Cleanup of config/includes.

Remove a use of AH_BOTTOM from configure.ac. This macro is used by
autoheader to add '#include' of some include file to the end of
config.h.in and then to config.h. OpenOCD can be built with a custom
config.h, so it's preferable to move these '#include' statement directly
in the C files that need them dropping this unneeded dependency.

It also causes problems when I want to use the gnulib library (which
comes with its own Makefile, and does not have the same include path as
the top-level Makefile).

So this change touches a lot of files, but is actually really simple. It
does not affect functionality at all.

Change-Id: I52c70bf15eb2edc1dd10e0fde23b2bcd4caec000
Signed-off-by: Tim Newsome <tim@sifive.com>
Reviewed-on: http://openocd.zylin.com/6171
Tested-by: jenkins
Reviewed-by: Antonio Borneo <borneo.antonio@gmail.com>