Report contig merges and name changes at the end.

[donkirkby]

I find the verbose output really helpful for learning how IVA works. I found a few steps that weren't included, though, and this pull request adds three new messages to let you trace from the verbose output all the way to the final contigs.

• Merging contigs: seeded.00001[0->1000] + seeded.00002[500<-0] ==> seeded.00001[0->1500] during _coords_to_new_contig() reports which parts of the contigs get combined and in which direction.
• Removing contained contig: seeded.00002 during _remove_contained_contigs() reports when a contig gets removed completely.
• Reported seeded.00001 as contig.00001 (reversed). at the end reports which contigs get renumbered after ordering by longest open reading frames. It also reports whether or not they get reverse complemented.

I'm happy to adjust the verbosity level or wording if you like.

I also documented what I learned about IVA's work flow for our project's documentation. If that would be helpful for your documentation, I'm happy to contribute it.

[puethe]

Thanks, looks all sensible to me!