This is an old question, but unfortunately the only answer he received was incorrect.
You can definitely read and write files using HTML5 in Chrome, without the mentioned "uncertainty" issues. The HTML5 file system creates a secure sandbox in which you write and read virtual files: you can think of it as files that are written to a database based on files managed by Chrome and are not accessible to other Chrome applications or extensions, or to other applications on OS base. The user will not be able to copy or move these files using his OS file browser, since they are inside the DB file of the web browser.
You cannot read (or write) arbitrary files from (to) a disk based on any given file path. If you need a file from disk, you can allow the user to select it by himself using chrome.fileSystem.chooseEntry ()
However, you can read (and write) your own files from (to) the HTML5 file system.
So, to answer your question: no, you do not need user interaction to write your configuration file to the browser file system. An alternative to files can be chrome storage, localstorage, or even indexedDB to store your (stored) key-value configuration pairs.
Here are some useful links to start reading about it:
Playing with the HTML5 File System
HTML5 Rocks
HTML5 demos
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