Put in preliminary changes for empty-input-dir-valid flag
input-dir-valid: fix logic bug, nix nils from empty dir, Cloudera hadoop
Merge branch 'feature/empty-dir-ok-mod' into feature/empty-dir-checkpoints

Conflicts:
	src/drake/core.clj
Merge branch 'develop' into feature/empty-dir-checkpoints
Bumped version for branch feature/empty-dir-checkpoints
Prototype checkpoint implementation #80

Also turned off logging when running unit tests
Put in temp file deleting code for #88 and fixed some bugs
More comments for checkpointing, fixed small bug #88

Unit tests pass
Turned off some logging, option to keep temp files, tests #88¬
Put in regression tests, fixed small bugs, improved exceptions #88
Removed ability to specify temp files in inputs #88
Added checkpoints testing to run-all regtest script #88
Final merge fixes
Some final merge fixes
More merge fixes
Fixed an old String -> Integer bug which I thought was fixed
Add unique ID (GUID) to each step
Fix logic error in adding step IDs
Fix another logic error with adding unique step IDs
Fixing problem with exception throwing