- Improve docs by avoiding confusion with distutils
- Update dependency management docs
- Update userguide on miscellaneous and extension

This is a continuation of the update effort to de-emphasize `distutils`
and make the documentation more consistent.

The main targets of the changes are the files
`docs/userguide/miscellaneous` and `docs/userguide/extension`.

Changes:

- Extracted text about automatic resource extraction and the zip-safe flag
  from `userguide/miscellaneous` to `deprecated/resource_extraction` and
  `deprecated/zip_safe`.
  - These configuration parameters are commonly associated with
    ``eggs``/``easy_install``/``pkg_resources``, and therefore are
    obsolete. Leaving them around in the main parts of the documentation
    just confuses users.
  - The text in the new files were updated.
- Extracted text about additional metadata from
  `userguide/miscellaneous` into the existing `userguide/extension`
  document.
- Updated `userguide/extension` to better reflect the status of the
  setuptools project.
  The text was also changed to explain a little bit more what is the
  relationship between ``setuptools`` and ``distutils``.
- Removed `userguide/functionalities_rewrite`.
  This file was virtually empty and not bringing any extra value to the
  docs.

- Extract `depencency_liks` section to a new file:
  `deprecated/dependency_links.rst`
- Add note about directly URLs not being accepted in PyPI.
- Simplify intro about build system requirement.
- Simplify intro about optional dependencies.
- Fix confusion in example about "Project" and "Package".
- "Demote" section about extras in entry-points to a note.