well you can always use file system api. http://www.html5rocks.com/en/tutorials/file/filesystem/ but its chrome only

For what it's worth, TiddlyWiki can save itself on the filesystem even with Firefox (user gets prompted to allow access). I don't know how it works though and when I tried it seemed to be quite buggy.

According to Wikipedia they use FileI/O, a Mozilla API for accessing the filesystem, which from what I can tell it's more directed at Addons than webpages.

What about security? I assume its not possible to read and write arbitrary files in the fs?

From parent's link:

If you're calling requestFileSystem() for the first time, new storage is created for your app. It's important to remember that this file system is sandboxed, meaning one web app cannot access another app's files. This also means you cannot read/write files to an arbitrary folder on the user's hard drive (for example My Pictures, My Documents, etc.).

Thank you for pointing it out. I assumed it would be like this but didn't find it scanning the page.