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 may have found a way for the broken test (with a timeout).