Variables to control semaphore limits and reduce limits
By default, generate unique IDs even if there are duplicates in the input
Stubs for utility scripts
Comment/question
Critical hash collision fixed in Step IDs, 207 smaple T1D completes.
Hash digest[:5] was used to generate Step directory names,
which occsionally resulted in identical directory names
for different steps, and one Step dir being overwritten,
and essentially dissapearing from the output. This manifested
itself in downstream Mothur error about sequence IDs present
in group file but not present in name file (Step for one sample
name file was overwritten and never concatenated).

Other changes in this commit:

- Implementation of FileMerger with skipping of header rows
(needed for Mothur upgrade).
- Reduced wait times in spin loops. Some steps are still present
in "running" state in monitor thread for a very long time
even after their batch jobs have finished.
Merging "shared" files in 454 after Mothur upgrade
Swithched off Step ID cutting in logging
Assert for duplicate registration of Step IDs (to catch name collisions)