Not sure if you found your solution or not. Have you tried using the File API: Directories and System API?
In April 2014 it was announced as dead
Work on this document has been discontinued and it should not be referenced or used as a basis for implementation.
But it still functions in Chrome v36. If this is something that you're wanting to use for a personal project, then it should be sufficient. Not sure if you'd want to rely on this API if you plan on releasing it to others, as Chrome could remove support for it. If you do release to others, at least do feature detection to ensure their browser supports it.
Here's a tutorial on exploring the filesystem api. I have not used this with an extension.