Refactor code to keep more things in memory

[hlasimpk]

Some of the results are stored in temporary files - try and keep this in memory

[fsimkovic]

what are you aiming to get from this? reduce disk space or r/w overhead?

[hlasimpk]

Reduce overhead - I think there are a few areas where I write everything to a file and then read out the results - especially moving between the rotation step and the MR step - but I'm not sure how feasible this is with clusters. Again, something to explore.