Fix the behavior of Markdown extensions.

There was several issues here:
- `self.extensions` was adding 'meta' multiple times (ref #1058)
- `self.extensions` was keeping a reference to `self.settings['MD_EXTENSIONS']`,
  so adding 'meta' to it.
- the `%s_EXTENSIONS` block coming after, it was overriding `self.extensions`
  with `self.settings['EXTENSIONS']` (while it was a reference, it was working,
  but ...). As this is currently used only for Mardown, the simplest solution is
  to remove this, and let each reader manage its `_EXTENSIONS` setting.
Merge pull request #1066 from saimn/markdown

Fix the behavior of Markdown extensions.