Makefiles should not touch .output, etc... unless operation completed successfully

[ahmadia]

No description provided.

[mandli]

This is a general problem for all pure Fortran examples. We need to capture the correct return code from the Fortran and probably assume that if it's not 0 we should return non-zero from the python run command. Currently I do not believe we capture the return code leading to erroneous "touching" of the .output phony target.