Reading and writing "files" from flash memory from Espruino

There's http://www.espruino.com/FlashEEPROM

That only uses a single page of flash, but could easily be extended to handle multiple pages. What it does do is allow you to use the data directly from flash, without having to load it into RAM first.

There's also the Flash API so you can always access things directly: http://www.espruino.com/Reference#Flash

If you're really bothered about 'named' files you could just write your own JS library to handle a simple filesystem - but FlashEEPROM does contain some fancy stuff to help reduce repeated flash erases for things that change frequently.