Create symlink to `allpairs_multicore`

Without this the prepare step of both allpairs tests fail on OS X with 'allpairs_multicore not in path' error.
New method for allpairs test.

Check that each input file occurs n times (where n is the total number of input files) in the first two columns of the output, which is the expected pattern for an allpairs run.
remove 'horrible, horrible' testing method
remove makeflowlog generated during testing