mpileup: Long options

[Add long options as per eb2b30907ada8dc77b2d373dcf36ea6b8b9d64d2, but
without removing existing -a/-D/-M/-S/-V/--ff/--rf options or creating
new -1/-2 short options --- @jmarshall]
Create a print_usage() function for usage printing

The source code text is unchanged, modulo whitespace and s/./->/g.
Reformat usage to (mostly) fit in 80 columns

This uses the typical GNU-style spacing (e.g., two leading spaces on
option lines) and removes brackets around <FILE> etc, as the capitals
used distinguishes them without using up characters.
Minor rewording of usage to fit in 80 columns
Deprecate `-S`, `-D`, `-V` in favour of `-t DP,DV,SP`

- Deprecate `-S`, `-D`, `-V` by hiding in short help.
- Options still exist, but warning to stderr is printed when used.
- Updated man for (just) these options.
Fix long option has_arg inconsistencies
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.
Remove mpileup -M option, which has never been implemented

(Fixes #132.)
Add lowercase synonyms for --VCF etc long options
Add output mode parameter to bam_merge_core2 and bam_sort_core_ext

Instead of a compression level, these now take a sam_open()-style
mode string (e.g., "wb0" for uncompressed BAM).  This allows calling
code to ask for e.g. CRAM output.
Overhaul samtools sort options and invocation

New set of samtools sort options, with a more typical -o FILE option,
separate options for final output and temporary files, and the ability
to write SAM, BAM, or CRAM.  Fixes #171.

The old usage is deprecated but still present, and is assumed when
neither -O nor -T options are present.

Updated documentation to list all options, and mention that the old
usage is now old.
Merge mpileup long options (PR #205)

Fixes #127, fixes #134, fixes #136.