Hi David,
you mean building with make files or batch files?
Yes, you can run the compiler/linker/etc in command line mode too.
E.g. you can run the compiler from the DOS shell with
prog\piper.exe chc12.exe foo.c
Apart of that, you need to set up a batch file or a make file.
How to use make files, here is a background article (Make my Make with Eclipse and MCU10 | MCU on Eclipse). It is using Eclipse, but the same principles apply for your classic CodeWarrior.
I hope this helps.