Code cleaning and bug fixes

Some cleaning and fixes including:
- Cleaned up code for ContinuousLR factor which is not supported yet.
- Fixed the well-known Akka non-terminating bugs by try-catch in `DeepDive.run`
- Reduced test output by using --quiet in sampler
- Fixed a warning that happens for a clean `make build`
- Skipped chunking on GP to ensure `make test` work on GP
- Fixed some occasional testing bugs

See the commit messages for detail.
I will try if I can add a unit test for this. It could be hard. 

Actually this is also captured by the big catch block in DeepDive.scala. I can change it back if necessary. There are many catch blocks like this that can be removed now that the big try-catch block works.