cnspath mode doesn't create/copy all output files

[brianwalenz]

Running verkko in --paths mode does not generate the same output files as a 'normal' run. The 'cnspath' rule does not create a noseq.gfa output - and probably others. This caused @skoren's get*sh scripts to fail.

[skoren]

See also #170, the output doesn't created partitioned haplotypes even if the labels are in the paths/fasta files. It should auto-discover the labels and use them. Going to close #170 and track both here.