Move some patching from Makefile.in to configure

Give user some space between configure and make to fix things up
and also fits better in the overall autotools expectations. Minor
style fixes to configure.
Don't change dir in wrapper.

Previous code (changing dir + relative path) messes things up for
argument paths.
Updating README and include it in installation.
configure: revise cli interface. New --package option.

Instead of the awkward 'file' and 'version' variables + the --local
option use a unified --package= option which implies local operation
and determines version from package path.
bundling bugfix
bundling bugfix
README update