Improve alternate build-dir support

Improve alternate build-dir support

We now put the configure.sh, config.h.in, and aclocal.m4 files in the
alternate build dir along with the other generated files.  This requires
that we create symlinks for configure.ac & m4 in the build dir, which is
handled on the first run of configure or prepare-source.  I also changed
the patch-branch handling away from the .gen-stash dir to an automatic
build/$PATCH subdir idiom that will keep each branch's configuration
separated.  These automatic build dirs are only used when there is a
.git dir, a build/master dir, and no top-dir Makefile.  You'll also
want to have package/make early on your path for optimal ease of use.