correct_reads.c using indel+qual safe code; Minor bug fixes.

0x0. cmd.c clones input arguments array

0x1. JSON header: better reporting of command line args - use array of strings
     instead of merging into a string without escaping spaces.

0x2. Print STDOUT/STDIN instead of "-" in lots of places.

0x4. scripts/seq2pdf.sh: fix some bugs when running not in scripts dir

0x8. Don't try to get file size when reading from STDIN ("-")

0x10. objbuf_macro.h: added FUNC_shift() function for shifting elements

0x20. ctx_exp_abc.c: report GraphWalker state at the end of traversals

0x40. util.c: added function util_print_nums() to report numbers nicely aligned

0x80. correct_reads.c: lots of work on correcting reads. Now using new version of
      code. Indels still not printing correctly though. Just a bit of tweaking
      required. Soon will handle indels and quality scores nicely.