Better stats output from ctx_clean.c + uses getopt_long()

ctx_clean.c:
- handles arguments manually with getopt_long()
- changed some command line arguments
- add number of kmers to coverage histogram
- options to save before/after covg/len histograms

scripts/plot-covg-hist.R:
- updated to include a plot of kmer count

clean_graph.c:
- Record before/after covg/len histograms as we go

supernode.c:
- don't need separate method here to get supernode length distribution

graph_reader.c:
- safer / cleaner parsing of threshold values in header

graph_info.c: Fixed not setting supernode threshold correctly