Updates for bamboo changes

The latest bamboo version has some interface-breaking changes, these are the updates needed on our side. You should upgrade your bamboo install after this is merged.

The main change is related to the new version-tracking feature in bamboo:

Instead of having the driver fill in the sample template (and make necessary changes), then dump the resulting config in the working directory and have the workers jobs open that one, have all the workers open the template and fill in/change the content.

This is because with the tracking system the analysis config should be tracked by git in the analysis repository (which would not be the case of the file dumped in the working dir).