Ruthlessly tidied up the examples directory.

The Makefile and C programs are gone. They didn't build and mostly
were redundant anyway. Arguably chk_indel.c and bam2bed.c could still
have a use, but as toy examples they would belong in an htslib rather
than here anyway.

The README file was updated to use more modern command alternatives
(view vs import, mpileup vs pileup), but does not yet contain any
references to CRAM.  This can be added once -T is working.
Revert to ex1.sam.gz; fix mpileup command lines

At present there doesn't seem to be any way to get mpileup to read
@SQ-headerless SAM files, so use the BAM files in the example instead.
Merge examples/ tidy up (PR #226)

(Cherry-picked from the pull request so as to avoid introducing ex1.sam,
which is uncompressed and voluminous.  Closes #226.)
Add seq_cache_populate.pl

seq_cache_populate.pl builds a cache of reference files for the CRAM
codec to use.  It can be given a list of fasta files to read on the
command line, or alternatively it can be made to search a directory
tree for anything that looks like a fasta file.

The sequences in the resulting cache are stored in files named after
the MD5 of the sequence itself.  Samtools/htslib can be made to use the
cache by appropriate setting of the REF_PATH environment varaiable.
Add seq_cache_populate.pl (PR #224), add it to "make install"
mpileup: Updated tests
Merge branch 'develop' into QS-vs-PL