Beginning work on LSF batching

Code is all written down right from my head. Now need to test and push and break in earnest

Flags for output and error files

More thoughts on a daemon process

First (as far as I can tell) working LSF submission system

Reporting unknown status. Also, everything's nice and tested now on chained jobs, and multiple workers

Now saving directories as parameters doesn't act funny

Added a local LSF task, for debugging.

Can now pass extra args to the batch submission

Removed unnecessary whitespace
Merged LSF submission into dev
Various changes that have been helpful