After reading you post I did a quick Google search and if I understand what I found it seems that there is now a File API for HTML5 that would allow me to do read/write files from the local machine.
There is no unfettered file access to the local system. You can use <input type=file multiple> to allow selection of files to make available to script (read-only). File writes are limited to download actions.
Chrome did define a "sandboxed" virtual file system but that didn't get traction with other browser vendors. There is a standardized database API that can persist files. (Caveat: it's pretty buggy in Safari)
And that there seems to be one for JavaScript as well. Is that correct?
Without getting too pedantic: HTML is a markup language, and the HTML specification defines that language and provides hooks JavaScript to interact with it via DOM and places for other specifications such as the File API to plug in. So "as well" is nonsensical. It's all one big hairball, where "HTML5" is really a marketing term and reality is spread across multiple specs.
Disclaimer: Making this all suck less is literally my day job. I'm manager for (and engineer on) the team at Google that implements "storage" APIs for Chrome, as well as an editor on some of the Web Platform specifications.
So... I can answer some questions here.
