some progress for mpileup documentation

- add missing options to the command line summary
- add missing and long options to the man page (#127)
- option `-a` removed as it implemented the default and was hidden anyway (#127)
- change to pileup output description in response to (#134)
- pileup command long since deprecated in favour of mpileup
- still needs work
Use getopt.h's descriptive constants in long options array

Also fix --illumina1.3+ short option equivalent.