Jira ticketing

After testing help from @kosiaris, here is the jira integration which seems to work satisfactorily. I merged the master branch into it because if I rebase on master I suspect the history of our inline comments will be lost (as the commits they are based on would all be lost). If that is preferred anyway in order to avoid the presence of the merge-commit let me know and I will rebase it. Closes issue #60