Longbow

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1. Update to the supported command line arguments to support non and GNU
standard options for help and version number.

2. Update to allow the creation of repX directories when they are missing
(Stops gromacs etc from exiting with path not found error).

3. Fix for bugs in python 3, there were two issues, one a python name change
and the second was due to garbled output coming from the linux shell
environment.

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1. Modifications to how Longbow accepts the help and version command line
parameters, some people don't follow GNU standards and thus so that we can
show them the help message/version we have allowed -v, -version, --version,
-h, -help and --help.

2. Longbow now creates missing repX directories if they are missing in cases
where all input files are global. This would allow jobs that might use
different random seeds on the same input files to be efficient on transfers.

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1. Fix for overwritten rsync-includes (developers only).

2. Bad character length on PBS now has an error message to inform the user what
went wrong. Job names longer than 15 chars would be rejected.

3. Jobs that failed in a multi job would bring down the whole lot due to a bad
initialisation now fixed.

4. Command line Longbow is submitted with is now logged to the log file for
debugging purposes.

5. Bug fix with a bad initialisation in job processing code.

6. New ini parsers that don't rely on python std lib parser, this means
comments are no longer deleted.

7. The following methods; loadhosts(), loadjobs(), sortjobsconfigs(),
sorthostsconfigs(), amendjobsconfigs() have been replaced with single method
processconfigs().

8. Fix for critical failure when the remoteworkdir did not exist.