Saving files locally using captive runtime?

Hi All,
I'm creating an app using Flash Builder 4.7 and trying to export as an Air-powered desktop executable (.exe / .app) using Captive Runtime. End users won't have permissions for an Air installer.
Part of the app uses a gallery where users can upload images. These are stored locally on their computer, and a local XML file with reference to the images is updated.
This works fine with an Air Installer, as an application directory is created. My question is - does this work using Captive Runtime?  Is an application directory created on the end user's machine, and if so where is it (the applicationStorageDirectory)?
When I try to run from within FB 4.7 as an extendedDesktop I get the error below. Is this because it's not packaged up properly?
Error: Error #3003: File or directory does not exist. at flash.filesystem::File/copyTo()
Any advise would be great, I urgently need to get this project out.
Thanks a lot

Ok yeah, but...
Lets say the user runs the application from the jar file through JWS.
Its the first time he start the app. The app starts through the Main class inside the jar. Where on the local computer is the application running from? From which directory?
Since it is the first time he start it, we need to somehow check our /conf/ folder for the program to see if it contains a conf.ini file. So where is this folder? Where can we check for it? We need somewhere to know where it is... I don't even know from where the application is running, or where the jar files are stored when starting from JWS. Preferably, when starting the application it should check something like
/Programs/theapplication/conf/conf.ini for it.
But how do we know the "/Programs" is somewhere to be found...
Its kind of a real mess using the JWS compared to simply having the application running from its own folder somewhere on the computer. As in you simply compress your application into a .zip file and the user unzip it wherever he want it on the system and simply runs the application from inside it. Then you don't need to worry at all about anything outside of the application folder. You have your /application/conf/ directory and you run your jar file from the main folder so you can easilly access anything below it.
If someone could give an example on how to set it up i would be grateful.

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