The FileSystem extension has been updated with bug fixes and minor documentation changes. An intermittent critical flaw which kept returning an error whenever a FileSystem function was called has now been fixed, so hopefully people can now use it properly.
Macromedia's own implementation of the javascript encodeURI, decodeURI, encodeURIComponent and decodeURIComponent functions are flakey, and thus we had to write our own for encoding/decoding file paths etc... which was the main issue.
[update]
Just to clarify, the issues we found with the four javascript functions above are as follows. If your script attempts to encode/decode a large file path such as the following line of code:
[as]alert(encodeURI("file:///C:/Documents and Settings/Guy/Local Settings/Macromedia/en/configuration/Commands"));[/as]
You get an error alert that says something along the lines of "out of memory in file: test.jfl" and then flash crashes.
[/update]