Fixing most recent bug in Workflow Creation and other little bugs I stumbled over in the past

Most important modification here is the one that fixed the problem of the workflow (if pickle-problem is ignored). However, I also applied few modifications to regularize the code in the alignments section. These don't change the major behaviour but should reduce bad surprises when using the alignment module (align/multiple.py) of LingPy as well as the align/pairwise.py module.