Make calculate_runtime robust, see notes

Sometimes there are 4 columns, sometimes there are
5. I have no idea why (see Git blame).
But now it checks for this and if they aren't 4 or 5 it returns NA.
Switch some tests to optimized ss3sim

Tired of the slowness
datfile should be infile
Re-indent some ss3sim_base code
Add some output notes in test file
Add is_ssdat_file function throughout
Fix typo -> Fleet should now be Flt
Add a TODO
Fix FltSvy -> Flt in sample_mlacomp.R
Fix unit test for sample_mlacomp()