512] [byteswap] /path/to/outputfile
To save the ROM(s) ready for burning (or an emulator), for an emulator you might not need any options, as a single file with no byteswap might be OK, but if your burner can only burn in 512k chunks you might need to add the "512" option, and you can byterswap for burning
exit
Quit from the capcli tool
There's a load more commands, analyserom, analysecomponent, savecomponenthash, saveromhash, addreloc, editcomponent, loadadf, adflist, adfsavefile plus all the patching commands, so I'll add some more stuff here when I can be arsed.