MAKEFLOW_INPUTS=input
MAKEFLOW_OUTPUTS=mydir/1.txt mydir/2.txt mydir

# specify everything (directories and files) in the target file section, but directory at the end (order of the targets creation is not as specified). This should work.
mydir/1.txt mydir/2.txt mydir: input
	mkdir -p mydir; cp input/hello mydir/1.txt; cp input/hello mydir/2.txt