Fix bug in run_programs.pl

The script instructs to run it with, say, sys_llvm. However, when queried about compilation flags, the Makefile in sys_* directories returns 2 lines of output instead of the 1 line returned by the Makefile in source. This causes commands to be 4 lines instead of 1 for the sys_* directories, and the compilation to fail.

Capture only the last line of the Makefile output; compilation commands are 1 line then, and the script works as intended.