Matrix ordering fixes for heatmaps, now they are always square, no need to test for it when plotting a matrix created with reorder_mtx

Added all.x=TRUE to the merge command that helps order families in heatmaps from repeats.tab; this will allow families not listed in this file to be ordered at the end of the plotting order list.

Scripts for generating heatmaps were renamed to better reflect their function. Old versions of these scripts were deleted.