Forcing docs to use the cwd as file base

This is a pull request meant to add to the discussion on #4 

**This is a pretty ugly hack**

The only way I was able to get gulp-yuidoc to write docs with relative path names is to set the base on my files in this plugin. Doing it via `gulp.src` would cause weird behavior where I would have to check `vinyl.base` in `lib/parser.js` and pass `vinyl.path` or `vinyl.relative` and that felt like an even bigger hack.

This solution just sets the file base to `vinyl.cwd` and then passes the relative path into the `filemap` and `dirmap`.

**Concerns**: I'm very concerned that doing this will result in problems if people try to chain other commands in their pipes.