Merge conflict

Created by: s-mm

This branch has the master branch and feature/ensembl_friendly branches merged.

1. Lot of files show change in the license comments. This was done to make it uniform across the entire code base.

2. Ignore all the formatting issues in modules/Bio/Otter/Lace/OnTheFly/QueryValidator.pm

3. I inadvertently changed the file mode of many files. This has been fixed.