Redesign file format for improved I/O performance

[hamishmorgan]

The file format needs to be completely re-structured to improve I/O performance. Specifically, the write speed needs to be reduced by a factor of ≈ 24 to make efficient use of the new (apollo.hpc.susx.ac.uk) cluster nodes, and by a factor of ≈ 4 for the old (dragon.inf.susx.ac.uk/crescent.inf.susx.ac.uk) machines.

Further evaluation has shown that the I/O bottleneck is not as severe as previously thought. However, some file-format redesign is likely to be required.

Relates to #1