added tile_sort() routine for qsort
removed some unused variable warnings
dropped explict skip of purity=0.25 bin for subst and context
No longer require tile size, dropped intensity_dir and tile width/height CMD line
options. Region tables for each tile stored in a hash keyed on x/y region index.
Filter file and reports now ordered by tile
dropped intensity_dir from pb_align, no longer needed by spatial filter
dropped magic number from calibration_pu.c and some tidiying up
restored but deprecated -intensity_dir in pb_align script
Merge pull request #68 from srl147/devel

Devel