changed some protecteds to privates
removed some unused imports and residual workflow references
a little 'spring' cleaning
Merge branch 'master' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository
took out wasp-file module
Merge branch 'master' into waspTest
moved location of WaspStatus message
added file service methods to create samplefile
added more methods
Merge branch 'master' into genericDna
added delay for case where scheduler doesn't know about the
job but the NFS hasn't registered the presence of the semaphore
file yet.  Needs improvement.
wait longer, more
Merge branch 'master' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository
added fastqService, should probably have own config file.
added some new methods for checking if sample is a cell and also for
getting setting a success status on a cell and getting all libraries on
a run which have been marked successful
reset
Merge branch 'master' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository into filework

Conflicts:
	wasp-core/src/main/java/edu/yu/einstein/wasp/service/impl/SampleServiceImpl.java
fixed up broken SampleService and Impl from last commit
Merge branch 'master' into genericDna
Merge branch 'master' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository into filework