Move detected NO_STH and NEED_STH variables, which we always output,
either setting or unsetting (setting to empty string) to config.mak.in
and use setting appropriately named variables and doing AC_SUBST
instead of adding them via GIT_CONF_APPEND_LINE macro and
config.mak.append temporary file.

Variables which might and might not be set are still added via
config.mak.append; this include all STH_PATH variables.
Signed-off-by: NJakub Narebski <jnareb@gmail.com>
Signed-off-by: NJunio C Hamano <junkio@cox.net>