merge changes from bioperl-live

Hi

when this repository was split from bioperl-live some 3 years ago, the development continued on both branches. This pull request merges the changes from both. The changes caused by the merge are on the commit carandraug/Bio-FeatureIO@86a32c56516009f40f5b5c971121af7b061685d8

Also, when this repository was created, all the previous history was lost. This pull request retrieves all that history (hence the 171 commits: 169 of old history + 1 of reorganizing the files for the merge + 1 for the actual merge). I did this by starting with bioperl-live and filtering the commits repeatedly with `filter-branch` a couple of times until only those files remained (I did not track file renames by the way). The commit date of the old stuff will look recent but its author date will show its true age.

There is one commit that I was unable to merge and someone should take a look at it, make sure is of any use: bioperl/bioperl-live@7218728b66ad297953676236077fd0ec757378c0

I already have received push access to the Bio-FeatureIO repository but would still like someone to take a look at the merge. After it's accepted, I'll push a commit removing the files from bioperl-live.

Carnë