Avoid autogen.sh and the forced initial configure

This commit adds back the already built Makefile that calls
base/config/kconfig/Makefile.kconfig for *config targets directly
without any need for Makefile generations.  Once configured, GNUmakefile
takes precedence and that makefile would never get called again.

In the process of figuring things out, it turned out Philippe Gerum had
already done this, but in the process of cleaning up generated files,
this was lost.  The same old file is retrieved and shortened.

Basically, the only thing left of autogen.sh was running autoreconf
which is rather unnecessary and anyone can just do autoreconf -i on
their own.

A very minor update is that since 108fdef, RTAI doesn't just "Display"
execution times, but "Track"s them.  During merges from upstream, this
had been reverted which is now fixed.

Signed-off-by: Shahbaz Youssefi <ShabbyX@gmail.com>