Updated to match the fixed version from the parallel layout. Also
discovered a `</div>` tag was missing.
Fixes jashkenas#302.

In the output html files, any directory separators will be replaced
with underscores (rather than replicating the folder structure, which
would create unnecessary headaches with linking). Fixes jashkenas#309, fixes
jashkenas#303. Also includes some previous changes that were in
`docco.litcoffee` but hadn’t found their way into `docco.js`.
Theoretically it would still create a naming conflict in cases where
you had two files, `foo_bar.coffee` and `foo/index.coffee` which could
be precluded with a double-underscore or similar, but I don’t think
there’s a strong likelihood of that occurring.

Applied change from previous commit (re: jashkenas#309 and jashkenas#303) to the classic
and linear templates.

I’m not sure if some people have a preference for just showing the
basename, but that option isn’t really compatible with multi-directory
sites. For single-folder sites (say, if everything is in `app/`, and
you don’t want `app/` at the front of all your links) you can get
around it simply by running docco from within the folder containing the
files (at least with the CLI).

Makes all links accessible on large sites. Additional change for jashkenas#302.