Use full file path, underscored, for output files

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 #309, fixes
#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.