This is an old question but unfortunately the only response it got was wrong.
It's definitely possible to read and write files using HTML5 in Chrome, without the vague "security" issues mentioned. The HTML5 Filesystem creates a protected sandbox in which you write and read virtual files: you can think of it as files being written in file based database managed by Chrome and not accessible by either other Chrome apps & extensions or other OS based applications. The user won't be able to copy or move these files using his OS file explorer since they reside inside the web browser's file DB.
You can't read (or write) arbitrary files from (to) disk based on any given file path.
If you need a file from disk you can only let the user select it himself by using chrome.fileSystem.chooseEntry()
You can however read (and write) your own files from (to) the HTML5 Filesystem.
So to answer your question: no you don't need user interaction to write your config file to the browser's file system.
An alternative to files could be chrome storage, localstorage or even indexedDB to store your (persisted) config key-value pairs.
Here are a couple of useful links to start reading about it:
Toying with the HTML5 filesystem
HTML5 Rocks
HTML5 demos