This does not have to do with the filesystem.
One of the libraries you use (Axis) tries to read a property but this is not allowed by the security manager. You might be able to circumvent this by using another way to deliver properties to Axis then having it try to find them by itself. Or by changing the security settings, which is something you cannot do when running in the Mendix cloud.
Looks like the library attempts to read from the file system. When you place those files (not the JARs!) in the resources folder of your project it should work. Of course you need an option to tell that library where to look for its stuff. I hope it supports that. Note that writing to the file system is not allowed.