The morse trainer software, which consists of one C file (morse.c) and one assembler file (irq.s) will need the following separate steps to compile into an executable named morse:
cc65 -g -Oi -t c64 morse.c ca65 -g morse.s ca65 -g irq.s ld65 -o morse -t c64 c64.o morse.o irq.o c64.lib
When using cl65, this is simplified to
cl65 -g -Oi morse.c irq.s
As a general rule, you may use cl65 instead of cc65 at most times, especially in makefiles to build object files directly from C files. Use
.c.o: cl65 -g -Oi $<
to do this.