Fixed #63 - `use_directory_urls` option has no effect.

- The `use_directory_urls` option is now passed forward to the
SiteNavigation object in order to correctly generate links to the
target file when needed.
- The post-processing of the HTML generated by converting from Markdown
now takes the `use_directory_urls` option passed to the SiteNavigation
object into account when changing anchor targets.
- The dev server mode (mkdocs serve) still ignores the
`use_directory_urls` option in order to have user-friendly URLs.
- There is a new test case for post-processing converted Markdown when
  `use_directory_urls` is `False`.