Preserve Directory Structure

[avivkeller]

Right now, doc-kit creates all files at the top-level. We should preserve the directory structure relative to the input. For example, if the input is docs/**/*.md, a file in a docs/my-subdirectory should be generated at out/my-subdirectory.

This is blocking nodejs/nodejs.org#8612

[avivkeller]

After investigating this issue, it's a lot harder than it sounds, since we use api to generate a lot of file names, when, in reality, a path would be needed to resolve this.