Slurm-pipeline

Added `sbatch.py` utility script (and `remove-repeated-headers.py` helper).

Added `--printOutput` option to tell `slurm-pipeline.py` to print the
output of running each step.

The distinction between simulated and skipped steps has been removed as it
was too subtle and complicated. Only step skipping remains now, and step
scripts need to decide what to do based on the value of `SP_SKIP`. For
backwards compatibility, the `SP_SIMULATE` variable is still set in the
environment, but its value is always identical to `SP_SKIP`.

Removed use of now-outdated ugly mocking code for `open`. This might break
Python 2 compatibility, but at this point I don't care.

The `--nice` argument put into the `SP_NICE_ARG` environment variable
changed to be e.g., `--nice=50` (used to be `--nice 50` which causes
`sbatch` to complain "sbatch: error: Unable to open file 50").

Removed unused `specification` argument to `SAcct` class.

Added missing `--scriptArgs` to `README.md`. Thanks
[avatar-lavventura](https://github.com/avatar-lavventura)!