Bioperl bundle refactor and removal of many options:

* drop hack overriding parent BUILDARGS
* recognize options with equal syntax of the bundled plugins
* drop many disable options and recommend to use the Filter bundle instead
* set defaults in one single place
* use AutoMetaResources. All the repository code is now part of this plugin
so we can use it. We still don't implement all of its options since it does
not make sense for us.
* commented large portions of unused code meant for podweaver
* write configuration section of documentation
* drop Method::Signatures::Simple because it only saved 1 line of code and
forced `with` to the bottom of the file
doc: fix typo
maint: update Changes file
doc: document what each plugin on the bundle does
filter [Readme] out of [@Basic]