Updates in FragmentLength, logo generation, memory usage tracking and report generation.

FragmentLength: I modified the script that calculates shift correlation. It is a lot faster now.
Logos: RunPhyloGibbs and MotifRefinement components now use the R package to create sequence logos. It produces neater logos without artefacts.
Memory tracking: Crunch now tracks for every component that is submitted to the cluster the usage of memory (Thierry's monmem script). This feature was added to the wrapper template.
Report: make_output.py script is now able to find whole report for shifted bedweight files.
Added files to track.