Use config.h for configuration options

Add the rudiments of a configuration header for _USE_KNETFILE,
BGZF_MT, and BGZF_CACHE instead of needing a special rule for bgzf.o.

Use it also in faidx.c, which had lost its _USE_KNETFILE define in htslib
and so lost its net functionality.  Also restore mistakenly removed #include
in faidx.c.

Fix makefile thinko: .pico files need prerequisites too.  Also fix
dependencies that were not updated with recent bgzf.c and faidx.c changes.