starting to shift from system_call to run_command (which has more checks and a hash for parameters)
switching to run_command from system_call
replacing system_call with run_command
Make fork_cmd a two-arg function as well.
syncing test_format.txt with this branch.
Merge branch 'master' into issue-127

This reverts commit bf62e39245fcd5ca564f8f6136be05389b02b581.
Apparently not all "which" versions have a -s flag.
simplifying calls to Configuration.pm
take out more -s flags for which
Ha, all that effort to set up "which" when all I really wanted to check was to see that a value was given.
test basicpipeline first; also just count the # of lines in the results instead of diffing.
take out the long failure messages.
close the log file if you need to.
centralized failure system; also prints the last logged lines for debugging.
might as well always be in debug mode for testing.
print to log, then die.
we don't need to log details about "cat"
random extra print.
Merge pull request #130 from juliema/issue-127

Giant pile of fixes