Remaining application code also moving repository

The remaining application-level code is moving to the samtools project,
in the samtools/samtools repository.  A duplicate of bamshuf.c is already
there; related existing functionality there will be extended to provide
the functionality provided by bam2bed.c, bam2fq.c, and bamidx.c; and
abreak.c will be included in samtools as appropriate.
Lift library source to the top-level directory

The htslib repository will be solely for htslib library code, so the
source code should be at the top level.  In particular, public API
headers remain down in htslib/ so that they are physically separate
from library-private source files and headers.
New non-recursive build infrastructure

This new makefile arrangement facilitates listing correct prerequisties
both for htslib code and code using it, such as samtools.
Build shared libraries, add "make install" target

Currently implemented for Unix .so and Darwin .dylib shared libraries;
could also be implemented e.g. for DLLs in Windows and Cygwin flavours.

Further work is required in version number infrastructure and to install
documentation etc -- currently only headers and libraries are installed.

There is now nothing significant remaining from the original makefile.