Cleanup and standardize omnibus-software definitions

you should also be defaulting to with_embedded_path() everywhere as well, even if the previous software description didn't use it.  if we build and install a tool like autoconf then if the software definition uses autoconf we always want to be picking up our version of it, and not escaping from the embedded path and using one in the distro that just happens to work...  same for pkg-config and everything else.

really the embedded path should have been baked into every command you run from the start, and then we should have later added an option to override it in those few special cases where it breaks something (e.g. looking at you zlib.rb...)